annotate FileConverter.xml @ 11:f2388622d581 draft

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

<?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: [File Handling]-->
<tool id="FileConverter" name="FileConverter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
  <description>Converts between different MS file formats.</description>
  <macros>
    <token name="@EXECUTABLE@">FileConverter</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)' &&
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($in.ext)'
-out
'out/output.${out_type}'

## Postprocessing
&& mv 'out/output.${out_type}' '$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[{"ThermoRaw_executable": "ThermoRawFileParser.exe", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
  </configfiles>
  <inputs>
    <param name="in" argument="-in" type="data" format="consensusxml,dta,dta2d,edta,featurexml,kroenik,mgf,ms2,mzdata,mzml,mzxml,peplist,tabular,thermo.raw" optional="false" label="Input file to convert" help=" select consensusxml,dta,dta2d,edta,featurexml,kroenik,mgf,ms2,mzdata,mzml,mzxml,peplist,tabular,thermo.raw data sets(s)"/>
    <param name="out_type" argument="-out_type" type="select" optional="false" label="Output file type -- default: determined from file extension or content" help="Note: that not all conversion paths work or make sense">
      <option value="consensusXML">consensusxml</option>
      <option value="csv">csv</option>
      <option value="dta2d">dta2d</option>
      <option value="edta">edta</option>
      <option value="featureXML">featurexml</option>
      <option value="mgf">mgf</option>
      <option value="mzData">mzdata</option>
      <option value="mzML">mzml</option>
      <option value="mzXML">mzxml</option>
      <expand macro="list_string_san"/>
    </param>
    <expand macro="adv_opts_macro">
      <param name="UID_postprocessing" argument="-UID_postprocessing" display="radio" type="select" optional="false" label="unique ID post-processing for output data" help="'none' keeps current IDs even if invalid.. 'ensure' keeps current IDs but reassigns invalid ones.. 'reassign' assigns new unique IDs">
        <option value="none">none</option>
        <option value="ensure" selected="true">ensure</option>
        <option value="reassign">reassign</option>
        <expand macro="list_string_san"/>
      </param>
      <param name="TIC_DTA2D" argument="-TIC_DTA2D" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Export the TIC instead of the entire experiment in mzML/mzData/mzXML -&gt; DTA2D conversions" help=""/>
      <param name="MGF_compact" argument="-MGF_compact" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use a more compact format when writing MGF (no zero-intensity peaks, limited number of decimal places)" help=""/>
      <param name="force_MaxQuant_compatibility" argument="-force_MaxQuant_compatibility" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[mzXML output only] Make sure that MaxQuant can read the mzXML and set the msManufacturer to 'Thermo Scientific'" help=""/>
      <param name="convert_to_chromatograms" argument="-convert_to_chromatograms" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[mzML output only] Assumes that the provided spectra represent data in SRM mode or targeted MS1 mode and converts them to chromatogram data" help=""/>
      <param name="force_TPP_compatibility" argument="-force_TPP_compatibility" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[mzML output only] Make sure that TPP parsers can read the mzML and the precursor ion m/z in the file (otherwise it will be set to zero by the TPP)" help=""/>
      <param name="change_im_format" argument="-change_im_format" display="radio" type="select" optional="false" label="[mzML output only] How to store ion mobility scans (none: no change in format, multiple: store each frame as multiple scans, one per drift time value, single: store whole frame as single scan with IM values in a FloatDataArray" help="">
        <option value="none" selected="true">none</option>
        <option value="multiple">multiple</option>
        <option value="single">single</option>
        <expand macro="list_string_san"/>
      </param>
      <param name="write_scan_index" argument="-write_scan_index" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Append an index when writing mzML or mzXML files" help="Some external tools might rely on it"/>
      <param name="lossy_compression" argument="-lossy_compression" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use numpress compression to achieve optimally small file size using linear compression for m/z domain and slof for intensity and float data arrays (attention: may cause small loss of precision; only for mzML data)" help=""/>
      <param name="lossy_mass_accuracy" argument="-lossy_mass_accuracy" type="float" optional="true" value="-1.0" label="Desired (absolute) m/z accuracy for lossy compression" help="(e.g. use 0.0001 for a mass accuracy of 0.2 ppm at 500 m/z, default uses -1.0 for maximal accuracy)"/>
      <param name="process_lowmemory" argument="-process_lowmemory" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether to process the file on the fly without loading the whole file into memory first (only for conversions of mzXML/mzML to mzML)" help="Note: this flag will prevent conversion from spectra to chromatograms"/>
      <param name="no_peak_picking" argument="-no_peak_picking" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Disables vendor peak picking for raw files" help=""/>
      <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 ${on_string}: out">
      <change_format>
        <when input="out_type" value="consensusXML" format="consensusxml"/>
        <when input="out_type" value="csv" format="csv"/>
        <when input="out_type" value="dta2d" format="dta2d"/>
        <when input="out_type" value="edta" format="edta"/>
        <when input="out_type" value="featureXML" format="featurexml"/>
        <when input="out_type" value="mgf" format="mgf"/>
        <when input="out_type" value="mzData" format="mzdata"/>
        <when input="out_type" value="mzML" format="mzml"/>
        <when input="out_type" value="mzXML" format="mzxml"/>
      </change_format>
    </data>
    <data name="ctd_out" format="xml" label="${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_FileConverter"/>
    <expand macro="manutest_FileConverter"/>
  </tests>
  <help><![CDATA[Converts between different MS file formats.


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