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integrated_tool_panel.xml
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integrated_tool_panel.xml
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<?xml version="1.0"?>
<toolbox>
<!--
This is Galaxy's integrated tool panel and should be modified directly only for
reordering tools inside a section. Each time Galaxy starts up, this file is
synchronized with the various tool config files: tools, sections and labels
added to one of these files, will be added also here in the appropriate place,
while elements removed from the tool config files will be correspondingly
deleted from this file.
To modify locally managed tools (e.g. from tool_conf.xml) modify that file
directly and restart Galaxy. Whenever possible Tool Shed managed tools (e.g.
from shed_tool_conf.xml) should be managed from within the Galaxy interface or
via its API - but if changes are necessary (such as to hide a tool or re-assign
its section) modify that file and restart Galaxy.
-->
<section id="getext" name="Get Data" version="">
<tool id="upload1" />
<tool id="ucsc_table_direct1" />
<tool id="ucsc_table_direct_archaea1" />
<tool id="ebi_sra_main" />
<tool id="flymine" />
<tool id="modENCODEfly" />
<tool id="modmine" />
<tool id="mousemine" />
<tool id="ratmine" />
<tool id="yeastmine" />
<tool id="modENCODEworm" />
<tool id="wormbase" />
<tool id="zebrafishmine" />
<tool id="eupathdb" />
<tool id="genomespace_importer" />
<tool id="genomespace_push" />
</section>
<section id="send" name="Send Data" version="">
<tool id="genomespace_exporter" />
</section>
<section id="liftOver" name="Lift-Over" version="">
<tool id="liftOver1" />
</section>
<section id="collection_operations" name="Collection Operations" version="">
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3" />
<tool id="__UNZIP_COLLECTION__" />
<tool id="__ZIP_COLLECTION__" />
<tool id="__FILTER_FAILED_DATASETS__" />
<tool id="__FLATTEN__" />
<tool id="__MERGE_COLLECTION__" />
<tool id="__RELABEL_FROM_FILE__" />
<tool id="__FILTER_FROM_FILE__" />
<tool id="__SORTLIST__" />
<tool id="__TAG_FROM_FILE__" />
<tool id="__APPLY_RULES__" />
<tool id="toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.1" />
</section>
<section id="textutil" name="Text Manipulation" version="">
<tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/1.1.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_unfold_column_tool/1.1.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/1.1.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/1.1.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.1.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/bgruening/uniprot_rest_interface/uniprot/0.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tac/1.1.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.1.0" />
<tool id="cat1" />
<tool id="addValue" />
<tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tac/1.0.0" />
<tool id="Condense characters1" />
<tool id="Cut1" />
<tool id="Convert characters1" />
<tool id="mergeCols1" />
<tool id="Remove beginning1" />
<tool id="createInterval" />
<tool id="Show beginning1" />
<tool id="Show tail1" />
<tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.0.0" />
<tool id="ChangeCase" />
<tool id="Paste1" />
<tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.0.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.0.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.0.0" />
<tool id="random_lines1" />
<tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.0.0" />
<tool id="trimmer" />
<tool id="wc_gnu" />
<tool id="secure_hash_message_digest" />
<tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.0.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/1.0.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/1.0.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/1.0.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.0.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.0.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_unfold_column_tool/1.0.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.0.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.0.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.0.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.0.0" />
</section>
<section id="datamash" name="Datamash" version="">
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.0.6" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.0.6" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.0.6" />
</section>
<section id="convert" name="Convert Formats" version="">
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/fastq_to_fasta/cshl_fastq_to_fasta/1.0.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fastq/tabular_to_fastq/1.1.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/fastqtofasta/fastq_to_fasta_python/1.1.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/fastq_to_tabular/fastq_to_tabular/1.1.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/bam_to_scidx/bam_to_scidx/1.0.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fastq/tabular_to_fastq/1.0.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/fastq_to_tabular/fastq_to_tabular/1.1.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/fastq_to_fasta/cshl_fastq_to_fasta/1.0.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/fastqtofasta/fastq_to_fasta_python/1.0.0" />
<tool id="bed2gff1" />
<tool id="gff2bed1" />
<tool id="MAF_To_BED1" />
<tool id="MAF_To_Interval1" />
<tool id="MAF_To_Fasta1" />
<tool id="Sff_extractor" />
<tool id="wig_to_bigWig" />
<tool id="bed_to_bigBed" />
</section>
<section id="filter" name="Filter and Sort" version="">
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/dna_filtering/histogram_rpy/1.0.3" />
<tool id="sort1" />
<tool id="Grep1" />
<tool id="Filter1" />
<label id="gff" text="GFF" version="" />
<tool id="gff_filter_by_attribute" />
<tool id="gff_filter_by_feature_count" />
<tool id="Extract_features1" />
<tool id="gtf_filter_by_attribute_values_list" />
</section>
<section id="group" name="Join, Subtract and Group" version="">
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/subtract_query/subtract_query1/0.1" />
<tool id="join1" />
<tool id="comp1" />
<tool id="Grouping1" />
</section>
<section id="fetchAlignSeq" name="Fetch Alignments/Sequences" version="">
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/extract_genomic_dna/Extract genomic DNA 1/3.0.3" />
<tool id="Interval2Maf_pairwise1" />
<tool id="Interval2Maf1" />
<tool id="Interval_Maf_Merged_Fasta2" />
<tool id="GeneBed_Maf_Fasta2" />
<tool id="maf_stats1" />
<tool id="MAF_Thread_For_Species1" />
<tool id="MAF_Limit_To_Species1" />
<tool id="maf_limit_size1" />
<tool id="maf_by_block_number1" />
<tool id="MAF_filter" />
<tool id="MAF_Reverse_Complement_1" />
<tool id="Extract genomic DNA 1" />
</section>
<section id="cshl_library_information" name="NGS: QC and manipulation" version="">
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/pear/iuc_pear/0.9.6.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.6" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/flash/flash/1.2.11.3" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/fastx_trimmer/cshl_fastx_trimmer/1.0.2" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/fastx_reverse_complement/cshl_fastx_reverse_complement/1.0.2" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/fastx_clipper/cshl_fastx_clipper/1.0.3" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/fastq_quality_filter/cshl_fastq_quality_filter/1.0.2" />
<tool id="toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.3" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/length_and_gc_content/length_and_gc_content/0.1.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.36.5" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/fastx_trimmer/cshl_fastx_trimmer/1.0.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/fastx_reverse_complement/cshl_fastx_reverse_complement/1.0.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/fastx_renamer/cshl_fastx_renamer/0.0.14+galaxy0" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/fastx_quality_statistics/cshl_fastx_quality_statistics/1.0.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/fastx_nucleotides_distribution/cshl_fastx_nucleotides_distribution/1.0.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/fastx_clipper/cshl_fastx_clipper/1.0.2" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/fastx_barcode_splitter/cshl_fastx_barcode_splitter/1.0.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/fastx_artifacts_filter/cshl_fastx_artifacts_filter/1.0.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/fastq_quality_filter/cshl_fastq_quality_filter/1.0.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/fastq_quality_converter/cshl_fastq_quality_converter/1.0.1" />
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<tool id="toolshed.g2.bx.psu.edu/repos/devteam/fastx_barcode_splitter/cshl_fastx_barcode_splitter/1.0.0" />
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<tool id="toolshed.g2.bx.psu.edu/repos/devteam/fastx_collapser/cshl_fastx_collapser/1.0.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/fastx_nucleotides_distribution/cshl_fastx_nucleotides_distribution/1.0.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/fastx_quality_statistics/cshl_fastx_quality_statistics/1.0.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/fastx_renamer/cshl_fastx_renamer/0.0.11" />
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<tool id="toolshed.g2.bx.psu.edu/repos/devteam/fastx_trimmer/cshl_fastx_trimmer/1.0.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/fastq_combiner/fastq_combiner/1.0.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.0.0" />
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<tool id="toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.0.4" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/fastq_masker_by_quality/fastq_masker_by_quality/1.0.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_joiner/fastq_paired_end_joiner/1.0.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_splitter/fastq_paired_end_splitter/1.0.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/fastq_stats/1.0.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/fastq_trimmer/fastq_trimmer/1.0.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/fastq_trimmer_by_quality/fastq_quality_trimmer/1.0.0" />
<tool id="solid2fastq" />
<tool id="solid_qual_stats" />
<tool id="solid_qual_boxplot" />
<label id="generic_fastq" text="Generic FASTQ manipulation" version="" />
<label id="fastx_toolkit_fastq" text="FASTX-Toolkit for FASTQ data" version="" />
<label id="illumina" text="Illumina data" version="" />
<label id="454" text="Roche-454 data" version="" />
<label id="solid" text="AB-SOLiD data" version="" />
</section>
<section id="ngs:_deeptools" name="NGS: DeepTools" version="">
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</section>
<section id="ngs_mapping" name="NGS: Mapping" version="">
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<tool id="toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.3.2" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_d_wrapper/1.3.2" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_d_wrapper/1.3.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.3.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/star_fusion/star_fusion/0.5.4-3" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_d_wrapper/1.3" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.3" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.2.2" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.15.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.15.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.2.6.2" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.12.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.12.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.2.6" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.4.2" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.4.2" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/0.4" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/0.3" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/megablast_xml_parser/megablast_xml_parser/1.0.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/megablast_wrapper/megablast_wrapper/1.2.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_color_wrapper/1.0.2" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.1.2" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/bowtie_color_wrappers/bowtie_color_wrapper/1.1.2" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.2.2" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/0.2" />
<label id="illumina" text="Illumina" version="" />
<label id="roche_454" text="Roche-454" version="" />
<label id="ab_solid" text="AB-SOLiD" version="" />
</section>
<section id="ngs-rna-tools" name="NGS: RNA Analysis" version="">
<tool id="toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/0.11.2" />
<tool id="toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond_makedb/0.8.24" />
<tool id="toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond/0.8.24.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/0.9.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.43.1.3" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.43.1.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/bgruening/sailfish/sailfish/0.10.1.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.34.9.7" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.20.7.2" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.26.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.2" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.0.6" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/1.3.3.2" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.6.0b-1" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.0.3" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/1.3.3.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.9.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.0.2" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.0.5.2" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.0.5.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.5.2b-0" />
<tool id="toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/0.8.2" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.39" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/1.3.3" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/1.3.3" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/gffcompare/gffcompare/0.9.8" />
<tool id="toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.6.1galaxy3" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/dexseq/dexseq_count/1.20.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/dexseq/dexseq/1.20.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/0.7.2" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.4.6.p5" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/0.1.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/1.2.3" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.38" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.1.8.4" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.0.3" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/1.0.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.1.8.3" />
<tool id="toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.6.1galaxy1" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/1.0.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/1.0.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/bgruening/sailfish/sailfish/0.7.6.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/1.1.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/1.0.3" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/cuffcompare/cuffcompare/0.0.5" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/0.0.6" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/cuffmerge/cuffmerge/0.0.5" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/filter_transcripts_via_tracking/filter_combined_via_tracking/0.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/tophat/tophat/1.5.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/0.6" />
</section>
<section id="samtools" name="NGS: SAMtools" version="">
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.4.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/samtools_bedcov/samtools_bedcov/2.0.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/samtools_split/samtools_split/1.3.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/samtools_reheader/samtools_reheader/2.0.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.3" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.1.2" />
<tool id="toolshed.g2.bx.psu.edu/repos/boris/filter_on_md/MDtag_filter/1.0.2" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/sam_merge/sam_merge2/1.2.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/pileup_interval/pileup_interval/1.0.2" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/gregory-minevich/bcftools_view/bcftools_view/0.0.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/samtools_reheader/samtools_reheader/2.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/samtools_split/samtools_split/1.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/samtools_bedcov/samtools_bedcov/2.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/1.0.3" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/pileup_interval/pileup_interval/1.0.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/pileup_parser/pileup_parser/1.0.2" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/sam2interval/sam2interval/1.0.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/sam_bitwise_flag_filter/sam_bw_filter/1.0.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/sam_merge/sam_merge2/1.1.2" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/sam_pileup/1.1.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/1.1.2" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/1.0.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/0.0.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/1.0.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/0.0.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.1.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/sam_pileup/1.1.2" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/1.1.3" />
</section>
<section id="ngs:_bam_tools" name="NGS: BamTools" version="">
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.4.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamSplit/0.0.2" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/0.0.2" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/0.0.2" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/0.0.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/0.0.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamSplit/0.0.1" />
</section>
<section id="ngs:_picard" name="NGS: Picard" version="">