comparison jackhmmer.xml @ 9:9fdeca68a6b5 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 721504306833ba97c91f285e5bfd86efc04875ee

8:5cbef50c0c63

<?xml version="1.0"?>
<tool id="hmmer_jackhmmer" name="jackhmmer" version="@TOOL_VERSION@+galaxy0">
  <description>iteratively search a protein sequence against a protein database (PSIBLAST-like)</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="bio_tools"/>
  <expand macro="requirements"/>
  <expand macro="stdio"/>
  <command><![CDATA[
@ADDTHREADS@
jackhmmer
-N $N
@OFORMAT_WITH_OPTS@
@HSSI@

> '$output'
  ]]></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="N" type="integer" value="5" min="1" label="Maximum number of iterations" help="(-N)"/>
    <param name="seqdb" type="data" format="fasta" label="Sequence Database"/>
    <expand macro="oformat_with_opts_dom"/>
    <expand macro="hssi"/>
    <expand macro="thresholds_xml"/>
    <expand macro="accel_heur_xml"/>

      <expand macro="oformat_test" />
      <expand macro="seed_test" />
      <output name="output" file="jackhmmer.out" lines_diff="180">
          <expand macro="assert_out" tool="jackhmmer"/>
      </output>
      <output name="domtblout" file="jackhmmer.domtblout" lines_diff="10">
          <expand macro="assert_tblout" tool="jackhmmer"/>
      </output>
      <output name="tblout" file="jackhmmer.tblout" lines_diff="10">
          <expand macro="assert_tblout" tool="jackhmmer"/>
      </output>
    </test>
    <test expect_num_outputs="1">
      <param name="seqfile" value="uniprot_matches.fasta"/>

9:9fdeca68a6b5

<?xml version="1.0"?>
<tool id="hmmer_jackhmmer" name="jackhmmer" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
  <description>iteratively search a protein sequence against a protein database (PSIBLAST-like)</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="bio_tools"/>
  <expand macro="requirements"/>
  <command detect_errors="aggressive"><![CDATA[
@ADDTHREADS@
jackhmmer
-N $N
@OFORMAT_WITH_OPTS@
@HSSI@

> '$output'
  ]]></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 argument="-N" type="integer" value="5" min="1" label="Maximum number of iterations" help="(-N)"/>
    <param name="seqdb" type="data" format="fasta" label="Sequence Database"/>
    <expand macro="oformat_with_opts_dom"/>
    <expand macro="hssi"/>
    <expand macro="thresholds_xml"/>
    <expand macro="accel_heur_xml"/>

      <expand macro="oformat_test" />
      <expand macro="seed_test" />
      <output name="output" file="jackhmmer.out" lines_diff="180">
          <expand macro="assert_out" tool="jackhmmer"/>
      </output>
      <output name="domtblout" file="jackhmmer.domtblout" lines_diff="12">
          <expand macro="assert_tblout" tool="jackhmmer"/>
      </output>
      <output name="tblout" file="jackhmmer.tblout" lines_diff="12">
          <expand macro="assert_tblout" tool="jackhmmer"/>
      </output>
    </test>
    <test expect_num_outputs="1">
      <param name="seqfile" value="uniprot_matches.fasta"/>