Skip to content

Commit

Permalink
Update test and fetch mutable config changes.
Browse files Browse the repository at this point in the history
  • Loading branch information
@natefoo
natefoo committed Dec 12, 2014
1 parent b78a21b commit 483a94e
Show file tree
Hide file tree
Showing 6 changed files with 30 additions and 195 deletions.
25 changes: 4 additions & 21 deletions files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -183,12 +183,12 @@
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/cuffcompare/cuffcompare/0.0.6" />
</section>
<section id="samtools" name="NGS: SAM Tools" version="">
<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/sam_pileup/sam_pileup/1.1.1" />
<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/samtools_rmdup/samtools_rmdup/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_flagstat/samtools_flagstat/1.0.0" />
<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/sam_pileup/sam_pileup/1.1.1" />
<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_bitwise_flag_filter/sam_bw_filter/1.0.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/sam2interval/sam2interval/1.0.1" />
Expand Down Expand Up @@ -239,17 +239,16 @@
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/table_annovar/table_annovar/0.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/varscan_version_2/varscan/0.1" />
<tool id="testtoolshed.g2.bx.psu.edu/repos/boris/phylorelatives/phylorelatives/0.0.1" />
<tool id="testtoolshed.g2.bx.psu.edu/repos/nick/allele_counts_1/allele_counts_1/1.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/gregory-minevich/ems_variant_density_mapping/ems_variant_density_mapping/1.0.0" />
<tool id="testtoolshed.g2.bx.psu.edu/repos/boris/getalleleseq/getalleleseq/0.0.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/gregory-minevich/snp_mapping_using_wgs/snp_mapping_using_wgs/1.0.0" />
<tool id="testtoolshed.g2.bx.psu.edu/repos/boris/hetbox/hetbox/1.0" />
<tool id="testtoolshed.g2.bx.psu.edu/repos/blankenberg/naive_variant_detector/naive_variant_detector/0.0.1" />
<tool id="testtoolshed.g2.bx.psu.edu/repos/nick/allele_counts_1/allele_counts_1/1.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/gregory-minevich/cloudmap_variant_discovery_mapping/cloudmap_variant_discovery_mapping/1.0.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/gregory-minevich/cloudmap_in_silico_complementation/in_silico_complementation/1.0.0" />
</section>
<section id="regVar" name="Regional Variation" version="">
<tool id="testtoolshed.g2.bx.psu.edu/repos/guru-ananda/rhmm/hmm_1/1.0.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/weightedaverage/wtavg/1.0.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/substitutions/substitutions1/1.0.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/substitution_rates/subRate1/1.0.0" />
Expand All @@ -269,8 +268,6 @@
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/windowsplitter/winSplitter/1.0.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/microsats_alignment_level/microsats_align1/1.0.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/getindels_2way/getIndels_2way/1.0.0" />
<tool id="testtoolshed.g2.bx.psu.edu/repos/guru-ananda/karyotype_plot/karyotype_Plot_1/1.0.0" />
<tool id="testtoolshed.g2.bx.psu.edu/repos/guru-ananda/heatmap/heatmap_1/1.0.0" />
</section>
<section id="genome_diversity" name="Genome Diversity" version="">
<label id="gd_init" text="Basic analyses" version="" />
Expand Down Expand Up @@ -433,19 +430,6 @@
<tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_chimera_uchime/1.22.0" />
</section>
<section id="picard_beta" name="NGS: Picard (beta)" 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="testtoolshed.g2.bx.psu.edu/repos/devteam/picard1106/picard_ARRG/1.106.0" />
<tool id="testtoolshed.g2.bx.psu.edu/repos/devteam/picard1106/picard_mergevcfs/1.106.0" />
<tool id="testtoolshed.g2.bx.psu.edu/repos/devteam/picard1106/PicardASMetrics/1.106.0" />
Expand Down Expand Up @@ -514,6 +498,7 @@
<tool id="testtoolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgpeakcall/2.0.10.0" />
<tool id="testtoolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_refinepeak/2.0.10.0" />
<tool id="testtoolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_predictd/2.0.10.0" />
<tool id="testtoolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.0.10.0" />
<tool id="testtoolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_filterdup/2.0.10.0" />
<tool id="testtoolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_randsample/2.0.10.0" />
<tool id="testtoolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgdiff/2.0.10.0" />
Expand All @@ -525,7 +510,6 @@
</section>
<section id="anton-vcftoolset" name="anton-vcftoolset" version="">
<tool id="toolshed.g2.bx.psu.edu/repos/anton/vcfselectsamples/vcfselectsamples/0.0.2" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/bamleftalign/bamleftalign/0.0.2" />
<tool id="toolshed.g2.bx.psu.edu/repos/anton/vcfcombine/vcfcombine/0.0.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/anton/vcfleftalign/vcfleftalign/0.0.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/anton/vcfcommonsamples/vcfcommonsamples/0.0.1" />
Expand All @@ -546,7 +530,6 @@
<tool id="toolshed.g2.bx.psu.edu/repos/anton/vcfbedintersect/vcfbedintersect/0.0.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/anton/vcfvcfintersect/vcfvcfintersect/0.0.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/anton/vcfselectsamples/vcfselectsamples/0.0.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/freebayes-0.9.14" />
</section>
<tool id="echo_test_handler0" />
<tool id="echo_test_handler1" />
Expand Down
109 changes: 2 additions & 107 deletions files/galaxy/test.galaxyproject.org/var/migrated_tools_conf.xml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -51,113 +51,6 @@
</tool>
</section>

<section id="picard_beta" name="NGS: Picard (beta)" version="">
<tool file="toolshed.g2.bx.psu.edu/repos/devteam/picard/1cd7f3b42609/picard/picard_FastqToSam.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FastqToSam/1.56.0">
<tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
<repository_name>picard</repository_name>
<repository_owner>devteam</repository_owner>
<installed_changeset_revision>1cd7f3b42609</installed_changeset_revision>
<id>toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FastqToSam/1.56.0</id>
<version>1.56.0</version>
</tool>
<tool file="toolshed.g2.bx.psu.edu/repos/devteam/picard/1cd7f3b42609/picard/picard_SamToFastq.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/1.56.1">
<tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
<repository_name>picard</repository_name>
<repository_owner>devteam</repository_owner>
<installed_changeset_revision>1cd7f3b42609</installed_changeset_revision>
<id>toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/1.56.1</id>
<version>1.56.1</version>
</tool>
<tool file="toolshed.g2.bx.psu.edu/repos/devteam/picard/1cd7f3b42609/picard/picard_BamIndexStats.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BamIndexStats/1.56.0">
<tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
<repository_name>picard</repository_name>
<repository_owner>devteam</repository_owner>
<installed_changeset_revision>1cd7f3b42609</installed_changeset_revision>
<id>toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BamIndexStats/1.56.0</id>
<version>1.56.0</version>
</tool>
<tool file="toolshed.g2.bx.psu.edu/repos/devteam/picard/1cd7f3b42609/picard/rgPicardASMetrics.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/picard/PicardASMetrics/1.56.0">
<tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
<repository_name>picard</repository_name>
<repository_owner>devteam</repository_owner>
<installed_changeset_revision>1cd7f3b42609</installed_changeset_revision>
<id>toolshed.g2.bx.psu.edu/repos/devteam/picard/PicardASMetrics/1.56.0</id>
<version>1.56.0</version>
</tool>
<tool file="toolshed.g2.bx.psu.edu/repos/devteam/picard/1cd7f3b42609/picard/rgPicardGCBiasMetrics.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/picard/PicardGCBiasMetrics/1.56.0">
<tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
<repository_name>picard</repository_name>
<repository_owner>devteam</repository_owner>
<installed_changeset_revision>1cd7f3b42609</installed_changeset_revision>
<id>toolshed.g2.bx.psu.edu/repos/devteam/picard/PicardGCBiasMetrics/1.56.0</id>
<version>1.56.0</version>
</tool>
<tool file="toolshed.g2.bx.psu.edu/repos/devteam/picard/1cd7f3b42609/picard/rgPicardLibComplexity.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/picard/rgEstLibComp/1.56.0">
<tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
<repository_name>picard</repository_name>
<repository_owner>devteam</repository_owner>
<installed_changeset_revision>1cd7f3b42609</installed_changeset_revision>
<id>toolshed.g2.bx.psu.edu/repos/devteam/picard/rgEstLibComp/1.56.0</id>
<version>1.56.0</version>
</tool>
<tool file="toolshed.g2.bx.psu.edu/repos/devteam/picard/1cd7f3b42609/picard/rgPicardInsertSize.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/picard/PicardInsertSize/1.56.0">
<tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
<repository_name>picard</repository_name>
<repository_owner>devteam</repository_owner>
<installed_changeset_revision>1cd7f3b42609</installed_changeset_revision>
<id>toolshed.g2.bx.psu.edu/repos/devteam/picard/PicardInsertSize/1.56.0</id>
<version>1.56.0</version>
</tool>
<tool file="toolshed.g2.bx.psu.edu/repos/devteam/picard/1cd7f3b42609/picard/rgPicardHsMetrics.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/picard/PicardHsMetrics/1.56.0">
<tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
<repository_name>picard</repository_name>
<repository_owner>devteam</repository_owner>
<installed_changeset_revision>1cd7f3b42609</installed_changeset_revision>
<id>toolshed.g2.bx.psu.edu/repos/devteam/picard/PicardHsMetrics/1.56.0</id>
<version>1.56.0</version>
</tool>
<tool file="toolshed.g2.bx.psu.edu/repos/devteam/picard/1cd7f3b42609/picard/picard_AddOrReplaceReadGroups.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ARRG/1.56.0">
<tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
<repository_name>picard</repository_name>
<repository_owner>devteam</repository_owner>
<installed_changeset_revision>1cd7f3b42609</installed_changeset_revision>
<id>toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ARRG/1.56.0</id>
<version>1.56.0</version>
</tool>
<tool file="toolshed.g2.bx.psu.edu/repos/devteam/picard/1cd7f3b42609/picard/picard_ReorderSam.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReorderSam/1.56.0">
<tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
<repository_name>picard</repository_name>
<repository_owner>devteam</repository_owner>
<installed_changeset_revision>1cd7f3b42609</installed_changeset_revision>
<id>toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReorderSam/1.56.0</id>
<version>1.56.0</version>
</tool>
<tool file="toolshed.g2.bx.psu.edu/repos/devteam/picard/1cd7f3b42609/picard/picard_ReplaceSamHeader.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReplaceSamHeader/1.56.0">
<tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
<repository_name>picard</repository_name>
<repository_owner>devteam</repository_owner>
<installed_changeset_revision>1cd7f3b42609</installed_changeset_revision>
<id>toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReplaceSamHeader/1.56.0</id>
<version>1.56.0</version>
</tool>
<tool file="toolshed.g2.bx.psu.edu/repos/devteam/picard/1cd7f3b42609/picard/rgPicardFixMate.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicFixMate/1.56.0">
<tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
<repository_name>picard</repository_name>
<repository_owner>devteam</repository_owner>
<installed_changeset_revision>1cd7f3b42609</installed_changeset_revision>
<id>toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicFixMate/1.56.0</id>
<version>1.56.0</version>
</tool>
<tool file="toolshed.g2.bx.psu.edu/repos/devteam/picard/1cd7f3b42609/picard/rgPicardMarkDups.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicardMarkDups/1.56.0">
<tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
<repository_name>picard</repository_name>
<repository_owner>devteam</repository_owner>
<installed_changeset_revision>1cd7f3b42609</installed_changeset_revision>
<id>toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicardMarkDups/1.56.0</id>
<version>1.56.0</version>
</tool>
</section>

<section id="solexa_tools" name="NGS: Mapping" version="">
<tool file="toolshed.g2.bx.psu.edu/repos/devteam/lastz/0801f8207d30/lastz/lastz_wrapper.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.2.2">
<tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
Expand Down Expand Up @@ -804,6 +697,8 @@








Expand Down
19 changes: 19 additions & 0 deletions files/galaxy/test.galaxyproject.org/var/shed_data_manager_conf.xml
View file
Original file line number Diff line number Diff line change
@@ -1,3 +1,22 @@
<?xml version="1.0"?>
<data_managers>
<data_manager guid="toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_all_fasta/data_manager/fetch_genome_all_fasta/0.0.1" id="fetch_genome_all_fasta" shed_conf_file="/home/g2test/var/shed_tool_conf.xml">
<tool file="toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_all_fasta/2ebc856bce29/data_manager_fetch_genome_all_fasta/data_manager/data_manager_fetch_genome_all_fasta.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_all_fasta/data_manager_fetch_genome_all_fasta/0.0.1"><tool_shed>toolshed.g2.bx.psu.edu</tool_shed><repository_name>data_manager_fetch_genome_all_fasta</repository_name><repository_owner>devteam</repository_owner><installed_changeset_revision>2ebc856bce29</installed_changeset_revision><id>toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_all_fasta/data_manager_fetch_genome_all_fasta/0.0.1</id><version>0.0.1</version></tool><data_table name="all_fasta">
<output>
<column name="value" />
<column name="dbkey" />
<column name="name" />
<column name="path" output_ref="out_file">
<move type="file">
<source>${path}</source>
<target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${dbkey}/seq/${path}</target>
</move>
<value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${dbkey}/seq/${path}</value_translation>
<value_translation type="function">abspath</value_translation>
</column>
</output>
</data_table>
</data_manager>


</data_managers>

0 comments on commit 483a94e

Please sign in to comment.