comparison NovorAdapter.xml @ 6:fa544e12732f draft default tip

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

5:34dda034b019

<?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="NovorAdapter" name="NovorAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
  <description>Performs de novo sequencing of peptides from MS/MS data with Novor.</description>
  <macros>
    <token name="@EXECUTABLE@">NovorAdapter</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>

@EXT_FOO@
#import re

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

## Main program call

set -o pipefail &&

  <configfiles>
    <inputs name="args_json" data_style="paths"/>
    <configfile name="hardcoded_json"><![CDATA[{"executable": "/home/berntm/Downloads/novor/lib/novor.jar", "java_executable": "java", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
  </configfiles>
  <inputs>
    <param argument="-in" type="data" format="mzml" optional="false" label="MzML Input file" help=" select mzml data sets(s)"/>
    <param argument="-enzyme" type="select" optional="true" label="Digestion enzyme - currently only Trypsin is supported" help="">
      <option value="Trypsin" selected="true">Trypsin</option>
      <expand macro="list_string_san" name="enzyme"/>
    </param>
    <param argument="-fragmentation" type="select" optional="true" label="Fragmentation method" help="">
      <option value="CID" selected="true">CID</option>
      <option value="HCD">HCD</option>
      <expand macro="list_string_san" name="fragmentation"/>
    </param>
    <param argument="-massAnalyzer" type="select" optional="true" label="MassAnalyze" help="e.g. (Oritrap CID-Trap, CID-FT, HCD-FT; QTof CID-TOF)">
      <option value="Trap" selected="true">Trap</option>
      <option value="TOF">TOF</option>
      <option value="FT">FT</option>
      <expand macro="list_string_san" name="massAnalyzer"/>
    </param>
    <param argument="-fragment_mass_tolerance" type="float" optional="true" value="0.5" label="Fragmentation error tolerance  (Da)" help=""/>
    <param argument="-precursor_mass_tolerance" type="float" optional="true" value="15.0" label="Precursor error tolerance  (ppm or Da)" help=""/>
    <param argument="-precursor_error_units" type="select" optional="true" label="Unit of precursor mass tolerance" help="">
      <option value="ppm" selected="true">ppm</option>
      <option value="Da">Da</option>
      <expand macro="list_string_san" name="precursor_error_units"/>
    </param>
    <param argument="-variable_modifications" multiple="true" type="select" optional="true" label="Variable modifications" help="">
      <option value="Acetyl (K)">Acetyl (K)</option>
      <option value="Acetyl (N-term)">Acetyl (N-term)</option>
      <option value="Amidated (C-term)">Amidated (C-term)</option>
      <option value="Ammonia-loss (N-term C)">Ammonia-loss (N-term C)</option>
      <option value="Biotin (K)">Biotin (K)</option>

      <option value="Sodium (DE)">Sodium (DE)</option>
      <option value="Sulfo (STY)">Sulfo (STY)</option>
      <option value="Trimethyl (RK)">Trimethyl (RK)</option>
      <expand macro="list_string_san" name="variable_modifications"/>
    </param>
    <param argument="-fixed_modifications" multiple="true" type="select" optional="true" label="Fixed modifications" help="">
      <option value="Acetyl (K)">Acetyl (K)</option>
      <option value="Acetyl (N-term)">Acetyl (N-term)</option>
      <option value="Amidated (C-term)">Amidated (C-term)</option>
      <option value="Ammonia-loss (N-term C)">Ammonia-loss (N-term C)</option>
      <option value="Biotin (K)">Biotin (K)</option>

      <option value="Sodium (DE)">Sodium (DE)</option>
      <option value="Sulfo (STY)">Sulfo (STY)</option>
      <option value="Trimethyl (RK)">Trimethyl (RK)</option>
      <expand macro="list_string_san" name="fixed_modifications"/>
    </param>
    <param argument="-forbiddenResidues" display="checkboxes" multiple="true" type="select" optional="true" label="Forbidden Resiudes" help="">
      <option value="I">I</option>
      <option value="U">U</option>
      <expand macro="list_string_san" name="forbiddenResidues"/>
    </param>
    <param argument="-novorFile" type="data" format="txt" optional="true" label="File to introduce customized algorithm parameters for advanced users (otional .novor file)" help=" select txt 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" 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 ${on_string}: out" format="idxml"/>
    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
    </data>
  </outputs>
  <tests><!-- TOPP_NovorAdapter_1 -->
  </tests>
  <help><![CDATA[Performs de novo sequencing of peptides from MS/MS data with Novor.


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

6:fa544e12732f

<!--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 of Proteins/Peptides (SearchEngines)]-->
<tool id="NovorAdapter" name="NovorAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
  <description>Performs de novo sequencing of peptides from MS/MS data with Novor</description>
  <macros>
    <token name="@EXECUTABLE@">NovorAdapter</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>

@EXT_FOO@
#import re

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

## Main program call

set -o pipefail &&

  <configfiles>
    <inputs name="args_json" data_style="paths"/>
    <configfile name="hardcoded_json"><![CDATA[{"executable": "/home/berntm/Downloads/novor/lib/novor.jar", "java_executable": "java", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
  </configfiles>
  <inputs>
    <param argument="-in" type="data" format="mzml" label="MzML Input file" help=" select mzml data sets(s)"/>
    <param argument="-enzyme" type="select" label="Digestion enzyme - currently only Trypsin is supported" help="">
      <option value="Trypsin" selected="true">Trypsin</option>
      <expand macro="list_string_san" name="enzyme"/>
    </param>
    <param argument="-fragmentation" type="select" label="Fragmentation method" help="">
      <option value="CID" selected="true">CID</option>
      <option value="HCD">HCD</option>
      <expand macro="list_string_san" name="fragmentation"/>
    </param>
    <param argument="-massAnalyzer" type="select" label="MassAnalyze" help="e.g. (Oritrap CID-Trap, CID-FT, HCD-FT; QTof CID-TOF)">
      <option value="Trap" selected="true">Trap</option>
      <option value="TOF">TOF</option>
      <option value="FT">FT</option>
      <expand macro="list_string_san" name="massAnalyzer"/>
    </param>
    <param argument="-fragment_mass_tolerance" type="float" value="0.5" label="Fragmentation error tolerance  (Da)" help=""/>
    <param argument="-precursor_mass_tolerance" type="float" value="15.0" label="Precursor error tolerance  (ppm or Da)" help=""/>
    <param argument="-precursor_error_units" type="select" label="Unit of precursor mass tolerance" help="">
      <option value="ppm" selected="true">ppm</option>
      <option value="Da">Da</option>
      <expand macro="list_string_san" name="precursor_error_units"/>
    </param>
    <param argument="-variable_modifications" type="select" multiple="true" optional="true" label="Variable modifications" help="">
      <option value="Acetyl (K)">Acetyl (K)</option>
      <option value="Acetyl (N-term)">Acetyl (N-term)</option>
      <option value="Amidated (C-term)">Amidated (C-term)</option>
      <option value="Ammonia-loss (N-term C)">Ammonia-loss (N-term C)</option>
      <option value="Biotin (K)">Biotin (K)</option>

      <option value="Sodium (DE)">Sodium (DE)</option>
      <option value="Sulfo (STY)">Sulfo (STY)</option>
      <option value="Trimethyl (RK)">Trimethyl (RK)</option>
      <expand macro="list_string_san" name="variable_modifications"/>
    </param>
    <param argument="-fixed_modifications" type="select" multiple="true" optional="true" label="Fixed modifications" help="">
      <option value="Acetyl (K)">Acetyl (K)</option>
      <option value="Acetyl (N-term)">Acetyl (N-term)</option>
      <option value="Amidated (C-term)">Amidated (C-term)</option>
      <option value="Ammonia-loss (N-term C)">Ammonia-loss (N-term C)</option>
      <option value="Biotin (K)">Biotin (K)</option>

      <option value="Sodium (DE)">Sodium (DE)</option>
      <option value="Sulfo (STY)">Sulfo (STY)</option>
      <option value="Trimethyl (RK)">Trimethyl (RK)</option>
      <expand macro="list_string_san" name="fixed_modifications"/>
    </param>
    <param argument="-forbiddenResidues" type="select" multiple="true" optional="true" label="Forbidden Resiudes" help="">
      <option value="I">I</option>
      <option value="U">U</option>
      <expand macro="list_string_san" name="forbiddenResidues"/>
    </param>
    <param argument="-novorFile" type="data" format="txt" optional="true" label="File to introduce customized algorithm parameters for advanced users (otional .novor file)" help=" select txt 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>

    <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/>
    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
    </data>
  </outputs>
  <tests>
    <!-- TOPP_NovorAdapter_1 -->
  </tests>
  <help><![CDATA[Performs de novo sequencing of peptides from MS/MS data with Novor.


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