annotate HighResPrecursorMassCorrector.xml @ 13:cdbd06d8cbd5 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
author galaxyp
date Tue, 13 Oct 2020 20:28:49 +0000
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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: [Signal processing and preprocessing]-->
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4 <tool id="HighResPrecursorMassCorrector" name="HighResPrecursorMassCorrector" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
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5 <description>Corrects the precursor mass and charge determined by the instrument software.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">HighResPrecursorMassCorrector</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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17
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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($in.ext)' &&
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21 mkdir out &&
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22 #if "out_csv_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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23 mkdir out_csv &&
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24 #end if
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25 #if $feature.in:
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26 mkdir feature.in &&
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27 ln -s '$feature.in' 'feature.in/${re.sub("[^\w\-_]", "_", $feature.in.element_identifier)}.$gxy2omsext($feature.in.ext)' &&
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28 #end if
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30 ## Main program call
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32 set -o pipefail &&
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33 @EXECUTABLE@ -write_ctd ./ &&
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34 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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35 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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36 -in
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37 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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38 -out
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39 'out/output.${gxy2omsext("mzml")}'
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40 #if "out_csv_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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41 -out_csv
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42 'out_csv/output.${gxy2omsext("csv")}'
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43 #end if
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44 #if $feature.in:
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45 -feature:in
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46 'feature.in/${re.sub("[^\w\-_]", "_", $feature.in.element_identifier)}.$gxy2omsext($feature.in.ext)'
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47 #end if
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48 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
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49 | tee '$stdout'
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50 #end if
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51
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52 ## Postprocessing
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53 && mv 'out/output.${gxy2omsext("mzml")}' '$out'
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54 #if "out_csv_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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55 && mv 'out_csv/output.${gxy2omsext("csv")}' '$out_csv'
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56 #end if
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57 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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58 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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59 #end if]]></command>
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60 <configfiles>
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61 <inputs name="args_json" data_style="paths"/>
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62 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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63 </configfiles>
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64 <inputs>
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65 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="Input file (centroided data)" help=" select mzml data sets(s)"/>
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66 <section name="feature" title="Use features for precursor mass correction" help="" expanded="false">
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67 <param name="in" argument="-feature:in" type="data" format="featurexml" optional="true" label="Features used to correct precursor masses" help=" select featurexml data sets(s)"/>
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68 <param name="mz_tolerance" argument="-feature:mz_tolerance" type="float" optional="true" value="5.0" label="The precursor mass tolerance" help="Used to determine matching to feature mass traces"/>
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69 <param name="mz_tolerance_unit" argument="-feature:mz_tolerance_unit" display="radio" type="select" optional="false" label="Unit of precursor mass tolerance" help="">
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70 <option value="Da">Da</option>
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71 <option value="ppm" selected="true">ppm</option>
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72 <expand macro="list_string_san"/>
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73 </param>
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74 <param name="rt_tolerance" argument="-feature:rt_tolerance" type="float" optional="true" value="0.0" label="Additional retention time tolerance added to feature boundaries" help=""/>
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75 <param name="max_trace" argument="-feature:max_trace" type="integer" optional="true" value="2" label="Maximum isotopic trace considered in matching a precursor to a feature" help=""/>
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76 <param name="believe_charge" argument="-feature:believe_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Assume precursor charge to be correct" help=""/>
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77 <param name="keep_original" argument="-feature:keep_original" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Make a copy of the precursor and MS2 (true) or discard the original (false)" help=""/>
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78 <param name="assign_all_matching" argument="-feature:assign_all_matching" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Correct a precursor using all matching features (true) or only the nearest (false)" help="Only evaluated if copies are created (feature:keep_original)"/>
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79 </section>
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80 <section name="nearest_peak" title="Use nearest centroided MS1 peak for precursor mass correction" help="" expanded="false">
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81 <param name="mz_tolerance" argument="-nearest_peak:mz_tolerance" type="float" optional="true" value="0.0" label="The precursor mass tolerance to find the closest MS1 peak" help="(Disable method by setting value to 0.0)"/>
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82 <param name="mz_tolerance_unit" argument="-nearest_peak:mz_tolerance_unit" display="radio" type="select" optional="false" label="Unit of precursor mass tolerance" help="">
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83 <option value="Da">Da</option>
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84 <option value="ppm" selected="true">ppm</option>
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85 <expand macro="list_string_san"/>
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86 </param>
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87 </section>
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88 <section name="highest_intensity_peak" title="Use centroided MS1 peak with the highest intensity in a certrain mass range - for precursor mass correction" help="" expanded="false">
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89 <param name="mz_tolerance" argument="-highest_intensity_peak:mz_tolerance" type="float" optional="true" value="0.0" label="The precursor mass tolerance to find the highest intensity MS1 peak" help="Suggested value 1/max. expected charge. (Disable method by setting value to 0.0)"/>
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90 <param name="mz_tolerance_unit" argument="-highest_intensity_peak:mz_tolerance_unit" display="radio" type="select" optional="false" label="Unit of precursor mass tolerance" help="">
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91 <option value="Da">Da</option>
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92 <option value="ppm" selected="true">ppm</option>
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93 <expand macro="list_string_san"/>
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94 </param>
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95 </section>
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96 <expand macro="adv_opts_macro">
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97 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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98 <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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99 <expand macro="list_string_san"/>
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100 </param>
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101 </expand>
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102 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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103 <option value="out_csv_FLAG">out_csv (Optional CSV output file for results on 'nearest_peak' or 'highest_intensity_peak' algorithm (see corresponding subsection) containing columns: RT, uncorrectedMZ, correctedMZ, deltaMZ)</option>
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104 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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105 </param>
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106 </inputs>
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107 <outputs>
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108 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/>
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109 <data name="out_csv" label="${tool.name} on ${on_string}: out_csv" format="csv">
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110 <filter>OPTIONAL_OUTPUTS is not None and "out_csv_FLAG" in OPTIONAL_OUTPUTS</filter>
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111 </data>
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112 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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113 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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114 </data>
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115 </outputs>
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116 <tests>
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117 <expand macro="autotest_HighResPrecursorMassCorrector"/>
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118 <expand macro="manutest_HighResPrecursorMassCorrector"/>
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119 </tests>
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120 <help><![CDATA[Corrects the precursor mass and charge determined by the instrument software.
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121
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122
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123 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_HighResPrecursorMassCorrector.html]]></help>
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124 <expand macro="references"/>
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125 </tool>