comparison macros.xml @ 5:b4fe2f703b4b draft

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

4:be0cc39776f9

    <requirements>
      <requirement type="package" version="@TOOL_VERSION@">hmmer</requirement>
      <yield/>
    </requirements>
  </xml>
  <token name="@TOOL_VERSION@">3.2</token>
  <xml name="stdio">
    <stdio>
      <!-- Anything other than zero is an error -->
      <exit_code range="1:"/>
      <exit_code range=":-1"/>

    <param argument="--EvN" type="integer" min="1" value="200" label="Number of sequences for Viterbi Gumbel mu fit" />
    <param argument="--EfL" type="integer" min="1" value="100" label="Length of sequences for Forward exp tail tau fit" />
    <param argument="--EfN" type="integer" min="1" value="200" label="Number of sequences for Forward exp tail tau fit" />
    <param argument="--Eft" type="float" min="0" max="1" value="0.04" label="tail mass for Forward exponential tail tau fit" />
  </xml>
  <token name="@OFORMAT_WITH_OPTS_NOPFAM@">
#if 'tblout' in str($oformat):
    --tblout '$tblout'
#end if

#if 'domtblout' in str($oformat):
    --domtblout '$domtblout'
#end if

$acc $noali $notextw
  </token>
  <xml name="oformat_with_opts_nopfam">
    <!-- Options directing output -->
    <param name="oformat" multiple="true" display="checkboxes" label="Output Formats" type="select">
      <option value="tblout" selected="true">Table of per-sequence hits (--tblout)</option>
      <option value="domtblout" selected="true">Table of per-domain hits (--domtblout)</option>
    </param>
    <param argument="--acc" type="boolean" truevalue="--acc" falsevalue="" label="Prefer accessions over names in output" />
    <param argument="--noali" type="boolean" truevalue="--noali" falsevalue="" label="Don't output alignments, so output is smaller" />
    <param argument="--notextw" type="boolean" truevalue="--notextw" falsevalue="" label="Unlimited ASCII text output line width" />
  </xml>
  <token name="@OFORMAT_WITH_OPTS@">
#if 'tblout' in str($oformat):
    --tblout '$tblout'
#end if

#if 'domtblout' in str($oformat):
    --domtblout '$domtblout'
#end if

#if 'pfamtblout' in str($oformat):
    --pfamtblout '$pfamtblout'
#end if

$acc $noali $notextw
  </token>
  <xml name="oformat_with_opts">
    <!-- Options directing output -->
    <param name="oformat" type="select" multiple="true" display="checkboxes" label="Output Formats">
      <option value="tblout" selected="true">Table of per-sequence hits (--tblout)</option>
      <option value="domtblout" selected="true">Table of per-domain hits (--domtblout)</option>
      <option value="pfamtblout" selected="true">Table of hits and domains in Pfam format (--pfamtblout)</option>
    </param>
    <param argument="--acc" type="boolean" truevalue="--acc" falsevalue="" label="Prefer accessions over names in output" />
    <param argument="--noali" type="boolean" truevalue="--noali" falsevalue="" label="Don't output alignments, so output is smaller" />
    <param argument="--notextw" type="boolean" truevalue="--notextw" falsevalue="" label="Unlimited ASCII text output line width" />
  </xml>
  <xml name="oformat_test">
      <param name="notextw" value="true" />
  </xml>
  <!-- TODO: tblout will match 'pfamtblout,dfamtblout' -->
  <token name="@OFORMAT_WITH_OPTS_N@">
#if 'tblout' in str($oformat):
    --tblout '$tblout'
#end if

#if 'dfamtblout' in str($oformat):
    --dfamtblout '$dfamtblout'
#end if

#if 'aliscoresout' in str($oformat):
    --aliscoresout '$aliscoresout'
#end if

$acc $noali $notextw
  </token>
  <xml name="oformat_with_opts_n">
    <!-- Options directing output -->
    <param name="oformat" type="select" multiple="true" display="checkboxes" label="Output Formats">
      <option value="tblout" selected="true">Table of hits (--tblout)</option>
      <option value="dfamtblout" selected="true">Table of hits in Dfam format (--dfamtblout)</option>
      <option value="aliscoresout">Scores for each position in each alignment to file (--aliscoresout)</option>
    </param>
    <param argument="--acc" type="boolean" truevalue="--acc" falsevalue="" label="Prefer accessions over names in output" />
    <param argument="--noali" type="boolean" truevalue="--noali" falsevalue="" label="Don't output alignments, so output is smaller" />
    <param argument="--notextw" type="boolean" truevalue="--notextw" falsevalue="" label="Unlimited ASCII text output line width" />
  </xml>
  <token name="@HSSI@">
#if $hssi.hssi_select == "singlemx":
    --popen $hssi.popen
    --pextend $hssi.pextend

    # HMMER 3.1 (February 2013); http://hmmer.org/
    # Copyright (C) 2011 Howard Hughes Medical Institute.
    # Freely distributed under the GNU General Public License (GPLv3).
    # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

The wrappers were written by Eric Rasche and is licensed under Apache2_. The
documentation is copied from the HMMER3 documentation.

.. _Apache2: http://www.apache.org/licenses/LICENSE-2.0
.. _HMMER3: http://hmmer.org/

5:b4fe2f703b4b

    <requirements>
      <requirement type="package" version="@TOOL_VERSION@">hmmer</requirement>
      <yield/>
    </requirements>
  </xml>
  <token name="@TOOL_VERSION@">3.3</token>
  <xml name="stdio">
    <stdio>
      <!-- Anything other than zero is an error -->
      <exit_code range="1:"/>
      <exit_code range=":-1"/>

    <param argument="--EvN" type="integer" min="1" value="200" label="Number of sequences for Viterbi Gumbel mu fit" />
    <param argument="--EfL" type="integer" min="1" value="100" label="Length of sequences for Forward exp tail tau fit" />
    <param argument="--EfN" type="integer" min="1" value="200" label="Number of sequences for Forward exp tail tau fit" />
    <param argument="--Eft" type="float" min="0" max="1" value="0.04" label="tail mass for Forward exponential tail tau fit" />
  </xml>
  <token name="@OFORMAT_WITH_OPTS@">
#if $oformat:      
    #for o in str($oformat).split(','):
        --$o '$getVar($o, 'MISSING_OUTPUT'+$o)'
    #end for
#end if
$acc $noali $notextw
  </token>
  <xml name="oformat_with_opts">
    <!-- Options directing output -->
    <param name="oformat" type="select" multiple="true" display="checkboxes" label="Output Formats">
      <option value="tblout" selected="true">Table of per-sequence hits (--tblout)</option>
      <yield/>
    </param>
    <param argument="--acc" type="boolean" truevalue="--acc" falsevalue="" label="Prefer accessions over names in output" />
    <param argument="--noali" type="boolean" truevalue="--noali" falsevalue="" label="Don't output alignments, so output is smaller" />
    <param argument="--notextw" type="boolean" truevalue="--notextw" falsevalue="" label="Unlimited ASCII text output line width" />
  </xml>

  <xml name="oformat_with_opts_dom">
    <expand macro="oformat_with_opts">
      <option value="domtblout" selected="true">Table of per-domain hits (--domtblout)</option>
      <yield/>
    </expand>
  </xml>

  <xml name="oformat_with_opts_dom_pfam">
    <expand macro="oformat_with_opts_dom">
      <option value="pfamtblout" selected="true">Table of hits and domains in Pfam format (--pfamtblout)</option>
    </expand>
  </xml>  

  <xml name="oformat_with_opts_dfam_alisc">
    <!-- Options directing output -->
    <expand macro="oformat_with_opts">
      <option value="dfamtblout" selected="true">Table of hits in Dfam format (--dfamtblout)</option>
      <option value="aliscoresout">Scores for each position in each alignment to file (--aliscoresout)</option>
    </expand>
  </xml>

  <xml name="output" token_tool="">
    <data name="output" format="txt" label="@TOOL@ on ${on_string}"/>
    <data name="tblout" format="txt" label="@TOOL@ on ${on_string}: per-sequence hits from HMM matches">
      <filter>oformat and 'tblout' in oformat</filter>
    </data>
    <yield/>
  </xml>
  <xml name="output_dom" token_tool="">
    <expand macro="output" tool="@TOOL@">
      <data name="domtblout" format="txt" label="@TOOL@ on ${on_string}: per-domain hits from HMM matches">
        <filter>oformat and 'domtblout' in oformat</filter>
      </data>
    </expand>
    <yield/>
  </xml>
  <xml name="output_dom_pfam" token_tool="">
    <expand macro="output_dom" tool="@TOOL@">
      <data name="pfamtblout" format="txt" label="@TOOL@ on ${on_string}: per-sequence/per-domain hits from HMM matches">
        <filter>oformat and 'pfamtblout' in oformat</filter>
      </data>
    </expand>
  </xml>
  <xml name="output_dfam_alisc" token_tool="" token_ofvar="seqfile" token_invar="seqdb">
    <expand macro="output" tool="@TOOL@">
      <data name="dfamtblout" format="txt" label="@TOOL@ on ${on_string}: per-sequence/per-domain hits from HMM matches">
        <filter>oformat and 'dfamtblout' in oformat</filter>
      </data>
      <data name="aliscoresout" format="txt" label="@TOOL@ on ${on_string}: scores for positional matches">
        <filter>oformat and 'aliscoresout' in oformat</filter>
      </data>
    </expand>
  </xml>

  <xml name="assert_out" token_tool="">
    <assert_contents>
      <has_line_matching expression="# @TOOL@.*"/>
      <has_line_matching expression="\[ok\]"/>
    </assert_contents>
  </xml> 

  <xml name="assert_tblout" token_tool="">
    <assert_contents>
      <has_line_matching expression="# Program:         @TOOL@"/>
      <has_line_matching expression="# \[ok\]"/>
    </assert_contents>
  </xml> 

  <xml name="oformat_test">
      <param name="notextw" value="true" />
  </xml>
  <token name="@HSSI@">
#if $hssi.hssi_select == "singlemx":
    --popen $hssi.popen
    --pextend $hssi.pextend

    # HMMER 3.1 (February 2013); http://hmmer.org/
    # Copyright (C) 2011 Howard Hughes Medical Institute.
    # Freely distributed under the GNU General Public License (GPLv3).
    # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

The wrappers were written by the IUC and are licensed under Apache2_. The
documentation is copied from the HMMER3 documentation.

.. _Apache2: http://www.apache.org/licenses/LICENSE-2.0
.. _HMMER3: http://hmmer.org/