Mercurial > repos > iuc > hmmer_hmmbuild
view hmmbuild.xml @ 4:d0875d3f6544 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7c3ac4ad5a64b737e1b8f73c522e006097596f1d
author | iuc |
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date | Mon, 11 Jun 2018 15:52:17 -0400 |
parents | 7ea31fc35394 |
children | 750269125dc9 |
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<?xml version="1.0"?> <tool id="hmmer_hmmbuild" name="hmmbuild" version="@TOOL_VERSION@"> <description>Build a profile HMM from an input multiple alignment</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> <command><![CDATA[ hmmbuild #if $hmmname: -n '$hmmname' #end if @FORMAT_SELECTOR@ @MCSS@ @ARSWS@ @AEEWS@ @PRIOR@ @HSSI@ @EVAL_CALIB@ @CPU@ @SEED@ @LENGTHS@ #if str($maxinsertlen): --maxinsertlen $maxinsertlen #end if '$hmmout' '$msafile' ]]></command> <inputs> <expand macro="input_msa" /> <param name="hmmname" argument="-n" type="text" optional="true" label="Name for the HMM" /> <expand macro="format_selector"/> <expand macro="mcss"/> <expand macro="arsws"/> <expand macro="aeews"/> <expand macro="prior"/> <expand macro="hssi"/> <expand macro="eval_calib_xml"/> <expand macro="seed"/> <expand macro="lengths" /> <param argument="--maxinsertlen" type="integer" optional="true" label="Pretend all inserts are length <= n" /> </inputs> <outputs> <data name="hmmout" format="hmm3" label="HMM profile from $msafile.name"/> </outputs> <tests> <test> <param name="msafile" value="globins4.sto"/> <expand macro="seed_test" /> <output name="hmmout" file="globins4.hmm" lines_diff="10"/> </test> <test> <param name="msafile" value="MADE1.sto"/> <param name="input_format_select" value="--dna"/> <expand macro="seed_test" /> <output name="hmmout" file="MADE1.hmm" lines_diff="14"/> </test> </tests> <help><![CDATA[ @HELP_PRE@ For each multiple sequence alignment in <msafile> build a profile HMM and save it to a new file <hmmfile out>. @HELP_PRE_OTH@ @FORMAT_SELECTOR_HELP@ @MCSS_HELP@ @ARSWS_HELP@ @AEEWS_HELP@ @PRIOR_HELP@ @HSSI_HELP@ @EVAL_CALIB_HELP@ @SEED_HELP@ @LENGTHS_HELP@ @ATTRIBUTION@ ]]></help> <expand macro="citation"/> </tool>