comparison macros.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 name="bio_tools">
      <xrefs>
          <xref type="bio.tools">hmmer3</xref>
      </xrefs>
  </xml>
  <token name="@TOOL_VERSION@">3.3.2</token>
  <xml name="stdio">
    <stdio>
      <!-- Anything other than zero is an error -->
      <exit_code range="1:"/>
      <exit_code range=":-1"/>
      <!-- In case the return code has not been set propery check stderr too -->
      <regex match="Error:"/>
      <regex match="Exception:"/>
    </stdio>
  </xml>

  <!-- command line for thresholds_* -->
  <token name="@THRESHOLDS@">
#if $repopt.repopt_sel == "evalue"
  -E $repopt.E
  #if str($repopt.incE) != ""

        <option value="--wgsc">Gerstein/Sonnhammer/Chothia tree weights (--wgsc)</option>
        <option value="--wblosum">Henikoff simple filter weights (--wblosum)</option>
        <option value="--wnone">don't do any relative weighting; set all to 1 (--wnnoe)</option>
        <option value="--wgiven">use weights as given in MSA file (--wgiven)</option>
      </param>
      <when value="--wpb">
      </when>
      <when value="--wgsc">
      </when>
      <when value="--wblosum">
        <param argument="--wid" type="float" value="0.62" label="Set identity cutoff" />
      </when>
      <when value="--wnone">
      </when>
      <when value="--wgiven">
      </when>
    </conditional>
  </xml>
  <token name="@AEEWS@">
#if $aeews.aeews_select != "":
--$aeews.aeews_select

9:9fdeca68a6b5

  <xml name="bio_tools">
      <xrefs>
          <xref type="bio.tools">hmmer3</xref>
      </xrefs>
  </xml>
  <token name="@TOOL_VERSION@">3.4</token>
  <token name="@PROFILE@">22.05</token>
  <!-- command line for thresholds_* -->
  <token name="@THRESHOLDS@">
#if $repopt.repopt_sel == "evalue"
  -E $repopt.E
  #if str($repopt.incE) != ""

        <option value="--wgsc">Gerstein/Sonnhammer/Chothia tree weights (--wgsc)</option>
        <option value="--wblosum">Henikoff simple filter weights (--wblosum)</option>
        <option value="--wnone">don't do any relative weighting; set all to 1 (--wnnoe)</option>
        <option value="--wgiven">use weights as given in MSA file (--wgiven)</option>
      </param>
      <when value="--wpb"/>
      <when value="--wgsc"/>
      <when value="--wblosum">
        <param argument="--wid" type="float" value="0.62" label="Set identity cutoff" />
      </when>
      <when value="--wnone"/>
      <when value="--wgiven"/>
    </conditional>
  </xml>
  <token name="@AEEWS@">
#if $aeews.aeews_select != "":
--$aeews.aeews_select