comparison nhmmscan.xml @ 2:c3075b7fdbdd draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6

1:4351ee79c942

<?xml version="1.0"?>
<tool id="hmmer_nhmmscan" name="nhmmscan" version="@WRAPPER_VERSION@.0">
  <description>search DNA sequence(s) against a DNA profile database</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <expand macro="stdio"/>
  <command><![CDATA[
hmmpress $hmmfile;

nhmmscan

@OFORMAT_WITH_OPTS_N@
@THRESHOLDS_NODOM@
@CUT@

@ADV_OPTS@
@LENGTHS@
@CPU@
@SEED@

$hmmfile
$seqfile
> $output
      ]]></command>
  <inputs>
    <expand macro="input_hmm" />
    <!-- todo use Galaxy features like data libraries/data tables/??? -->
    <param name="seqfile" type="data" format="fasta" label="Sequence file"/>
    <expand macro="oformat_with_opts_n"/>
    <expand macro="thresholds_nodom"/>
    <expand macro="cut"/>
    <expand macro="accel_heur_xml"/>

    <param name="B1" type="integer" label="window length for biased-composition modifier (MSV)" help="(--B1)" value="110"/>
    <param name="B2" type="integer" label="window length for biased-composition modifier (Vit)" help="(--B2)" value="240"/>
    <param name="B3" type="integer" label="window length for biased-composition modifier (Fwd)" help="(--B3)" value="1000"/>

    <expand macro="adv_opts"/>
    <expand macro="lengths"/>
    <expand macro="seed"/>
  </inputs>
  <outputs>
    <data format="txt" name="output" label="HMM matches 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>'tblout' in str(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>'pfamtblout' in str(oformat)</filter>
    </data>
    <data format="txt" name="aliscoresout" label="Scores for positional matches of $seqfile.name in $hmmfile.name">
      <filter>'aliscoresout' in str(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="MADE1.out" lines_diff="140"/>
      <output name="tblout" file="MADE1.out.tblout" lines_diff="30"/>
      <output name="domtblout" file="MADE1.out.domtblout" lines_diff="30"/>
      <output name="pfamtblout" file="MADE1.out.pfamtblout" lines_diff="36"/>
    </test>
  </tests>
  <help><![CDATA[
@HELP_PRE@

2:c3075b7fdbdd

<?xml version="1.0"?>
<tool id="hmmer_nhmmscan" name="nhmmscan" version="@TOOL_VERSION@">
  <description>search DNA sequence(s) against a DNA profile database</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <expand macro="stdio"/>
  <command><![CDATA[
@INPUTHMMCHOICE@
nhmmscan

@OFORMAT_WITH_OPTS_N@
@THRESHOLDS_NODOM@
@CUT@

@ADV_OPTS@
@LENGTHS@
@CPU@
@SEED@

'$input_hmm_filename'
'$seqfile'
> '$output'
  ]]></command>
  <inputs>
    <expand macro="input_hmm_choice" />
    <!-- todo use Galaxy features like data libraries/data tables/??? -->
    <param name="seqfile" type="data" format="fasta" label="Sequence file"/>
    <expand macro="oformat_with_opts_n"/>
    <expand macro="thresholds_nodom"/>
    <expand macro="cut"/>
    <expand macro="accel_heur_xml"/>

    <param argument="--B1" type="integer" value="110" label="window length for biased-composition modifier (MSV)" />
    <param argument="--B2" type="integer" value="240" label="window length for biased-composition modifier (Vit)" />
    <param argument="--B3" type="integer" value="1000" label="window length for biased-composition modifier (Fwd)" />

    <expand macro="adv_opts"/>
    <expand macro="lengths"/>
    <expand macro="seed"/>
  </inputs>
  <outputs>
    <data name="output" format="txt" label="HMM matches of $seqfile.name against the profile database"/>

    <data name="tblout" format="txt" label="Table of per-sequence hits from HMM matches of $seqfile.name against the profile database">
      <filter>oformat and 'tblout' in oformat</filter>
    </data>
    <data name="dfamtblout" format="txt" label="Table of per-sequence/per-domain hits from HMM matches of $seqfile.name against the profile database">
      <filter>oformat and 'dfamtblout' in oformat</filter>
    </data>
    <data name="aliscoresout" format="txt" label="Scores for positional matches of $seqfile.name against the profile database">
      <filter>oformat and 'aliscoresout' in oformat</filter>
    </data>
  </outputs>
  <tests>
    <test>
      <param name="input_hmm_conditional|input_hmm_source" value="history"/>
      <param name="input_hmm_conditional|hmmfile" value="MADE1.hmm"/>
      <param name="seqfile" value="dna_target.fa"/>
      <expand macro="oformat_test" />
      <expand macro="seed_test" />
      <output name="output" file="MADE1.nhmmscan_out" lines_diff="12" />
      <output name="tblout" file="MADE1.nhmmscan_out.tblout" lines_diff="10" />
      <output name="dfamtblout" file="MADE1.nhmmscan_out.dfamtblout" />
      <output name="aliscoresout" file="MADE1.nhmmscan_out.aliscoresout" lines_diff="10" />
    </test>
  </tests>
  <help><![CDATA[
@HELP_PRE@