view nhmmer.xml @ 3:c8e81e43bff1 draft

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author iuc
date Sat, 07 Apr 2018 03:50:51 -0400
parents ae4754e7c97a
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>
  <expand macro="requirements"/>
  <expand macro="stdio"/>


> '$output'
    <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"/>
    <data format="txt" name="output" label="NHMMER search of $ in $"/>

    <data format="txt" name="tblout" label="Table of per-sequence hits from HMM matches of $ in $">
      <filter>oformat and 'tblout' in oformat</filter>
    <data format="txt" name="dfamtblout" label="Table of per-sequence/per-domain hits from HMM matches of $ in $">
      <filter>oformat and 'pfamtblout' in oformat</filter>
    <data format="txt" name="aliscoresout" label="Scores for positional matches of $ in $">
      <filter>oformat and 'aliscoresout' in oformat</filter>
      <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" />

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.



  <expand macro="citation"/>