Mercurial > repos > iuc > hmmer_nhmmer
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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 15:52:05 -0400 |
parents | c8e81e43bff1 |
children | b4fe2f703b4b |
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<?xml version="1.0"?> <tool id="hmmer_nhmmer" name="nhmmer" version="@TOOL_VERSION@"> <description>search a DNA model or alignment against a DNA database (BLASTN-like)</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> <command><![CDATA[ nhmmer @OFORMAT_WITH_OPTS_N@ @HSSI@ @THRESHOLDS_NODOM@ @CUT@ @ACCEL_HEUR@ @FORMAT_SELECTOR@ @ADV_OPTS@ @LENGTHS@ @CPU@ @SEED@ '$hmmfile' '$seqfile' > '$output' ]]></command> <inputs> <expand macro="input_hmm" /> <param name="seqfile" type="data" format="fasta" label="Target sequence file"/> <expand macro="oformat_with_opts_n"/> <expand macro="hssi"/> <expand macro="thresholds_nodom"/> <expand macro="cut" /> <expand macro="accel_heur_xml"/> <expand macro="format_selector_noprot"/> <expand macro="adv_opts"/> <expand macro="lengths"/> <!-- TODO: block_length toponly bottomonly --> <expand macro="seed"/> </inputs> <outputs> <data format="txt" name="output" label="NHMMER search of $seqfile.name in $hmmfile.name"/> <data format="txt" name="tblout" label="Table of per-sequence hits from HMM matches of $seqfile.name in $hmmfile.name"> <filter>oformat and 'tblout' in oformat</filter> </data> <data format="txt" name="dfamtblout" label="Table of per-sequence/per-domain hits from HMM matches of $seqfile.name in $hmmfile.name"> <filter>oformat and 'pfamtblout' in oformat</filter> </data> <data format="txt" name="aliscoresout" label="Scores for positional matches of $seqfile.name in $hmmfile.name"> <filter>oformat and 'aliscoresout' in oformat</filter> </data> </outputs> <tests> <test> <param name="hmmfile" value="MADE1.hmm"/> <param name="seqfile" value="dna_target.fa"/> <expand macro="oformat_test" /> <expand macro="seed_test" /> <output name="output" file="nhmmer.out" lines_diff="10" /> <output name="tblout" file="nhmmer.out.tblout" lines_diff="10" /> <output name="dfamtblout" file="nhmmer.out.dfamtblout" lines_diff="10" /> </test> </tests> <help><![CDATA[ @HELP_PRE@ nhmmer is used to search one or more nucleotide queries against a nucleotide sequence database. For each query in <queryfile>, use that query to search the target database of sequences in <seqdb>, and output a ranked list of the hits with the most significant matches to the query. A query may be either a profile model built using hmmbuild, a sequence alignment, or a single sequence. Sequence based queries can be in a number of formats (see --qformat), and can typically be autodetected. Note that only Stockholm format supports the use of multiple sequence-based queries. @HELP_PRE_OTH@ @OFORMAT_WITH_OPTS_N_HELP@ @HSSI_HELP@ @THRESHOLDS_NODOM_HELP@ @CUT_HELP@ @ACCEL_HEUR_HELP@ @FORMAT_SELECTOR_HELP@ @ADV_OPTS_HELP@ @LENGTHS_HELP@ @SEED_HELP@ @ATTRIBUTION@ ]]></help> <expand macro="citation"/> </tool>