Mercurial > repos > galaxyp > sixgill
diff sixgill_merge.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_merge.xml Thu Oct 13 08:38:04 2016 -0400 @@ -0,0 +1,70 @@ +<tool id="sixgill_merge" name="sixgill merge" version="@VERSION@.0"> + <description>metapeptide databases</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> + <version_command>sixgill_merge --version</version_command> + <command><![CDATA[ + sixgill_merge + --nogzipout + --out=metapeptides_db_output.tsv + #for ($i,$metapeptide_db) in enumerate($metapeptide_dbs) + "$metapeptide_db" + #end for + #if 'fa' in str($output_choice): + && + sixgill_makefasta --type=aa --out="metapeptides_fa_output.fa" "metapeptides_db_output.tsv" + #end if + ]]></command> + <inputs> + <param name="metapeptide_dbs" type="data" format="tabular" multiple="true" optional="false" label="metapeptide databases" + help="Can be generated with sixgill_build"/> + <param name="output_choice" type="select" multiple="true" optional="false" label="select outputs"> + <option value="db" selected="true">metapeptide database</option> + <option value="fa">metapeptide protein fasta</option> + </param> + </inputs> + <outputs> + <data name="output_db" format="tabular" label="${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_dbs" ftype="tabular" + value="testdb_metagene.metapeptides.tsv,testdb_nometagene.metapeptides.tsv"/> + <output name="output_db"> + <assert_contents> + <has_text text="DLRILLRERLVAGDSDEAAVDFIVDR" /> + <has_text text="YHNFEGYRWR" /> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +usage: sixgill_merge [-h] --out OUT [--debug] + metapeptidedbfiles [metapeptidedbfiles ...] + +Merge multiple metapeptide database files into a single metapeptide database. +Optionally, filter simultaneously. + +positional arguments: + metapeptidedbfiles input metapeptide database files + +optional arguments: + -h, --help show this help message and exit + --out OUT output file + --debug Enable debug logging + + ]]></help> + <expand macro="citations" /> +</tool>