Mercurial > repos > iuc > stacks_genotypes
changeset 3:aa333a0a7d5a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
| author | iuc |
|---|---|
| date | Sat, 25 Jun 2016 17:28:58 -0400 |
| parents | dbe3901aace2 |
| children | 969a09779e3c |
| files | macros.xml stacks_genotypes.xml tool_dependencies.xml |
| diffstat | 3 files changed, 13 insertions(+), 10 deletions(-) [+] |
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--- a/macros.xml Wed Jun 15 06:25:01 2016 -0400 +++ b/macros.xml Sat Jun 25 17:28:58 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_genotypes.xml Wed Jun 15 06:25:01 2016 -0400 +++ b/stacks_genotypes.xml Sat Jun 25 17:28:58 2016 -0400 @@ -1,4 +1,4 @@ -<tool id="stacks_genotypes" name="Stacks: genotypes" version="@WRAPPER_VERSION@.0"> +<tool id="stacks_genotypes" name="Stacks: genotypes" version="@WRAPPER_VERSION@.1"> <description>analyse haplotypes or genotypes in a genetic cross ('genotypes' program)</description> <macros> <import>macros.xml</import> @@ -6,17 +6,20 @@ <expand macro="requirements"/> <expand macro="stdio"/> <command><![CDATA[ + #import re mkdir stacks_outputs && #for $input_file in $input_col: - #set $ext = "" - #if not str($input_file.name).endswith('.tsv'): - #set $ext = ".tsv" + #set $filename = str($input_file.element_identifier) + #if not $filename.endswith('.tsv'): + #set $filename = $filename + ".tsv" #end if - ln -s "${input_file}" "stacks_outputs/${input_file.name}${ext}" && + #if re.search('\.(tags|snps|alleles|matches)(\.tsv)?$', $filename): + ln -s "${input_file}" "stacks_outputs/${filename}" && + #end if #end for genotypes
--- a/tool_dependencies.xml Wed Jun 15 06:25:01 2016 -0400 +++ b/tool_dependencies.xml Sat Jun 25 17:28:58 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" />