Mercurial > repos > iuc > stacks_cstacks
changeset 3:6a7c5e218732 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
| author | iuc |
|---|---|
| date | Sat, 25 Jun 2016 17:28:35 -0400 |
| parents | 5bd1418f4227 |
| children | a62f7e799494 |
| files | macros.xml stacks_cstacks.xml tool_dependencies.xml |
| diffstat | 3 files changed, 24 insertions(+), 8 deletions(-) [+] |
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--- a/macros.xml Wed Jun 15 06:24:34 2016 -0400 +++ b/macros.xml Sat Jun 25 17:28:35 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>
--- a/stacks_cstacks.xml Wed Jun 15 06:24:34 2016 -0400 +++ b/stacks_cstacks.xml Sat Jun 25 17:28:35 2016 -0400 @@ -1,4 +1,4 @@ -<tool id="stacks_cstacks" name="Stacks: cstacks" version="@WRAPPER_VERSION@.0"> +<tool id="stacks_cstacks" name="Stacks: cstacks" version="@WRAPPER_VERSION@.2"> <description>build a catalogue of loci</description> <macros> <import>macros.xml</import> @@ -14,9 +14,9 @@ #set $samples = "" #for $input_file in $input_col: - #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" && @@ -49,6 +49,8 @@ #end if -o stacks_outputs + + > cstacks.log 2>&1 ]]></command> <inputs> @@ -71,6 +73,8 @@ </inputs> <outputs> + <data format="txt" name="output_log" label="cstacks.log with ${tool.name} on ${on_string}" from_work_dir="cstacks.log" /> + <data format="tabular" name="catalogtags" label="Catalog assembled loci (tags) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.catalog.tags.tsv" /> <data format="tabular" name="catalogsnps" label="Catalog model calls (snps) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.catalog.snps.tsv" /> <data format="tabular" name="catalogalleles" label="Catalog haplotypes (alleles) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.catalog.alleles.tsv" /> @@ -94,6 +98,12 @@ </collection> </param> + <output name="output_log"> + <assert_contents> + <has_text text="done." /> + </assert_contents> + </output> + <!-- catalog --> <output name="catalogtags"> <assert_contents> @@ -130,6 +140,12 @@ </param> <param name="gapped|use_gapped" value="true" /> + <output name="output_log"> + <assert_contents> + <has_text text="done." /> + </assert_contents> + </output> + <!-- catalog --> <output name="catalogtags"> <assert_contents>
--- a/tool_dependencies.xml Wed Jun 15 06:24:34 2016 -0400 +++ b/tool_dependencies.xml Sat Jun 25 17:28:35 2016 -0400 @@ -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" />