Mercurial > repos > galaxyp > sixgill
view sixgill_filter.xml @ 0:cf8eee8343fb draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
author | galaxyp |
---|---|
date | Thu, 13 Oct 2016 08:38:04 -0400 |
parents | |
children |
line wrap: on
line source
<tool id="sixgill_filter" name="sixgill filter" version="@VERSION@.0"> <description>a metapeptide database</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <expand macro="stdio" /> <version_command>sixgill_filter --version</version_command> <command><![CDATA[ sixgill_filter --nogzipout --out=metapeptides_db_output.tsv #if str($minorflength) != '': --minorflength=$minorflength #end if #if str($minaaseqlength) != '': --minaaseqlength=$minaaseqlength #end if #if str($minqualscore) != '': --minqualscore=$minqualscore #end if #if str($minlongesttryppeplen) != '': --minlongesttryppeplen=$minlongesttryppeplen #end if #if str($minreadcount) != '': --minreadcount=$minreadcount #end if #if str($maxmetapeptides) != '': --maxmetapeptides=$maxmetapeptides #end if $metapeptide_db #if 'fa' in str($output_choice): && sixgill_makefasta --type=aa --out="metapeptides_fa_output.fa" "metapeptides_db_output.tsv" #end if ]]></command> <inputs> <param name="metapeptide_db" type="data" format="tabular" label="metapeptide database" help="Can be generated with sixgill_build"/> <param name="minorflength" type="integer" value="40" min="0" optional="true" label="minorflength" help="min length of ORF-portion"/> <param name="minaaseqlength" type="integer" value="10" min="0" optional="true" label="minaaseqlength" help="min AA sequence length"/> <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="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="minmetagenescore" type="integer" value="" min="-1" optional="true" label="minmetagenescore" help="minimum MetaGene score"/> <param name="maxmetapeptides" type="integer" value="" optional="true" label="maxmetapeptides" help="maximum number of metapeptides to write"/> <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="metapeptide_db" ftype="tabular" value="metagene_nometagene_merged.metapeptides.tsv"/> <param name="minreadcount" value="2"/> <param name="minaaseqlength" value="12"/> <param name="output_choice" value="db"/> <output name="output_db"> <assert_contents> <has_text text="DLRILLRERLVAGDSDEAAVDFIVDR" /> <not_has_text text="YHNFEGYRWR" /> </assert_contents> </output> </test> </tests> <help><![CDATA[ usage: sixgill_filter [-h] --out OUT [--minorflength MINORFLENGTH] [--minaaseqlength MINAASEQLENGTH] [--minreadcount MINREADCOUNT] [--minqualscore MINQUALSCORE] [--minlongesttryppeplen MINLONGESTTRYPPEPLEN] [--minmetagenescore MINMETAGENESCORE] [--maxmetapeptides MAXMETAPEPTIDES] [--debug] metapeptidefile Filter a metapeptide database. positional arguments: metapeptidefile input metapeptide database file optional arguments: -h, --help show this help message and exit --out OUT output metapeptide database file --minorflength MINORFLENGTH minimum ORF length --minaaseqlength MINAASEQLENGTH minimum AA sequence length --minreadcount MINREADCOUNT minimum read count --minqualscore MINQUALSCORE minimum basecall quality --minlongesttryppeplen MINLONGESTTRYPPEPLEN minimum length of the longest tryptic peptide --minmetagenescore MINMETAGENESCORE Minimum MetaGene score (-1 for none) --maxmetapeptides MAXMETAPEPTIDES maximum number of metapeptides to write --debug Enable debug logging ]]></help> <expand macro="citations" /> </tool>