Mercurial > repos > iuc > hmmer_hmmsearch
diff hmmsearch.xml @ 0:1dde27bbdcba draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
author | iuc |
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date | Sat, 25 Jun 2016 15:06:44 -0400 |
parents | |
children | 4d2ba28f8c8c |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hmmsearch.xml Sat Jun 25 15:06:44 2016 -0400 @@ -0,0 +1,80 @@ +<?xml version="1.0"?> +<tool id="hmmer_hmmsearch" name="hmmsearch" version="@WRAPPER_VERSION@.0"> + <description>search profile(s) against a sequence database</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="stdio"/> + <command><![CDATA[ +hmmsearch + +@OFORMAT_WITH_OPTS@ +@THRESHOLDS@ +@CUT@ +@ACCEL_HEUR@ +@ADV_OPTS@ +@CPU@ +@SEED@ + +$hmmfile +$seqdb +> $output + ]]></command> + <inputs> + <expand macro="input_hmm" /> + <!-- todo use Galaxy features like data libraries/data tables/??? --> + <param name="seqdb" type="data" format="fasta" label="Sequence database to search against"/> + <expand macro="oformat_with_opts"/> + <expand macro="thresholds_xml"/> + <expand macro="cut"/> + <expand macro="accel_heur_xml"/> + <expand macro="adv_opts"/> + <expand macro="seed"/> + </inputs> + <outputs> + <data format="txt" name="output" label="HMM matches of $hmmfile.name in $seqdb.name"/> + <data format="txt" name="tblout" label="Table of per-sequence hits from HMM matches of $hmmfile.name in $seqdb.name"> + <filter>'tblout' in str(oformat)</filter> + </data> + <data format="txt" name="domtblout" label="Table of per-domain hits from HMM matches of $hmmfile.name in $seqdb.name"> + <filter>'domtblout' in str(oformat)</filter> + </data> + <data format="txt" name="pfamtblout" label="Table of per-sequence/per-domain hits from HMM matches of $hmmfile.name in $seqdb.name"> + <filter>'pfamtblout' in str(oformat)</filter> + </data> + </outputs> + <tests> + <test> + <param name="hmmfile" value="globins4.hmm"/> + <param name="seqdb" value="uniprot_matches.fasta"/> + <expand macro="oformat_test" /> + <expand macro="seed_test" /> + <output name="output" file="uniprot_globins_match.out" lines_diff="20"/> + <output name="domtblout" file="globins.domtblout" lines_diff="10"/> + <output name="pfamtblout" file="globins.pfamtblout" lines_diff="10"/> + <output name="tblout" file="globins.tblout" lines_diff="10"/> + </test> + </tests> + <help><![CDATA[ +@HELP_PRE@ + +hmmsearch is used to search one or more profiles against a sequence database. +For each profile in <hmmfile>, use that query profile to search the target +database of sequences in <seqdb>, and output ranked lists of the sequences with +the most significant matches to the profile. To build profiles from multiple +alignments, see hmmbuild. + +@HELP_PRE_OTH@ + +@OFORMAT_WITH_OPTS_HELP@ +@THRESHOLDS_HELP@ +@CUT_HELP@ +@ACCEL_HEUR_HELP@ +@ADV_OPTS_HELP@ +@SEED_HELP@ + +@ATTRIBUTION@ +]]></help> + <expand macro="citation"/> +</tool>