annotate SpecLibCreator.xml @ 14:5b237d23cb7d draft default tip

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

<!--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: [Identification Processing]-->
<tool id="SpecLibCreator" name="SpecLibCreator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
  <description>Creates an MSP formatted spectral library</description>
  <macros>
    <token name="@EXECUTABLE@">SpecLibCreator</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <expand macro="stdio"/>
  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
@EXT_FOO@
#import re

## Preprocessing
mkdir info &&
cp '$info' 'info/${re.sub("[^\w\-_]", "_", $info.element_identifier)}.$gxy2omsext($info.ext)' &&
mkdir spec &&
cp '$spec' 'spec/${re.sub("[^\w\-_]", "_", $spec.element_identifier)}.$gxy2omsext($spec.ext)' &&
mkdir out &&

## Main program call

set -o pipefail &&
@EXECUTABLE@ -write_ctd ./ &&
python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
@EXECUTABLE@ -ini @EXECUTABLE@.ctd
-info
'info/${re.sub("[^\w\-_]", "_", $info.element_identifier)}.$gxy2omsext($info.ext)'
-spec
'spec/${re.sub("[^\w\-_]", "_", $spec.element_identifier)}.$gxy2omsext($spec.ext)'
-out
'out/output.${gxy2omsext("msp")}'

## Postprocessing
&& mv 'out/output.${gxy2omsext("msp")}' '$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 argument="-info" type="data" format="csv" label="Holds id, peptide, retention time etc" help=" select csv data sets(s)"/>
    <param argument="-itemseperator" type="text" value="," label=" Separator between items. e.g. ," help="">
      <expand macro="list_string_san" name="itemseperator"/>
    </param>
    <param argument="-itemenclosed" type="boolean" truevalue="true" falsevalue="false" checked="false" label="'true' or 'false' if true every item is enclosed" help="e.g. '$peptide$,$run$"/>
    <param argument="-spec" type="data" format="mzdata,mzxml" label="spectra" help=" select mzdata,mzxml data sets(s)"/>
    <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>
    </param>
  </inputs>
  <outputs>
    <data name="out" label="${tool.name} on ${on_string}: out" format="msp"/>
    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
    </data>
  </outputs>
  <tests>
    <!--TODO could not find test data -->
  </tests>
  <help><![CDATA[Creates an MSP formatted spectral library.


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