comparison QCMerger.xml @ 14:86a29d233856 draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906

13:fbf1dfad22ce

<?xml version='1.0' encoding='UTF-8'?>
<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
<!--Proposed Tool Section: [Utilities]-->
<tool id="QCMerger" name="QCMerger" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
  <description>Merges two qcml files together.</description>
  <macros>
    <token name="@EXECUTABLE@">QCMerger</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>

## Preprocessing
mkdir in_cond.in &&
#if $in_cond.in_select == "no"
mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && 
${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
#else
ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
#end if
mkdir out &&

## Main program call

      <param name="in_select" type="select" label="Run tool in batch mode for -in">
        <option value="no">No: process all datasets jointly</option>
        <option value="yes">Yes: process each dataset in an independent job</option>
      </param>
      <when value="no">
        <param argument="-in" type="data" format="qcml" multiple="true" optional="false" label="List of qcml files to be merged" help=" select qcml data sets(s)"/>
      </when>
      <when value="yes">
        <param argument="-in" type="data" format="qcml" multiple="false" optional="false" label="List of qcml files to be merged" help=" select qcml data sets(s)"/>
      </when>
    </conditional>
    <param argument="-setname" type="text" optional="true" value="" label="Use only when all given qcml files belong to one set, which will be held under the given name" help="">
      <expand macro="list_string_san" name="setname"/>
    </param>
    <expand macro="adv_opts_macro">
      <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
        <expand macro="list_string_san" name="test"/>
      </param>
    </expand>
    <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>

    <data name="out" label="${tool.name} on ${on_string}: out" format="qcml"/>
    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
    </data>
  </outputs>
  <tests><test expect_num_outputs="1"><!-- just using 2 outputs from QCCalculator as input (no2 did not work) -->
    <param name="adv_opts|test" value="true"/>
    <param name="in" ftype="qcml" value="QCCalculator1.qcML,QCCalculator3.qcML"/>
    <output name="out" ftype="qcml" value="QCMerger.qcML"/>
  </test>
</tests>
  <help><![CDATA[Merges two qcml files together.


For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_QCMerger.html]]></help>
  <expand macro="references"/>
</tool>

14:86a29d233856

<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
<!--Proposed Tool Section: []-->
<tool id="QCMerger" name="QCMerger" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
  <description>Merges two qcml files together</description>
  <macros>
    <token name="@EXECUTABLE@">QCMerger</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>

## Preprocessing
mkdir in_cond.in &&
#if $in_cond.in_select == "no"
mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && 
${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
#else
cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
#end if
mkdir out &&

## Main program call

      <param name="in_select" type="select" label="Run tool in batch mode for -in">
        <option value="no">No: process all datasets jointly</option>
        <option value="yes">Yes: process each dataset in an independent job</option>
      </param>
      <when value="no">
        <param argument="-in" type="data" format="qcml" multiple="true" label="List of qcml files to be merged" help=" select qcml data sets(s)"/>
      </when>
      <when value="yes">
        <param argument="-in" type="data" format="qcml" label="List of qcml files to be merged" help=" select qcml data sets(s)"/>
      </when>
    </conditional>
    <param argument="-setname" type="text" optional="true" value="" label="Use only when all given qcml files belong to one set, which will be held under the given name" help="">
      <expand macro="list_string_san" name="setname"/>
    </param>
    <expand macro="adv_opts_macro">
      <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
        <expand macro="list_string_san" name="test"/>
      </param>
    </expand>
    <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>

    <data name="out" label="${tool.name} on ${on_string}: out" format="qcml"/>
    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
    </data>
  </outputs>
  <tests>
    <test expect_num_outputs="1">
      <!-- just using 2 outputs from QCCalculator as input (no2 did not work) -->
      <param name="adv_opts|test" value="true"/>
      <param name="in" ftype="qcml" value="QCCalculator1.qcML,QCCalculator3.qcML"/>
      <output name="out" ftype="qcml" value="QCMerger.qcML"/>
    </test>
  </tests>
  <help><![CDATA[Merges two qcml files together.


For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_QCMerger.html]]></help>
  <expand macro="references"/>
</tool>