Mercurial > repos > galaxyp > openms_fileconverter

annotate FileConverter.xml @ 13:62e19948b50f draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
author galaxyp
date Tue, 13 Oct 2020 19:48:09 +0000
parents f2388622d581
children 2a93a25f0599
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2ef180905190 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
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3 <!--Proposed Tool Section: [File Handling]-->
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4 <tool id="FileConverter" name="FileConverter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
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5 <description>Converts between different MS file formats.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">FileConverter</token>
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8 <import>macros.xml</import>
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9 <import>macros_autotest.xml</import>
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10 <import>macros_test.xml</import>
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11 </macros>
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12 <expand macro="requirements"/>
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13 <expand macro="stdio"/>
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14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
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15 @EXT_FOO@
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16 #import re
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18 ## Preprocessing
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19 mkdir in &&
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20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
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21 mkdir out &&
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23 ## Main program call
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25 set -o pipefail &&
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26 @EXECUTABLE@ -write_ctd ./ &&
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27 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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28 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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29 -in
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30 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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31 -out
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32 'out/output.${out_type}'
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33
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34 ## Postprocessing
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35 && mv 'out/output.${out_type}' '$out'
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36 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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37 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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38 #end if]]></command>
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39 <configfiles>
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40 <inputs name="args_json" data_style="paths"/>
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41 <configfile name="hardcoded_json"><![CDATA[{"ThermoRaw_executable": "ThermoRawFileParser.exe", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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42 </configfiles>
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43 <inputs>
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44 <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)"/>
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45 <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">
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46 <option value="consensusXML">consensusxml</option>
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47 <option value="csv">csv</option>
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48 <option value="dta2d">dta2d</option>
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49 <option value="edta">edta</option>
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50 <option value="featureXML">featurexml</option>
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51 <option value="mgf">mgf</option>
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52 <option value="mzData">mzdata</option>
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53 <option value="mzML">mzml</option>
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54 <option value="mzXML">mzxml</option>
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55 <expand macro="list_string_san"/>
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56 </param>
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57 <expand macro="adv_opts_macro">
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58 <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">
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59 <option value="none">none</option>
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60 <option value="ensure" selected="true">ensure</option>
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61 <option value="reassign">reassign</option>
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62 <expand macro="list_string_san"/>
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63 </param>
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64 <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=""/>
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65 <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=""/>
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66 <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=""/>
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67 <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=""/>
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68 <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=""/>
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69 <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="">
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70 <option value="none" selected="true">none</option>
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71 <option value="multiple">multiple</option>
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72 <option value="single">single</option>
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73 <expand macro="list_string_san"/>
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74 </param>
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75 <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"/>
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76 <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=""/>
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77 <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)"/>
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78 <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"/>
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79 <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=""/>
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80 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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81 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
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82 <expand macro="list_string_san"/>
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83 </param>
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84 </expand>
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85 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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86 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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87 </param>
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88 </inputs>
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89 <outputs>
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90 <data name="out" label="${tool.name} on ${on_string}: out">
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91 <change_format>
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92 <when input="out_type" value="consensusXML" format="consensusxml"/>
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93 <when input="out_type" value="csv" format="csv"/>
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94 <when input="out_type" value="dta2d" format="dta2d"/>
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95 <when input="out_type" value="edta" format="edta"/>
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96 <when input="out_type" value="featureXML" format="featurexml"/>
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97 <when input="out_type" value="mgf" format="mgf"/>
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98 <when input="out_type" value="mzData" format="mzdata"/>
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99 <when input="out_type" value="mzML" format="mzml"/>
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100 <when input="out_type" value="mzXML" format="mzxml"/>
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101 </change_format>
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102 </data>
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103 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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104 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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105 </data>
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106 </outputs>
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107 <tests>
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108 <expand macro="autotest_FileConverter"/>
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109 <expand macro="manutest_FileConverter"/>
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110 </tests>
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111 <help><![CDATA[Converts between different MS file formats.
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112
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113
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114 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_FileConverter.html]]></help>
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115 <expand macro="references"/>
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116 </tool>