Mercurial > repos > iuc > stacks_pstacks
changeset 3:fede8a808d36 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
| author | iuc |
|---|---|
| date | Sat, 25 Jun 2016 17:27:31 -0400 |
| parents | 0f16a6c30085 |
| children | 77e29e6a6101 |
| files | macros.xml stacks_pstacks.xml tool_dependencies.xml |
| diffstat | 3 files changed, 23 insertions(+), 13 deletions(-) [+] |
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--- a/macros.xml Wed Jun 15 06:23:05 2016 -0400 +++ b/macros.xml Sat Jun 25 17:27:31 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_pstacks.xml Wed Jun 15 06:23:05 2016 -0400 +++ b/stacks_pstacks.xml Sat Jun 25 17:27:31 2016 -0400 @@ -1,4 +1,4 @@ -<tool id="stacks_pstacks" name="Stacks: pstacks" version="@WRAPPER_VERSION@.0"> +<tool id="stacks_pstacks" name="Stacks: pstacks" version="@WRAPPER_VERSION@.2"> <description>find stacks from short reads mapped to a reference genome</description> <macros> <import>macros.xml</import> @@ -14,12 +14,12 @@ && #if $sample.ext == "sam": - #set $data_path = splitext($sample.name)[0] + #set $data_path = splitext($sample.element_identifier)[0] #set $data_path = re.sub(r'\.1$', '', $data_path) #set $data_path = "stacks_inputs/" + $data_path + ".sam" #set inputype = "sam" #else: - #set $data_path = splitext($sample.name)[0] + #set $data_path = splitext($sample.element_identifier)[0] #set $data_path = re.sub(r'\.1$', '', $data_path) #set $data_path = "stacks_inputs/" + $data_path + ".bam" #set inputype = "bam" @@ -58,8 +58,10 @@ -o stacks_outputs + > pstacks.log 2>&1 + ## If input is in bam format, stacks will output gzipped files (no option to control this) - && gunzip stacks_outputs/*.gz + && if ls stacks_outputs/*.gz > /dev/null 2>&1; then gunzip stacks_outputs/*.gz; fi ]]></command> <inputs> @@ -77,11 +79,13 @@ </inputs> <outputs> + <data format="txt" name="output_log" label="pstacks.log with ${tool.name} on ${on_string}" from_work_dir="pstacks.log" /> + <collection name="tabs" type="list" label="Stacks from ${on_string}"> - <discover_datasets pattern="(?P<name>.+\.tags)\.tsv" ext="tabular" directory="stacks_outputs" /> - <discover_datasets pattern="(?P<name>.+\.snps)\.tsv" ext="tabular" directory="stacks_outputs" />> - <discover_datasets pattern="(?P<name>.+\.alleles)\.tsv" ext="tabular" directory="stacks_outputs" /> - <discover_datasets pattern="(?P<name>.+\.models)\.tsv" ext="tabular" directory="stacks_outputs" /> + <discover_datasets pattern="(?P<name>.+\.tags)\.tsv$" ext="tabular" directory="stacks_outputs" /> + <discover_datasets pattern="(?P<name>.+\.snps)\.tsv$" ext="tabular" directory="stacks_outputs" />> + <discover_datasets pattern="(?P<name>.+\.alleles)\.tsv$" ext="tabular" directory="stacks_outputs" /> + <discover_datasets pattern="(?P<name>.+\.models)\.tsv$" ext="tabular" directory="stacks_outputs" /> </collection> </outputs> @@ -90,6 +94,12 @@ <param name="sample" value="refmap/PopA_01.bam" ftype="bam" /> <param name="sample_id" value="4" /> + <output name="output_log"> + <assert_contents> + <has_text text="done." /> + </assert_contents> + </output> + <output_collection name="tabs"> <element name="PopA_01.tags"> <assert_contents>
--- a/tool_dependencies.xml Wed Jun 15 06:23:05 2016 -0400 +++ b/tool_dependencies.xml Sat Jun 25 17:27:31 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" />