| Previous changeset 2:fea78fd36a05 (2016-06-15) Next changeset 4:ae705d244e28 (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_assembleperead.xml tool_dependencies.xml |
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| diff -r fea78fd36a05 -r ee52d9cfaffc macros.xml --- a/macros.xml Wed Jun 15 06:23:24 2016 -0400 +++ b/macros.xml Sat Jun 25 17:27:42 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> |
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| diff -r fea78fd36a05 -r ee52d9cfaffc stacks_assembleperead.xml --- a/stacks_assembleperead.xml Wed Jun 15 06:23:24 2016 -0400 +++ b/stacks_assembleperead.xml Sat Jun 25 17:27:42 2016 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="stacks_assembleperead" name="Stacks: assemble read pairs by locus" version="@WRAPPER_VERSION@.0"> +<tool id="stacks_assembleperead" name="Stacks: assemble read pairs by locus" version="@WRAPPER_VERSION@.1"> <description>run the STACKS sort_read_pairs.pl and exec_velvet.pl wrappers</description> <macros> <import>macros.xml</import> @@ -13,17 +13,24 @@ #for $input_file in $stacks_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 #for $input_file in $reads: - #set $name = str($input_file.name) - #if $name.endswith('.2.fq'): - ## sort_read_pairs is expecting strange fastq names... + #set $name = str($input_file.element_identifier) + ## sort_read_pairs is expecting strange fastq names: <sample_name>.fq_2 + #if $name.endswith('.1.fq'): + ## handle a common case + #set $name = $name[:-5]+".fq_1" + #else if $name.endswith('.2.fq'): + ## handle a common case #set $name = $name[:-5]+".fq_2" + #else if not $name.endswith('.fq') and not $name.endswith('.fq_2'): + ## no extension, consider it's a fq_2 file + #set $name = $name + ".fq_2" #end if ln -s "${input_file}" "reads/${name}" && #end for @@ -57,7 +64,7 @@ ]]></command> <inputs> <param name="stacks_col" argument="-p" format="tabular,txt" type="data_collection" collection_type="list" label="Output from previous Stacks pipeline steps (e.g. denovo_map or refmap)" /> - <param name="reads" argument="-s" format="fastqsanger" type="data" multiple="true" label="Files containing sequences" help="Files containing parent sequences from a mapping cross" /> + <param name="reads" argument="-s" format="fastqsanger" type="data" multiple="true" label="Files containing reads to assemble" help="only R2 reads" /> <param name="whitelist" argument="-w" format="txt,tabular" type="data" optional="true" label="White list of catalog IDs to include" /> <param name="threshold" argument="-r" type="integer" value="" optional="true" label="Minimum number of reads by locus"/> @@ -72,7 +79,8 @@ </inputs> <outputs> <collection name="collated" type="list" label="Collated FASTA files per locus on ${on_string}"> - <discover_datasets pattern="(?P<name>.+)\.fa(sta)?" ext="fasta" directory="stacks_outputs" /> + <filter>not velvet['use_velvet']</filter> + <discover_datasets pattern="(?P<name>.+)\.fa(sta)?$" ext="fasta" directory="stacks_outputs" /> </collection> <data format="fasta" name="contigs" label="Assembled contigs on ${on_string}" from_work_dir="assembled/collated.fa"> @@ -127,14 +135,6 @@ <param name="velvet|use_velvet" value="true" /> <param name="velvet|contig_length" value="20" /> - <output_collection name="collated"> - <element name="1"> - <assert_contents> - <has_text text="CCGATCAGCATCAGTAGTTTTCAACGAGCTGGCCCAATGGTGTATAACTATGTGGTAGAGAGAAACTGCTGCTATCACTCACGATATAAGCCCTCTGACG" /> - </assert_contents> - </element> - </output_collection> - <output name="contigs"> <assert_contents> <has_text text="TGTATTCTCCCATGCGACAGCAGGACATCCCATCCCCCTCTGATGTTATCAATCATAAGA" /> |
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| diff -r fea78fd36a05 -r ee52d9cfaffc tool_dependencies.xml --- a/tool_dependencies.xml Wed Jun 15 06:23:24 2016 -0400 +++ b/tool_dependencies.xml Sat Jun 25 17:27:42 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" /> |