| Previous changeset 2:e880ddd2d8fa (2016-06-15) Next changeset 4:679f97ac0dd5 (2016-09-26) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 |
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modified:
macros.xml stacks_sstacks.xml tool_dependencies.xml |
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| diff -r e880ddd2d8fa -r 344cfdb7dd48 macros.xml --- a/macros.xml Wed Jun 15 06:24:20 2016 -0400 +++ b/macros.xml Sat Jun 25 17:28:25 2016 -0400 |
| [ |
| @@ -117,11 +117,11 @@ ln -s batch_1.genotypes_*onemap.tsv batch_1.genotypes.onemap.tsv && ln -s batch_1.genotypes_*.onemap.txt batch_1.genotypes.onemap.txt && ln -s batch_1.genomic_*.tsv batch_1.genomic.tsv && - ln -s batch_1.genotypes_1.rqtl.tsv batch_1.genotypes.rqtl.tsv && - ln -s batch_1.haplotypes_1.tsv batch_1.haplotypes.tsv && + ln -s batch_1.genotypes_*.rqtl.tsv batch_1.genotypes.rqtl.tsv && + ln -s batch_1.haplotypes_*.tsv batch_1.haplotypes.tsv && ln -s batch_1.genotypes_*.loc batch_1.genotypes.loc && - ln -s batch_1.genotypes_1.txt batch_1.genotypes.txt && - ln -s batch_1.genotypes_1.tsv batch_1.genotypes.tsv && + ln -s batch_1.genotypes_*.txt batch_1.genotypes.txt && + ln -s batch_1.genotypes_*[^rqtl].tsv batch_1.genotypes.tsv && cd .. ]]> </token> |
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| diff -r e880ddd2d8fa -r 344cfdb7dd48 stacks_sstacks.xml --- a/stacks_sstacks.xml Wed Jun 15 06:24:20 2016 -0400 +++ b/stacks_sstacks.xml Sat Jun 25 17:28:25 2016 -0400 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="stacks_sstacks" name="Stacks: sstacks" version="@WRAPPER_VERSION@.0"> +<tool id="stacks_sstacks" name="Stacks: sstacks" version="@WRAPPER_VERSION@.1"> <description>match stacks to a catalog</description> <macros> <import>macros.xml</import> @@ -14,9 +14,9 @@ #set $catalog = "" #for $input_file in $input_cat: - #set $filename = str($input_file.name) + #set $filename = str($input_file.element_identifier) #if not filename.endswith('.tsv'): - #set $filename = ".tsv" + #set $filename = $filename + ".tsv" #end if #if re.search('catalog\.[a-z]+(\.tsv)?$', $filename): ln -s "${input_file}" "stacks_inputs/$filename" && @@ -29,9 +29,9 @@ #set $samples = "" #for $input_file in $input_tags: - #set $filename = str($input_file.name) + #set $filename = str($input_file.element_identifier) #if not filename.endswith('.tsv'): - #set $filename = ".tsv" + #set $filename = $filename + ".tsv" #end if #if not re.search('catalog\.[a-z]+(\.tsv)?$', $filename): ln -s "${input_file}" "stacks_inputs/$filename" && @@ -60,6 +60,8 @@ $gapped -o stacks_outputs + + > sstacks.log 2>&1 ]]></command> <inputs> @@ -74,8 +76,10 @@ </inputs> <outputs> + <data format="txt" name="output_log" label="sstacks.log with ${tool.name} on ${on_string}" from_work_dir="sstacks.log" /> + <collection name="matches" type="list" label="Matches to the catalog on ${on_string}"> - <discover_datasets pattern="(?P<name>.+\.matches)\.tsv" ext="tabular" directory="stacks_outputs" /> + <discover_datasets pattern="(?P<name>.+\.matches)\.tsv$" ext="tabular" directory="stacks_outputs" /> </collection> </outputs> @@ -101,6 +105,12 @@ </collection> </param> + <output name="output_log"> + <assert_contents> + <has_text text="Outputing to file" /> + </assert_contents> + </output> + <output_collection name="matches"> <element name="PopA_01.matches"> <assert_contents> @@ -133,6 +143,12 @@ <param name="gapped" value="true" /> <param name="check_haplo" value="true" /> + <output name="output_log"> + <assert_contents> + <has_text text="Outputing to file" /> + </assert_contents> + </output> + <output_collection name="matches"> <element name="PopA_01.matches"> <assert_contents> |
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| diff -r e880ddd2d8fa -r 344cfdb7dd48 tool_dependencies.xml --- a/tool_dependencies.xml Wed Jun 15 06:24:20 2016 -0400 +++ b/tool_dependencies.xml Sat Jun 25 17:28:25 2016 -0400 |
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| @@ -1,7 +1,7 @@ <?xml version="1.0"?> <tool_dependency> <package name="stacks" version="1.40"> - <repository changeset_revision="95cffefc0dfe" name="package_stacks_1_40" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="51d4ab2c4dcf" name="package_stacks_1_40" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="velvet" version="1.2.10"> <repository changeset_revision="93d32326537b" name="package_velvet_1_2_10" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> |