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Final Main tool panel fixes
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@natefoo
natefoo committed Feb 11, 2019
1 parent 76555e1 commit 0d9b413
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Showing 3 changed files with 87 additions and 55 deletions.
96 changes: 61 additions & 35 deletions env/main/files/galaxy/var/integrated_tool_panel.xml
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Expand Up @@ -35,7 +35,7 @@

<tool id="echo_main_bridges" />

<section id="get_data" name="Get Data">
<section id="get_data" name="Get Data" version="">

<tool id="upload1" />

Expand All @@ -47,6 +47,8 @@

<tool id="flymine" />

<tool id="intermine" />

<tool id="modENCODEfly" />

<tool id="modmine" />
Expand All @@ -65,6 +67,8 @@

<tool id="eupathdb" />

<tool id="hbvar" />

<tool id="genomespace_importer" />

<tool id="genomespace_push" />
Expand All @@ -77,7 +81,7 @@

</section>

<section id="send_data" name="Send Data">
<section id="send_data" name="Send Data" version="">

<tool id="genomespace_exporter" />

Expand All @@ -91,6 +95,8 @@

<tool id="__ZIP_COLLECTION__" />

<tool id="__FILTER_EMPTY_DATASETS__" />

<tool id="__FILTER_FAILED_DATASETS__" />

<tool id="__FLATTEN__" />
Expand All @@ -105,6 +111,10 @@

<tool id="__TAG_FROM_FILE__" />

<tool id="__BUILD_LIST__" />

<tool id="__EXTRACT_DATASET__" />

<tool id="__APPLY_RULES__" />

<tool id="toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.0" />
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</section>

<section id="join_subtract_and_group" name="Join, Subtract and Group">
<section id="join_subtract_and_group" name="Join, Subtract and Group" version="">

<tool id="toolshed.g2.bx.psu.edu/repos/devteam/subtract_query/subtract_query1/0.1" />

Expand All @@ -297,9 +307,7 @@

<label id="genomic_file_manipulation_label" text="Genomic File Manipulation" version="" />

<section id="fasta_fastq" name="FASTA/FASTQ">

<label id="generic_fastq" text="Generic FASTQ manipulation" version="" />
<section id="fasta_fastq" name="FASTA/FASTQ" version="">

<tool id="toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.5" />

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<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="fastx_toolkit_fastq" text="FASTX-Toolkit for FASTQ data" version="" />

<tool id="toolshed.g2.bx.psu.edu/repos/devteam/fasta_nucleotide_changer/cshl_fasta_nucleotides_changer/1.0.2" />

<tool id="toolshed.g2.bx.psu.edu/repos/devteam/fasta_nucleotide_changer/cshl_fasta_nucleotides_changer/1.0.1" />
Expand All @@ -445,11 +445,9 @@

<tool id="toolshed.g2.bx.psu.edu/repos/devteam/fasta_nucleotide_changer/cshl_fasta_nucleotides_changer/1.0.0" />

<tool id="toolshed.g2.bx.psu.edu/repos/devteam/fastx_collapser/cshl_fastx_collapser/1.0.0" />

</section>

<section id="fastq_quality_control" name="FASTQ Quality Control">
<section id="fastq_quality_control" name="FASTQ Quality Control" version="">

<tool id="toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.6" />

Expand Down Expand Up @@ -501,13 +499,9 @@

</section>

<section id="sam_bam" name="SAM/BAM">

<label id="samtools_label" name="SAMTools" version="" />
<section id="sam_bam" name="SAM/BAM" 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/gregory-minevich/bcftools_view/bcftools_view/0.0.1" />
<label id="samtools_label" text="SAMTools" version="" />

<tool id="toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.2" />

Expand Down Expand Up @@ -611,7 +605,7 @@

<tool id="toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/1.1.3" />

<label id="bamtools_label" name="BAMTools" version="" />
<label id="bamtools_label" text="BAMTools" version="" />

<tool id="toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamSplit/2.4.0" />

Expand All @@ -635,7 +629,7 @@

<section id="bed" name="BED" version="">

<label id="bedtools_label" name="BEDTools" version="" />
<label id="bedtools_label" text="BEDTools" version="" />

<tool id="toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.27.0.1" />

Expand Down Expand Up @@ -1073,6 +1067,8 @@

<tool id="toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.4.0" />

<tool id="toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.4.0" />

<tool id="toolshed.g2.bx.psu.edu/repos/iuc/bcftools_roh/bcftools_roh/1.4.0.0" />

<tool id="toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/bcftools_merge/1.4.0" />
Expand Down Expand Up @@ -1119,7 +1115,9 @@

</section>

<section id="nanopore" name="Nanopore">
<section id="nanopore" name="Nanopore" version="">

<label id="poretools_label" text="poretools" version="" />

<tool id="toolshed.g2.bx.psu.edu/repos/iuc/poretools_yield_plot/poretools_yield_plot/0.6.1a1.0" />

Expand Down Expand Up @@ -1149,7 +1147,7 @@

</section>

<section id="convert_formats" name="Convert Formats">
<section id="convert_formats" name="Convert Formats" version="">

<tool id="toolshed.g2.bx.psu.edu/repos/iuc/bam_to_scidx/bam_to_scidx/1.0.1" />

Expand Down Expand Up @@ -1203,7 +1201,7 @@

<label id="common_genomics_tools_label" text="Common Genomics Tools" version="" />

<section id="operate_on_genomic_intervals" name="Operate on Genomic Intervals">
<section id="operate_on_genomic_intervals" name="Operate on Genomic Intervals" version="">

<tool id="toolshed.g2.bx.psu.edu/repos/devteam/merge/gops_merge_1/1.0.0" />

Expand Down Expand Up @@ -1365,6 +1363,10 @@

<section id="variant_calling" name="Variant Calling" version="">

<tool id="toolshed.g2.bx.psu.edu/repos/pcingola/snpeff/snpSift_filter/1.0" />

<tool id="toolshed.g2.bx.psu.edu/repos/pcingola/snpeff/snpEff/1.0" />

<tool id="toolshed.g2.bx.psu.edu/repos/devteam/varscan_version_2/varscan/2.4.2" />

<tool id="toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3+T.galaxy2" />
Expand Down Expand Up @@ -1445,10 +1447,6 @@

<tool id="toolshed.g2.bx.psu.edu/repos/devteam/table_annovar/table_annovar/0.1" />

<tool id="toolshed.g2.bx.psu.edu/repos/pcingola/snpeff/snpSift_filter/1.0" />

<tool id="toolshed.g2.bx.psu.edu/repos/pcingola/snpeff/snpEff/1.0" />

</section>

<section id="chip_seq" name="ChIP-seq" version="">
Expand Down Expand Up @@ -1673,7 +1671,7 @@

<tool id="toolshed.g2.bx.psu.edu/repos/devteam/tophat/tophat/1.5.0" />

<label id="structurefold_label" text="RNA Structure Prediction" />
<label id="structurefold_label" text="RNA Structure Prediction" version="" />

<tool id="toolshed.g2.bx.psu.edu/repos/tyty/structurefold/iterative_map_pipeline/1.0" />

Expand Down Expand Up @@ -2727,6 +2725,32 @@

<section id="picard" name="Picard" version="">

<tool id="toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FastqToSam/1.56.0" />

<tool id="toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/1.56.1" />

<tool id="toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BamIndexStats/1.56.0" />

<tool id="toolshed.g2.bx.psu.edu/repos/devteam/picard/PicardASMetrics/1.56.0" />

<tool id="toolshed.g2.bx.psu.edu/repos/devteam/picard/PicardGCBiasMetrics/1.56.0" />

<tool id="toolshed.g2.bx.psu.edu/repos/devteam/picard/rgEstLibComp/1.56.0" />

<tool id="toolshed.g2.bx.psu.edu/repos/devteam/picard/PicardInsertSize/1.56.0" />

<tool id="toolshed.g2.bx.psu.edu/repos/devteam/picard/PicardHsMetrics/1.56.0" />

<tool id="toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ARRG/1.56.0" />

<tool id="toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReorderSam/1.56.0" />

<tool id="toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReplaceSamHeader/1.56.0" />

<tool id="toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicFixMate/1.56.0" />

<tool id="toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicardMarkDups/1.56.0" />

<tool id="toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FastqToSam/2.18.2.1" />

<tool id="toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectBaseDistributionByCycle/2.18.2.1" />
Expand Down Expand Up @@ -3917,7 +3941,7 @@

<tool id="Count1" />

<label id="multiple_regression_label" text="Multiple Regression" />
<label id="multiple_regression_label" text="Multiple Regression" version="" />

<tool id="toolshed.g2.bx.psu.edu/repos/devteam/linear_regression/LinearRegression1/1.0.1" />

Expand All @@ -3929,7 +3953,7 @@

<tool id="toolshed.g2.bx.psu.edu/repos/devteam/best_regression_subsets/BestSubsetsRegression1/1.0.0" />

<label id="multivariate_analysis_label" text="Multivariate Analysis" />
<label id="multivariate_analysis_label" text="Multivariate Analysis" version="" />

<tool id="toolshed.g2.bx.psu.edu/repos/devteam/canonical_correlation_analysis/cca1/1.0.0" />

Expand Down Expand Up @@ -4047,6 +4071,8 @@

<tool id="toolshed.g2.bx.psu.edu/repos/gregory-minevich/check_snpeff_candidates/check_snpeff_candidates/1.0.0" />

<tool id="toolshed.g2.bx.psu.edu/repos/gregory-minevich/bcftools_view/bcftools_view/0.0.1" />

</section>

<section id="metagenomic_analysis_deprecated" name="Metagenomic Analysis (deprecated)" version="">
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2 changes: 1 addition & 1 deletion env/main/files/galaxy/var/migrated_tools_conf.xml
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Expand Up @@ -494,7 +494,7 @@
</tool>
</section>

<section id="picard_beta" name="NGS: Picard (beta)">
<section id="picard" name="Picard">
<tool file="toolshed.g2.bx.psu.edu/repos/devteam/picard/e0232cbac965/picard/picard_FastqToSam.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FastqToSam/1.56.0" hidden="true">
<tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
<repository_name>picard</repository_name>
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44 changes: 25 additions & 19 deletions env/main/files/galaxy/var/shed_tool_conf.xml
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@@ -1,15 +1,19 @@
<?xml version="1.0" ?>
<toolbox tool_path="/cvmfs/main.galaxyproject.org/shed_tools">
<section id="bed" name="BED" version="">
<label id="bedtools_label" text="BEDTools" version="" />
<section id="sam_bam" name="SAM/BAM">
<label id="samtools_label" text="SAMTools" />
<label id="bamtools_label" text="BAMTools" />
</section>
<section id="bed" name="BED">
<label id="bedtools_label" text="BEDTools" />
</section>
<section id="vcf_bcf" name="VCF/BCF">
<label id="vcflib_label" text="vcflib" version="" />
<label id="vcftools_label" text="VCFTools" version="" />
<label id="bcftools_label" text="BCFTools" version="" />
<label id="vcflib_label" text="vcflib" />
<label id="vcftools_label" text="VCFTools" />
<label id="bcftools_label" text="BCFTools" />
</section>
<section id="nanopore" name="Nanopore" version="">
<label id="poretools_label" text="poretools" version="" />
<section id="nanopore" name="Nanopore">
<label id="poretools_label" text="poretools" />
</section>
<section id="rna_seq" name="RNA-seq">
<label id="structurefold_label" text="RNA Structure Prediction" />
Expand All @@ -19,9 +23,9 @@
<label id="multivariate_analysis_label" text="Multivariate Analysis" />
</section>
<label id="genomics_toolkits_label" text="Genomics Toolkits" />
<label id="metagenomics_label" text="Metagenomics" version="" />
<label id="deprecated_tools_label" text="Deprecated Tools" version="" />
<section id="snpeff" name="snpEff" version="">
<label id="metagenomics_label" text="Metagenomics" />
<label id="deprecated_tools_label" text="Deprecated Tools" />
<section id="variant_calling" name="Variant Calling" version="">
<tool file="toolshed.g2.bx.psu.edu/repos/pcingola/snpeff/c052639fa666/snpeff/snpEff_2_1a/snpEff_2_1a/galaxy/snpSift_filter.xml" guid="toolshed.g2.bx.psu.edu/repos/pcingola/snpeff/snpSift_filter/1.0" hidden="true">
<tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
<repository_name>snpeff</repository_name>
Expand Down Expand Up @@ -98,14 +102,6 @@
</tool>
</section>
<section id="sam_bam" name="SAM/BAM">
<tool file="toolshed.g2.bx.psu.edu/repos/gregory-minevich/bcftools_view/69e3ff62728f/bcftools_view/bcftools_view.xml" guid="toolshed.g2.bx.psu.edu/repos/gregory-minevich/bcftools_view/bcftools_view/0.0.1">
<tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
<repository_name>bcftools_view</repository_name>
<repository_owner>gregory-minevich</repository_owner>
<installed_changeset_revision>69e3ff62728f</installed_changeset_revision>
<id>toolshed.g2.bx.psu.edu/repos/gregory-minevich/bcftools_view/bcftools_view/0.0.1</id>
<version>0.0.1</version>
</tool>
<tool file="toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/890d97772e2a/sam_pileup/sam_pileup.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/sam_pileup/1.1.2">
<tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
<repository_name>sam_pileup</repository_name>
Expand Down Expand Up @@ -164,6 +160,14 @@
<id>toolshed.g2.bx.psu.edu/repos/gregory-minevich/check_snpeff_candidates/check_snpeff_candidates/1.0.0</id>
<version>1.0.0</version>
</tool>
<tool file="toolshed.g2.bx.psu.edu/repos/gregory-minevich/bcftools_view/69e3ff62728f/bcftools_view/bcftools_view.xml" guid="toolshed.g2.bx.psu.edu/repos/gregory-minevich/bcftools_view/bcftools_view/0.0.1">
<tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
<repository_name>bcftools_view</repository_name>
<repository_owner>gregory-minevich</repository_owner>
<installed_changeset_revision>69e3ff62728f</installed_changeset_revision>
<id>toolshed.g2.bx.psu.edu/repos/gregory-minevich/bcftools_view/bcftools_view/0.0.1</id>
<version>0.0.1</version>
</tool>
</section>
<section id="variant_calling" name="Variant Calling" version="">
<tool file="toolshed.g2.bx.psu.edu/repos/devteam/freebayes/28e422c589ac/freebayes/freebayes.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/0.0.3" hidden="true">
Expand Down Expand Up @@ -222,6 +226,8 @@
<id>toolshed.g2.bx.psu.edu/repos/devteam/table_annovar/table_annovar/0.1</id>
<version>0.1</version>
</tool>
</section>
<section id="vcf_bcf" name="VCF/BCF" version="">
<tool file="toolshed.g2.bx.psu.edu/repos/devteam/vcftools_annotate/bc178c43e4fe/vcftools_annotate/vcftools_annotate.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/vcftools_annotate/vcftools_annotate/0.1">
<tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
<repository_name>vcftools_annotate</repository_name>
Expand Down Expand Up @@ -14427,7 +14433,7 @@
<version>0.72</version>
</tool>
</section>
<section id="sam_bam" name="SAM/BAM">
<section id="vcf_bcf" name="VCF/BCF">
<tool file="toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/b03984136ce4/bcftools_call/bcftools_call.xml" guid="toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.4.0">
<tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
<repository_name>bcftools_call</repository_name>
Expand Down

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