comparison phmmer.xml @ 5:c1de05e20868 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"

4:74fc6d7d40f1

  ]]></command>
  <inputs>
    <param name="seqfile" type="data" format="fasta" label="Protein sequence to search with"/>
    <!-- todo use Galaxy features like data libraries/data tables/??? -->
    <param name="seqdb" type="data" format="fasta" label="Sequence Database"/>
    <expand macro="oformat_with_opts"/>
    <expand macro="hssi"/>
    <expand macro="thresholds_xml"/>
    <expand macro="accel_heur_xml"/>
    <expand macro="eval_calib_xml"/>
    <expand macro="adv_opts"/>
    <expand macro="seed"/>
  </inputs>
  <outputs>
    <data name="output" format="txt" label="PHMMER search of $seqfile.name in $seqdb.name"/>
    <data name="tblout" format="txt" label="Table of per-sequence hits from HMM matches of $seqfile.name in $seqdb.name">
      <filter>oformat and 'tblout' in oformat</filter>
    </data>
    <data name="domtblout" format="txt" label="Table of per-domain hits from HMM matches of $seqfile.name in $seqdb.name">
      <filter>oformat and 'domtblout' in oformat</filter>
    </data>
    <data name="pfamtblout" format="txt" label="Table of per-sequence/per-domain hits from HMM matches of $seqfile.name in $seqdb.name">
      <filter>oformat and 'pfamtblout' in oformat</filter>
    </data>
  </outputs>
  <tests>
    <test>
      <param name="seqfile" value="globins45.fa"/>
      <param name="seqdb" value="uniprot_matches.fasta"/>
      <expand macro="oformat_test" />
      <expand macro="seed_test" />
      <output name="output" file="phmmer.out" lines_diff="200"/>
      <!-- Lines diff is high due to a line of cpu/timing information for EACH sequence -->
      <output name="domtblout" file="phmmer.domtblout" lines_diff="10"/>
      <output name="pfamtblout" file="phmmer.pfamtblout" lines_diff="10"/>
      <output name="tblout" file="phmmer.tblout" lines_diff="10"/>
    </test>
  </tests>
  <help><![CDATA[
@HELP_PRE@

5:c1de05e20868

  ]]></command>
  <inputs>
    <param name="seqfile" type="data" format="fasta" label="Protein sequence to search with"/>
    <!-- todo use Galaxy features like data libraries/data tables/??? -->
    <param name="seqdb" type="data" format="fasta" label="Sequence Database"/>
    <expand macro="oformat_with_opts_dom_pfam"/>
    <expand macro="hssi"/>
    <expand macro="thresholds_xml"/>
    <expand macro="accel_heur_xml"/>
    <expand macro="eval_calib_xml"/>
    <expand macro="adv_opts"/>
    <expand macro="seed"/>
  </inputs>
  <outputs>
    <expand macro="output_dom_pfam" tool="PHMMER"/>
  </outputs>
  <tests>
    <test expect_num_outputs="4">
      <param name="seqfile" value="globins45.fa"/>
      <param name="seqdb" value="uniprot_matches.fasta"/>
      <expand macro="oformat_test" />
      <expand macro="seed_test" />
      <output name="output" file="phmmer.out" lines_diff="200">
          <expand macro="assert_out" tool="phmmer"/>
      </output>
      <!-- Lines diff is high due to a line of cpu/timing information for EACH sequence -->
      <output name="domtblout" file="phmmer.domtblout" lines_diff="12">
          <expand macro="assert_tblout" tool="phmmer"/>
      </output>
      <output name="pfamtblout" file="phmmer.pfamtblout" lines_diff="12">
          <expand macro="assert_tblout" tool="phmmer"/>
      </output>
      <output name="tblout" file="phmmer.tblout" lines_diff="12">
          <expand macro="assert_tblout" tool="phmmer"/>
      </output>
    </test>
    <test expect_num_outputs="1">
      <param name="seqfile" value="globins45.fa"/>
      <param name="seqdb" value="uniprot_matches.fasta"/>
      <expand macro="oformat_test" />
      <param name="oformat" value=""/>
      <expand macro="seed_test" />
      <output name="output" file="phmmer.out" lines_diff="200">
          <expand macro="assert_out" tool="phmmer"/>
      </output>
    </test>
  </tests>
  <help><![CDATA[
@HELP_PRE@