| Previous changeset 0:e1867440ed36 (2017-09-19) |
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Commit message:
planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 969557932bff35913d93068d16facb8da4d64123 |
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modified:
seqtk_nml.xml |
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| diff -r e1867440ed36 -r f49992c79fe4 seqtk_nml.xml --- a/seqtk_nml.xml Tue Sep 19 16:37:42 2017 -0400 +++ b/seqtk_nml.xml Thu Nov 02 14:09:07 2017 -0400 |
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| b'@@ -1,113 +1,114 @@\n-<tool id="seqtk_nml_sample" name="seqTK Sample NML" version="1.0.0">\n+<tool id="seqtk_nml_sample" name="seqTK Sample NML" version="1.0.1">\n <description>Runs seqTK sample if raw coverage is above user defined threshold </description>\n <requirements>\n <requirement type="package" version="1.2">seqtk</requirement>\n <requirement type="package" version="1.6.924">perl-bioperl</requirement>\n </requirements>\n- <stdio>\n- <exit_code range="1:" level="fatal" description="Unknown error has occured"/>\n- </stdio>\n- <command>\n-\t\tperl $__tool_directory__/seqtk_nml.pl --ref $fastar \n+ <command detect_errors="exit_code"><![CDATA[\n+ perl \'$__tool_directory__/seqtk_nml.pl\'\n+\n+ --ref \'$fastar\' \n+\n+ #if $single_or_paired.type == "single"\n+ --type single\n+ --forward \'$input_se\'\n+ --out_forward \'$output\'\n \n-\t\t#if $single_or_paired.type == "single"\n-\t\t\t--type single\n- \t\t\t--forward $input_se\n- \t\t\t--cov $coverage \n-\t\t\t--out_forward $output\n-\t\t\t--log $log\n-\t\t#elif $single_or_paired.type == "paired"\n-\t --type paired\n- \t--forward $single_or_paired.forward_pe \n-\t\t--reverse $single_or_paired.reverse_pe\n- \t--cov $coverage \n-\t\t--out_forward $output \n-\t\t--out_reverse $output_rev\n-\t\t--log $log\n- #else\n- collection\n- $single_or_paired.fastq_collection.forward $single_or_paired.fastq_collection.reverse\n- $coverage $output_collection.forward $output_collection.reverse\n- #end if\n+ #elif $single_or_paired.type == "paired"\n+ --type paired\n+ --forward \'$single_or_paired.forward_pe\'\n+ --reverse \'$single_or_paired.reverse_pe\'\n+ --out_forward \'$output\' \n+ --out_reverse \'$output_rev\'\n+ \n+ #else\n+ --type paired\n+ --forward \'$single_or_paired.fastq_collection.forward\' \n+ --reverse \'$single_or_paired.fastq_collection.reverse\'\n+ --out_forward \'$output_collection.forward\' \n+ --out_reverse \'$output_collection.reverse\'\n+ #end if\n \n- </command>\n+ --cov \'$coverage\'\n+ --log \'$log\'\n+\n+ ]]></command>\n <inputs>\n <conditional name="single_or_paired">\n <param name="type" type="select" label="Read type">\n-\t<option value="single">Single-end</option>\n- <option value="paired">Paired-end</option>\n- <option value="collection">Collection Paired-end</option>\n- </param>\n- <when value="single">\n-\t<param name="input_se" type="data" format="fastqsanger" label="Single end read file(s)"/>\n- </when>\n- <when value="paired">\n-\t<param name="forward_pe" type="data" format="fastqsanger" label="Forward paired-end read file"/>\n- <param name="reverse_pe" type="data" format="fastqsanger" label="Reverse paired-end read file"/>\n- </when>\n- <when value="collection">\n- <param name="fastq_collection" type="data_collection" label="Paired-end reads collection" optional="false" format="txt" collection_type="paired" />\n- </when>\n- </conditional>\n- <param name="fastar" type="data" label="Fasta Reference File" format="fasta" />\n- <param name="coverage" type="integer" label="Desired Coverage" value="50" />\n- </inputs>\n- <outputs>\n- <data format="fastqsanger" name="output" label="SubSampled Fastq" >\n- <filter>single_or_paired[\'type\']!="collection"</filter>\n- </data>\n- <data format="fastqsanger" name="output_rev" label="SubSampled Fastq Reverse">\n- <filter>single_or_paired[\'type\']=="paired"</filter>\n- </data>\n- <collection name="output_collection" type="paired" label="SubSampled Fastqs">\n- <data name="forward" format="fastqsanger"/>\n- <data name="reverse" format="fastqsanger"/>\n- <filter>single_or_paired[\'type\']=="collection"</filter>\n- </collection>\n- <data format="txt" name="log" label="Log file"/>\n- </outputs>\n- \n- <tests>\n- <test>\n- <param name="type" value="paired" />\n- <param name="forward_pe" value="inputforward.fastq" />\n- <param name="reverse_pe" value="inputreverse.fastq" />\n- '..b' name="coverage" value="50" />\n- <output name="output" file="outputforward.fastq" />\n- <output name="output_rev" file="outputreverse.fastq" />\n- <output name="log" file="lognosample.log" />\n- </test>\n- <test>\n- <param name="type" value="paired" />\n- <param name="forward_pe" value="inputforward.fastq" />\n- <param name="reverse_pe" value="inputreverse.fastq" />\n- <param name="fastar" value="testref.fasta"/>\n- <param name="coverage" value="25" />\n- <output name="output" file="outputdownsamepleforward.fastq" />\n- <output name="output_rev" file="outputdownsameplereverse.fastq" />\n- <output name="log" file="logdownsample.log" />\n- </test>\n- </tests>\n- <help>\n+ <option value="single">Single-end</option>\n+ <option value="paired">Paired-end</option>\n+ <option value="collection">Collection Paired-end</option>\n+ </param>\n+ <when value="single">\n+ <param name="input_se" type="data" format="fastqsanger" label="Single end read file(s)"/>\n+ </when>\n+ <when value="paired">\n+ <param name="forward_pe" type="data" format="fastqsanger" label="Forward paired-end read file"/>\n+ <param name="reverse_pe" type="data" format="fastqsanger" label="Reverse paired-end read file"/>\n+ </when>\n+ <when value="collection">\n+ <param name="fastq_collection" type="data_collection" label="Paired-end reads collection" optional="false" format="txt" collection_type="paired" />\n+ </when>\n+ </conditional>\n+ <param name="fastar" type="data" label="Fasta Reference File" format="fasta" />\n+ <param name="coverage" type="integer" label="Desired Coverage" value="50" />\n+</inputs>\n+<outputs>\n+ <data format="fastqsanger" name="output" label="SubSampled Fastq" >\n+ <filter>single_or_paired[\'type\']!="collection"</filter>\n+ </data>\n+ <data format="fastqsanger" name="output_rev" label="SubSampled Fastq Reverse">\n+ <filter>single_or_paired[\'type\']=="paired"</filter>\n+ </data>\n+ <collection name="output_collection" type="paired" label="SubSampled Fastqs">\n+ <data name="forward" format="fastqsanger"/>\n+ <data name="reverse" format="fastqsanger"/>\n+ <filter>single_or_paired[\'type\']=="collection"</filter>\n+ </collection>\n+ <data format="txt" name="log" label="Log file"/>\n+</outputs>\n+\n+<tests>\n+ <test>\n+ <param name="type" value="paired" />\n+ <param name="forward_pe" value="inputforward.fastq" />\n+ <param name="reverse_pe" value="inputreverse.fastq" />\n+ <param name="fastar" value="testref.fasta"/>\n+ <param name="coverage" value="50" />\n+ <output name="output" file="outputforward.fastq" />\n+ <output name="output_rev" file="outputreverse.fastq" />\n+ <output name="log" file="lognosample.log" />\n+ </test>\n+ <test>\n+ <param name="type" value="paired" />\n+ <param name="forward_pe" value="inputforward.fastq" />\n+ <param name="reverse_pe" value="inputreverse.fastq" />\n+ <param name="fastar" value="testref.fasta"/>\n+ <param name="coverage" value="25" />\n+ <output name="output" file="outputdownsamepleforward.fastq" />\n+ <output name="output_rev" file="outputdownsameplereverse.fastq" />\n+ <output name="log" file="logdownsample.log" />\n+ </test>\n+</tests>\n+<help><![CDATA[\n+============\n What it does\n ============\n-\n Calculates raw coverage. If the raw coverage is greater than desired coverage, runs seqTK sample to generate downsampled reads. \n \n-\n+=====\n Usage\n =====\n \n **Parameters**\n-\t- Fastq reads (single end, paired end, or paired end collection)\n-\t- Fasta reference file\n+- Fastq reads (single end, paired end, or paired end collection)\n+- Fasta reference file\n \n **Options**\n-\t- Desired coverage (50)\n- </help>\n- <citations>\n- <citation type="doi">doi.org/10.1371/journal.pone.0163962</citation>\n- </citations>\n-</tool>\n-\n+- Desired coverage (50)\n+]]></help>\n+<citations>\n+ <citation type="doi">10.1371/journal.pone.0163962</citation>\n+</citations>\n+</tool>\n\\ No newline at end of file\n' |