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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_makefasta" name="sixgill makefasta" version="@VERSION@.0"> <description>from a metapeptide database</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <expand macro="stdio" /> <version_command>sixgill_makefasta --version</version_command> <command><![CDATA[ sixgill_makefasta --out=metapeptides_fa_output.fa --type="$fa_type.fasta_type" #if $fa_type.fasta_type == 'peptide': --missedcleavages=$fa_type.missedcleavages --minpeptidelength=$fa_type.minpeptidelength #end if "$metapeptide_db" ]]></command> <inputs> <param name="metapeptide_db" type="data" format="tabular" label="metapeptide database" help="Can be generated with sixgill_build"/> <conditional name="fa_type"> <param name="fasta_type" type="select" label="fasta type"> <help> peptide with specified missed cleavages requires holding all peptides in the database in memory, as each is only written once </help> <option value="aa" selected="true">aa - amino acid</option> <option value="peptide">peptide - with specified missed cleavages</option> </param> <when value="aa"/> <when value="peptide"> <param name="missedcleavages" type="integer" value="0" min="0" max="6" label="missedcleavages"/> <param name="minpeptidelength" type="integer" value="7" min="1" label="minpeptidelength"/> </when> </conditional> </inputs> <outputs> <data name="output_fa" format="fasta" label="${tool.name} on ${on_string}: metapeptide.fa" from_work_dir="metapeptides_fa_output.fa"/> </outputs> <tests> <test> <param name="metapeptide_db" ftype="tabular" value="testdb_metagene.metapeptides.tsv"/> <param name="fasta_type" value="aa"/> <output name="output_fa"> <assert_contents> <has_text text="DLRILLRERLVAGDSDEAAVDFIVDR" /> </assert_contents> </output> </test> </tests> <help><![CDATA[ usage: sixgill_makefasta [-h] --out OUT --type {aa,peptide} [--missedcleavages MISSEDCLEAVAGES] [--minpeptidelength MINPEPTIDELENGTH] [--debug] metapeptidedbfile Build a fasta database from a metapeptide database. Either nucleotide or amino acid. positional arguments: metapeptidedbfile input metapeptide database file optional arguments: -h, --help show this help message and exit --out OUT output file --type {aa,peptide} database type --missedcleavages MISSEDCLEAVAGES missed cleavages (for type peptide only) --minpeptidelength MINPEPTIDELENGTH minimum peptide length (for type peptide only) --debug Enable debug logging ]]></help> <expand macro="citations" /> </tool>