Mercurial > repos > galaxyp > sixgill
diff 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 |
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date | Thu, 13 Oct 2016 08:38:04 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sixgill_filter.xml Thu Oct 13 08:38:04 2016 -0400 @@ -0,0 +1,120 @@ +<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>