Mercurial > repos > drosofff > msp_sr_bowtie
changeset 12:a0bde9b84ca6 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit b6de14061c479f0418cd89e26d6f5ac26e565a07
| author | drosofff |
|---|---|
| date | Wed, 09 Nov 2016 11:22:31 -0500 |
| parents | 88cdd6118bfe |
| children | 99009e0a7a4a |
| files | sRbowtie.py sRbowtie.xml tool_dependencies.xml |
| diffstat | 3 files changed, 26 insertions(+), 24 deletions(-) [+] |
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--- a/sRbowtie.py Mon Sep 28 16:47:11 2015 -0400 +++ b/sRbowtie.py Wed Nov 09 11:22:31 2016 -0500 @@ -181,7 +181,7 @@ else: tmp_dir, index_path = "dummy/dymmy", args.index_source command_line = bowtieCommandLiner(args.method, args.v_mismatches, args.output_format, - args.aligned, args.unaligned, args.input_format, args.input, + args.aligned, args.unaligned, args.input_format, args.input, index_path, args.output, args.num_threads) bowtie_alignment(command_line, flyPreIndexed=tmp_dir) F.close()
--- a/sRbowtie.xml Mon Sep 28 16:47:11 2015 -0400 +++ b/sRbowtie.xml Wed Nov 09 11:22:31 2016 -0500 @@ -1,27 +1,29 @@ -<tool id="bowtieForSmallRNA" name="sRbowtie" version="1.1.2"> +<tool id="bowtieForSmallRNA" name="sRbowtie" version="1.1.2.1"> <description>for FASTA small reads</description> <requirements> - <requirement type="package" version="0.12.7">bowtie</requirement> + <requirement type="package" version="1.1.2">bowtie</requirement> <requirement type="package" version="1.2">samtools</requirement> </requirements> - <command interpreter="python"> sRbowtie.py --input $input - --input-format $input.extension - --method $method - --v-mismatches $v_mismatches - --output-format $output_format - --output $output - --index-from $refGenomeSource.genomeSource - ## the very source of the index (indexed or fasta file) - --index-source - #if $refGenomeSource.genomeSource == "history": - $refGenomeSource.ownFile - #else: - $refGenomeSource.index.fields.path - #end if - --aligned $aligned - --unaligned $unaligned - --num-threads \${GALAXY_SLOTS:-4} ## number of processors to be handled by bowtie - </command> + <command><![CDATA[ + python '$__tool_directory__'/sRbowtie.py + --input '$input' + --input-format '$input.extension' + --method '$method' + --v-mismatches $v_mismatches + --output-format $output_format + --output '$output' + --index-from '$refGenomeSource.genomeSource' + ## the very source of the index (indexed or fasta file) + --index-source + #if $refGenomeSource.genomeSource == "history": + '$refGenomeSource.ownFile' + #else: + '$refGenomeSource.index.fields.path' + #end if + --aligned '$aligned' + --unaligned '$unaligned' + --num-threads \${GALAXY_SLOTS:-4} ## number of processors to be handled by bowtie + ]]></command> <inputs> <param format="fasta, fastq" help="Only with clipped, raw fasta files" label="Input fasta file: reads clipped from their adapter" name="input" type="data" /> <param help="bowtie parameters adjusted to the type of matching. RNA option match to only one strand" label="What kind of matching do you want to do?" name="method" type="select">
--- a/tool_dependencies.xml Mon Sep 28 16:47:11 2015 -0400 +++ b/tool_dependencies.xml Wed Nov 09 11:22:31 2016 -0500 @@ -1,9 +1,9 @@ <?xml version="1.0"?> <tool_dependency> - <package name="bowtie" version="0.12.7"> - <repository changeset_revision="f0faa5eea2eb" name="package_bowtie_0_12_7" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <package name="bowtie" version="1.1.2"> + <repository changeset_revision="8584a4574ab1" name="package_bowtie_1_1_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> <package name="samtools" version="1.2"> - <repository changeset_revision="9cd278d52bb6" name="package_samtools_1_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="5b7172f9b230" name="package_samtools_1_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> </tool_dependency>