comparison QCShrinker.xml @ 9:ccfc3e189087 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"

8:fd4184a9016b

<?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="QCShrinker" name="QCShrinker" version="2.3.0">
  <description>This application is used to remove the verbose table attachments from a qcml file that are not needed anymore, e.g. for a final report.</description>
  <macros>
    <token name="@EXECUTABLE@">QCShrinker</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command detect_errors="aggressive"><![CDATA[QCShrinker

#if $param_in:
  -in $param_in
#end if

#if $rep_param_qp_accessions:
-qp_accessions
  #for token in $rep_param_qp_accessions:
    #if " " in str(token):
      "$token.param_qp_accessions"
    #else
      $token.param_qp_accessions
    #end if
  #end for
#end if
#if $param_name:
  -name     "$param_name"
#end if
#if $param_run:
  -run $param_run
#end if
#if $param_out:
  -out $param_out
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
#end if
]]></command>
  <inputs>
    <param name="param_in" type="data" format="qcml" optional="False" label="Input qcml file" help="(-in) "/>
    <repeat name="rep_param_qp_accessions" min="0" title="param_qp_accessions">
      <param name="param_qp_accessions" type="text" size="30" label="A list of cv accessions that should be removed" help="(-qp_accessions) If empty, the usual suspects will be removed!">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
    </repeat>
    <param name="param_name" type="text" size="30" label="The name of the target run or set that contains the requested quality paramete" help="(-name) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_run" type="data" format="mzml" optional="True" label="The file from which the name of the target run that contains the requested quality parameter is taken" help="(-run) This overrides the name parameter!"/>
    <expand macro="advanced_options">
      <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" format="qcml"/>
  </outputs>
  <help>This application is used to remove the verbose table attachments from a qcml file that are not needed anymore, e.g. for a final report.


For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_QCShrinker.html</help>
</tool>

9:ccfc3e189087

<?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="QCShrinker" name="QCShrinker" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
  <description>This application is used to remove the verbose table attachments from a qcml file that are not needed anymore, e.g. for a final report.</description>
  <macros>
    <token name="@EXECUTABLE@">QCShrinker</token>
    <import>macros.xml</import>
    <import>macros_autotest.xml</import>
    <import>macros_test.xml</import>
  </macros>
  <expand macro="requirements"/>
  <expand macro="stdio"/>
  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
@EXT_FOO@
#import re

## Preprocessing
mkdir in &&
ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
#if $run:
  mkdir run &&
  ln -s '$run' 'run/${re.sub("[^\w\-_]", "_", $run.element_identifier)}.$gxy2omsext($run.ext)' &&
#end if
mkdir out &&

## Main program call

set -o pipefail &&
@EXECUTABLE@ -write_ctd ./ &&
python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
@EXECUTABLE@ -ini @EXECUTABLE@.ctd
-in
'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
#if $run:
  -run
  'run/${re.sub("[^\w\-_]", "_", $run.element_identifier)}.$gxy2omsext($run.ext)'
#end if
-out
'out/output.${gxy2omsext("qcml")}'

## Postprocessing
&& mv 'out/output.${gxy2omsext("qcml")}' '$out'
#if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
  && mv '@EXECUTABLE@.ctd' '$ctd_out'
#end if]]></command>
  <configfiles>
    <inputs name="args_json" data_style="paths"/>
    <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
  </configfiles>
  <inputs>
    <param name="in" argument="-in" type="data" format="qcml" optional="false" label="Input qcml file" help=" select qcml data sets(s)"/>
    <param name="qp_accessions" argument="-qp_accessions" type="text" optional="true" value="" label="A list of cv accessions that should be removed" help="If empty, the usual suspects will be removed! (space separated list, in order to allow for spaces in list items surround them by single quotes)">
      <expand macro="list_string_val"/>
      <expand macro="list_string_san"/>
    </param>
    <param name="name" argument="-name" type="text" optional="true" value="" label="The name of the target run or set that contains the requested quality paramete" help="">
      <expand macro="list_string_san"/>
    </param>
    <param name="run" argument="-run" type="data" format="mzml" optional="true" label="The file from which the name of the target run that contains the requested quality parameter is taken" help="This overrides the name parameter! select mzml data sets(s)"/>
    <expand macro="adv_opts_macro">
      <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
      <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
        <expand macro="list_string_san"/>
      </param>
    </expand>
    <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
    </param>
  </inputs>
  <outputs>
    <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>
    <expand macro="autotest_QCShrinker"/>
    <expand macro="manutest_QCShrinker"/>
  </tests>
  <help><![CDATA[This application is used to remove the verbose table attachments from a qcml file that are not needed anymore, e.g. for a final report.


For more information, visit http://www.openms.de/documentation/UTILS_QCShrinker.html]]></help>
  <expand macro="references"/>
</tool>