| Previous changeset 2:5d12647ff71f (2016-06-15) Next changeset 4:c2733bcc51f7 (2016-09-26) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 |
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modified:
macros.xml stacks_procrad.xml tool_dependencies.xml |
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| diff -r 5d12647ff71f -r 11642e18f2b0 macros.xml --- a/macros.xml Wed Jun 15 06:25:27 2016 -0400 +++ b/macros.xml Sat Jun 25 17:29:23 2016 -0400 |
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| @@ -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> |
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| diff -r 5d12647ff71f -r 11642e18f2b0 stacks_procrad.xml --- a/stacks_procrad.xml Wed Jun 15 06:25:27 2016 -0400 +++ b/stacks_procrad.xml Sat Jun 25 17:29:23 2016 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="stacks_procrad" name="Stacks: process radtags" version="@WRAPPER_VERSION@.1"> +<tool id="stacks_procrad" name="Stacks: process radtags" version="@WRAPPER_VERSION@.2"> <description>the Stacks demultiplexing script</description> <macros> <import>macros.xml</import> @@ -149,18 +149,18 @@ <data format="txt" name="output_log" label="results.log with ${tool.name} on ${on_string}: demultiplexed and cleaned reads" from_work_dir="stacks_outputs/process_radtags.log" /> <collection name="demultiplexed" type="list" label="Demultiplexed reads from ${on_string}"> - <discover_datasets pattern="(?P<name>.+(\.[12])?)\.fq" ext="fastqsanger" directory="stacks_outputs" /> - <discover_datasets pattern="(?P<name>.+(\.[12])?)\.fa" ext="fasta" directory="stacks_outputs" /> + <discover_datasets pattern="(?P<name>.+(\.[12])?)\.fq$" ext="fastqsanger" directory="stacks_outputs" /> + <discover_datasets pattern="(?P<name>.+(\.[12])?)\.fa$" ext="fasta" directory="stacks_outputs" /> </collection> <collection name="remaining" type="list" label="Remaining orphan reads from ${on_string}"> <filter>input_type['options_type_selector'] == "paired"</filter> - <discover_datasets pattern="(?P<name>.+\.rem(\.[12])?)\.fq" ext="fastqsanger" directory="stacks_outputs" /> - <discover_datasets pattern="(?P<name>.+\.rem(\.[12])?)\.fa" ext="fasta" directory="stacks_outputs" /> + <discover_datasets pattern="(?P<name>.+\.rem(\.[12])?)\.fq$" ext="fastqsanger" directory="stacks_outputs" /> + <discover_datasets pattern="(?P<name>.+\.rem(\.[12])?)\.fa$" ext="fasta" directory="stacks_outputs" /> </collection> <collection name="discarded" type="list" label="${tool.name}: discarded reads from ${on_string}"> <filter>capture is True</filter> - <discover_datasets pattern="(?P<name>.+)\.fq\.discards" ext="fastqsanger" directory="stacks_outputs" /> - <discover_datasets pattern="(?P<name>.+)\.fa\.discards" ext="fasta" directory="stacks_outputs" /> + <discover_datasets pattern="(?P<name>.+)\.fq\.discards$" ext="fastqsanger" directory="stacks_outputs" /> + <discover_datasets pattern="(?P<name>.+)\.fa\.discards$" ext="fasta" directory="stacks_outputs" /> </collection> </outputs> |
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| diff -r 5d12647ff71f -r 11642e18f2b0 tool_dependencies.xml --- a/tool_dependencies.xml Wed Jun 15 06:25:27 2016 -0400 +++ b/tool_dependencies.xml Sat Jun 25 17:29:23 2016 -0400 |
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| @@ -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" /> |