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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
author | galaxyp |
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date | Thu, 13 Oct 2016 08:38:04 -0400 |
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<tool id="sixgill_build" name="sixgill build" version="@VERSION@.0"> <description>a metapeptide database from metagenome fastq files</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <expand macro="stdio" /> <version_command>sixgill_build --version</version_command> <command><![CDATA[ sixgill_build --nogzipout --out=metapeptides_db_output.tsv #if 'fa' in str($output_choice): --outfasta=metapeptides_fa_output.fa #end if #if str($sec_filter.minlength): --minlength=$sec_filter.minlength #end if #if str($sec_filter.minqualscore): --minqualscore=$sec_filter.minqualscore #end if #if str($sec_filter.minorflength): --minorflength=$sec_filter.minorflength #end if #if str($sec_filter.minlongesttryppeplen): --minlongesttryppeplen=$sec_filter.minlongesttryppeplen #end if #if str($sec_filter.minreadcount): --minreadcount=$sec_filter.minreadcount #end if #if str($sec_filter.maxreads): --maxreads=$sec_filter.maxreads #end if #if $sec_mg.metagenefile: --metagenefile="$sec_mg.metagenefile" #if $sec_mg.minmetagenescore: --minmetagenescore=$sec_mg.minmetagenescore #end if #end if #for $i, $fastqfile in enumerate($fastqfiles): "$fastqfile" #end for ]]></command> <inputs> <param name="fastqfiles" type="data" format="fastq" multiple="true" optional="false" label="metagenomic fastq files" help=""/> <section name="sec_filter" expanded="false" title="filter"> <param name="minlength" type="integer" value="10" min="0" optional="true" label="minlength" help="min AA length of a metapeptide"/> <param name="minqualscore" type="integer" value="30" min="0" optional="true" label="minqualscore" help="min base-call phred score across any NT in a metapeptide"/> <param name="minorflength" type="integer" value="40" min="0" optional="true" label="minorflength" help="min length of ORF-portion"/> <param name="minlongesttryppeplen" type="integer" value="7" min="0" optional="true" label="minlongesttryppeplen" help="minimum length of the longest tryptic peptide"/> <param name="minreadcount" type="integer" value="2" min="1" optional="true" label="minreadcount" help="minimum read count"/> <param name="maxreads" type="integer" value="" optional="true" label="maxreads" help="stop early if we hit this many reads"/> </section> <section name="sec_mg" expanded="false" title="MetaGene Annotator"> <param name="metagenefile" type="data" format="txt" optional="true" label="metagenefile" help="MetaGene Annotator output file. Records must be in same linear order as reads in fastqfiles"/> <param name="minmetagenescore" type="integer" value="" min="-1" optional="true" label="minmetagenescore" help="minimum MetaGene score"/> </section> <param name="output_choice" type="select" multiple="true" optional="false" label="select outputs"> <option value="db" selected="true">metapeptide database</option> <option value="fa">metapeptide protein fasta</option> </param> </inputs> <outputs> <data name="output_db" format="tabular" label="${tool.name} on ${on_string}: metapeptides.tsv" from_work_dir="metapeptides_db_output.tsv"> <filter>'db' in output_choice</filter> <actions> <action name="comment_lines" type="metadata" default="1" /> <action name="column_names" type="metadata" default="sequence,length,min_qualscore,partial_orf_length,metagene_score,read_ids" /> </actions> </data> <data name="output_fa" format="fasta" label="${tool.name} on ${on_string}: metapeptides.fa" from_work_dir="metapeptides_fa_output.fa"> <filter>'fa' in output_choice</filter> </data> </outputs> <tests> <test> <param name="fastqfiles" ftype="fastq" value="small.fq"/> <param name="minreadcount" value="1"/> <param name="output_choice" value="db,fa"/> <output name="output_db"> <assert_contents> <has_text text="DLRILLRERLVAGDSDEAAVDFIVDR" /> </assert_contents> </output> <output name="output_fa"> <assert_contents> <has_text text="DLRILLRERLVAGDSDEAAVDFIVDR" /> </assert_contents> </output> </test> <test> <param name="fastqfiles" ftype="fastq" value="small.fq"/> <param name="minreadcount" value="1"/> <param name="metagenefile" ftype="fastq" value="metagene_output.txt"/> <param name="output_choice" value="db"/> <output name="output_db"> <assert_contents> <has_text text="DLRILLRERLVAGDSDEAAVDFIVDR" /> </assert_contents> </output> </test> </tests> <help><![CDATA[ usage: sixgill_build [-h] [--minlength MINLENGTH] [--minqualscore MINQUALSCORE] [--metagenefile METAGENEFILE] [--minmetagenescore MINMETAGENESCORE] [--minorflength MINORFLENGTH] [--minlongesttryppeplen MINLONGESTTRYPPEPLEN] [--maxreads MAXREADS] [--minreadcount MINREADCOUNT] --out OUT [--outfasta OUTFASTA] [--debug] fastqfiles [fastqfiles ...] Read in one or more fastq files. For each read, do a 6-frame translation and add all metapeptides that pass the specified filtering criteria. If --metagenefile is specified, start with the output of MetaGene Annotator instead of raw reads. positional arguments: fastqfiles input fastq file(s), bgzipped optional arguments: -h, --help show this help message and exit --minlength MINLENGTH min AA length of a metapeptide --minqualscore MINQUALSCORE min base-call phred score across any NT in a metapeptide --metagenefile METAGENEFILE input MetaGene Annotator output file. Records must be in same linear order as reads in fastqfiles --minmetagenescore MINMETAGENESCORE minimum MetaGene score --minorflength MINORFLENGTH min length of ORF-portion --minlongesttryppeplen MINLONGESTTRYPPEPLEN minimum length of the longest tryptic peptide --maxreads MAXREADS stop early if we hit this many reads --minreadcount MINREADCOUNT minimum read count --out OUT Output metapeptide database file --outfasta OUTFASTA Output metapeptide fasta database file --debug Enable debug logging ]]></help> <expand macro="citations" /> </tool>