Mercurial > repos > iuc > stacks_rxstacks
changeset 3:55814b6afe69 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
| author | iuc |
|---|---|
| date | Sat, 25 Jun 2016 17:27:52 -0400 |
| parents | 77f5db795774 |
| children | fec69a2d92d7 |
| files | macros.xml stacks_rxstacks.xml tool_dependencies.xml |
| diffstat | 3 files changed, 12 insertions(+), 12 deletions(-) [+] |
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--- a/macros.xml Wed Jun 15 06:23:37 2016 -0400 +++ b/macros.xml Sat Jun 25 17:27:52 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_rxstacks.xml Wed Jun 15 06:23:37 2016 -0400 +++ b/stacks_rxstacks.xml Sat Jun 25 17:27:52 2016 -0400 @@ -1,4 +1,4 @@ -<tool id="stacks_rxstacks" name="Stacks: rxstacks" version="@WRAPPER_VERSION@.0"> +<tool id="stacks_rxstacks" name="Stacks: rxstacks" version="@WRAPPER_VERSION@.1"> <description>make corrections to genotype and haplotype calls</description> <macros> <import>macros.xml</import> @@ -13,10 +13,10 @@ #for $input_file in $input_col: #set $ext = "" - #if not str($input_file.name).endswith('.tsv'): + #if not str($input_file.element_identifier).endswith('.tsv'): #set $ext = ".tsv" #end if - ln -s "${input_file}" "stacks_inputs/${input_file.name}${ext}" && + ln -s "${input_file}" "stacks_inputs/${input_file.element_identifier}${ext}" && #end for rxstacks @@ -95,19 +95,19 @@ </data> <collection name="tags" type="list" label="Assembled loci filtered from ${on_string}"> - <discover_datasets pattern="(?P<name>.+\.tags)\.tsv" ext="tabular" directory="stacks_outputs" /> + <discover_datasets pattern="(?P<name>.+\.tags)\.tsv$" ext="tabular" directory="stacks_outputs" /> </collection> <collection name="snps" type="list" label="Model calls from each locus filtered from ${on_string}"> - <discover_datasets pattern="(?P<name>.+\.snps)\.tsv" ext="tabular" directory="stacks_outputs" /> + <discover_datasets pattern="(?P<name>.+\.snps)\.tsv$" ext="tabular" directory="stacks_outputs" /> </collection> <collection name="alleles" type="list" label="Haplotypes/alleles recorded from each locus filtered from ${on_string}"> - <discover_datasets pattern="(?P<name>.+\.alleles)\.tsv" ext="tabular" directory="stacks_outputs" /> + <discover_datasets pattern="(?P<name>.+\.alleles)\.tsv$" ext="tabular" directory="stacks_outputs" /> </collection> <collection name="all_output" type="list" label="Full output from rxstacks on ${on_string}"> - <discover_datasets pattern="(?P<name>.+\.(tags|snps|alleles))\.tsv" ext="tabular" directory="stacks_outputs" /> + <discover_datasets pattern="(?P<name>.+\.(tags|snps|alleles))\.tsv$" ext="tabular" directory="stacks_outputs" /> </collection> </outputs>
--- a/tool_dependencies.xml Wed Jun 15 06:23:37 2016 -0400 +++ b/tool_dependencies.xml Sat Jun 25 17:27:52 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" />