| Previous changeset 2:dbe3901aace2 (2016-06-15) Next changeset 4:969a09779e3c (2016-09-26) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 |
|
modified:
macros.xml stacks_genotypes.xml tool_dependencies.xml |
| b |
| diff -r dbe3901aace2 -r aa333a0a7d5a macros.xml --- 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> |
| b |
| diff -r dbe3901aace2 -r aa333a0a7d5a stacks_genotypes.xml --- 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 |
| b |
| diff -r dbe3901aace2 -r aa333a0a7d5a tool_dependencies.xml --- a/tool_dependencies.xml Wed Jun 15 06:25:01 2016 -0400 +++ b/tool_dependencies.xml Sat Jun 25 17:28:58 2016 -0400 |
| b |
| @@ -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" /> |