Mercurial > repos > galaxyp > openms_highresprecursormasscorrector

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author galaxyp
date Fri, 14 Jun 2024 21:40:04 +0000
parents d3546bb9fd8e
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1 <!--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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2 <!--Proposed Tool Section: [Mass Correction and Calibration]-->
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3 <tool id="HighResPrecursorMassCorrector" name="HighResPrecursorMassCorrector" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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4 <description>Corrects the precursor mass and charge determined by the instrument software</description>
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5 <macros>
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6 <token name="@EXECUTABLE@">HighResPrecursorMassCorrector</token>
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7 <import>macros.xml</import>
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8 </macros>
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9 <expand macro="requirements"/>
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10 <expand macro="stdio"/>
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11 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
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12 @EXT_FOO@
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13 #import re
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14
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15 ## Preprocessing
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16 mkdir in &&
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17 cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
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18 mkdir out &&
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19 #if "out_csv_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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20 mkdir out_csv &&
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21 #end if
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22 #if $feature.in:
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23 mkdir feature.in &&
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24 cp '$feature.in' 'feature.in/${re.sub("[^\w\-_]", "_", $feature.in.element_identifier)}.$gxy2omsext($feature.in.ext)' &&
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25 #end if
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27 ## Main program call
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29 set -o pipefail &&
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30 @EXECUTABLE@ -write_ctd ./ &&
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31 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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32 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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33 -in
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34 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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35 -out
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36 'out/output.${gxy2omsext("mzml")}'
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37 #if "out_csv_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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38 -out_csv
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39 'out_csv/output.${gxy2omsext("csv")}'
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40 #end if
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41 #if $feature.in:
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42 -feature:in
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43 'feature.in/${re.sub("[^\w\-_]", "_", $feature.in.element_identifier)}.$gxy2omsext($feature.in.ext)'
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44 #end if
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45 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
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46 | tee '$stdout'
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47 #end if
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48
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49 ## Postprocessing
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50 && mv 'out/output.${gxy2omsext("mzml")}' '$out'
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51 #if "out_csv_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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52 && mv 'out_csv/output.${gxy2omsext("csv")}' '$out_csv'
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53 #end if
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54 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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55 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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56 #end if]]></command>
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57 <configfiles>
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58 <inputs name="args_json" data_style="paths"/>
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59 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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60 </configfiles>
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61 <inputs>
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62 <param argument="-in" type="data" format="mzml" label="Input file (centroided data)" help=" select mzml data sets(s)"/>
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63 <section name="feature" title="Use features for precursor mass correction" help="" expanded="false">
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64 <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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65 <param name="mz_tolerance" argument="-feature:mz_tolerance" type="float" value="5.0" label="The precursor mass tolerance" help="Used to determine matching to feature mass traces"/>
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66 <param name="mz_tolerance_unit" argument="-feature:mz_tolerance_unit" type="select" label="Unit of precursor mass tolerance" help="">
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67 <option value="Da">Da</option>
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68 <option value="ppm" selected="true">ppm</option>
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69 <expand macro="list_string_san" name="mz_tolerance_unit"/>
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70 </param>
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71 <param name="rt_tolerance" argument="-feature:rt_tolerance" type="float" value="0.0" label="Additional retention time tolerance added to feature boundaries" help=""/>
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72 <param name="max_trace" argument="-feature:max_trace" type="integer" value="2" label="Maximum isotopic trace considered in matching a precursor to a feature" help=""/>
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73 <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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74 <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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75 <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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76 </section>
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77 <section name="nearest_peak" title="Use nearest centroided MS1 peak for precursor mass correction" help="" expanded="false">
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78 <param name="mz_tolerance" argument="-nearest_peak:mz_tolerance" type="float" 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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79 <param name="mz_tolerance_unit" argument="-nearest_peak:mz_tolerance_unit" type="select" label="Unit of precursor mass tolerance" help="">
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80 <option value="Da">Da</option>
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81 <option value="ppm" selected="true">ppm</option>
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82 <expand macro="list_string_san" name="mz_tolerance_unit"/>
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83 </param>
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84 </section>
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85 <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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86 <param name="mz_tolerance" argument="-highest_intensity_peak:mz_tolerance" type="float" 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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87 <param name="mz_tolerance_unit" argument="-highest_intensity_peak:mz_tolerance_unit" type="select" label="Unit of precursor mass tolerance" help="">
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88 <option value="Da">Da</option>
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89 <option value="ppm" selected="true">ppm</option>
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90 <expand macro="list_string_san" name="mz_tolerance_unit"/>
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91 </param>
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92 </section>
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93 <expand macro="adv_opts_macro">
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94 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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95 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
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96 <expand macro="list_string_san" name="test"/>
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97 </param>
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98 </expand>
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99 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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100 <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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101 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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102 </param>
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103 </inputs>
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104 <outputs>
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105 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/>
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106 <data name="out_csv" label="${tool.name} on ${on_string}: out_csv" format="csv">
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107 <filter>OPTIONAL_OUTPUTS is not None and "out_csv_FLAG" in OPTIONAL_OUTPUTS</filter>
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108 </data>
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109 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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110 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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111 </data>
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112 </outputs>
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113 <tests>
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114 <!-- TOPP_HighResPrecursorMassCorrector_1 -->
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115 <test expect_num_outputs="2">
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116 <section name="adv_opts">
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117 <param name="force" value="false"/>
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118 <param name="test" value="true"/>
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119 </section>
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120 <param name="in" value="HighResPrecursorMassCorrector_2860_1103_3.mzML"/>
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121 <output name="out" value="HighResPrecursorMassCorrector_2860_1103_3_out.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
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122 <section name="feature">
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123 <param name="in" value="HighResPrecursorMassCorrector_2860_1103_3.featureXML"/>
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124 <param name="mz_tolerance" value="5.0"/>
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125 <param name="mz_tolerance_unit" value="ppm"/>
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126 <param name="rt_tolerance" value="0.0"/>
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127 <param name="max_trace" value="2"/>
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128 <param name="believe_charge" value="false"/>
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129 <param name="keep_original" value="false"/>
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130 <param name="assign_all_matching" value="false"/>
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131 </section>
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132 <section name="nearest_peak">
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133 <param name="mz_tolerance" value="0.0"/>
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134 <param name="mz_tolerance_unit" value="ppm"/>
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135 </section>
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136 <section name="highest_intensity_peak">
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137 <param name="mz_tolerance" value="0.0"/>
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138 <param name="mz_tolerance_unit" value="ppm"/>
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139 </section>
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140 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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141 <output name="ctd_out" ftype="xml">
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142 <assert_contents>
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143 <is_valid_xml/>
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144 </assert_contents>
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145 </output>
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146 <assert_stdout>
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147 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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148 </assert_stdout>
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149 </test>
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150 <!-- TOPP_HighResPrecursorMassCorrector_3 -->
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151 <test expect_num_outputs="2">
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152 <section name="adv_opts">
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153 <param name="force" value="false"/>
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154 <param name="test" value="true"/>
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155 </section>
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156 <param name="in" value="HighResPrecursorMassCorrector_2538_1091_2.mzML"/>
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157 <output name="out" value="HighResPrecursorMassCorrector_2538_1091_2_out.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
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158 <section name="feature">
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159 <param name="in" value="HighResPrecursorMassCorrector_2538_1091_2.featureXML"/>
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160 <param name="mz_tolerance" value="5.0"/>
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161 <param name="mz_tolerance_unit" value="ppm"/>
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162 <param name="rt_tolerance" value="0.0"/>
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163 <param name="max_trace" value="2"/>
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164 <param name="believe_charge" value="false"/>
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165 <param name="keep_original" value="false"/>
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166 <param name="assign_all_matching" value="false"/>
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167 </section>
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168 <section name="nearest_peak">
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169 <param name="mz_tolerance" value="0.0"/>
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170 <param name="mz_tolerance_unit" value="ppm"/>
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171 </section>
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172 <section name="highest_intensity_peak">
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173 <param name="mz_tolerance" value="0.0"/>
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174 <param name="mz_tolerance_unit" value="ppm"/>
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175 </section>
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176 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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177 <output name="ctd_out" ftype="xml">
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178 <assert_contents>
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179 <is_valid_xml/>
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180 </assert_contents>
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181 </output>
16
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182 <assert_stdout>
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183 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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184 </assert_stdout>
15
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185 </test>
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186 <!-- TOPP_HighResPrecursorMassCorrector_4 -->
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187 <test expect_num_outputs="2">
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188 <section name="adv_opts">
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189 <param name="force" value="false"/>
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190 <param name="test" value="true"/>
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191 </section>
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192 <param name="in" value="HighResPrecursorMassCorrector_2810_1091_3.mzML"/>
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193 <output name="out" value="HighResPrecursorMassCorrector_2810_1091_3_out.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
15
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194 <section name="feature">
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195 <param name="in" value="HighResPrecursorMassCorrector_2810_1091_3.featureXML"/>
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196 <param name="mz_tolerance" value="5.0"/>
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197 <param name="mz_tolerance_unit" value="ppm"/>
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198 <param name="rt_tolerance" value="0.0"/>
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199 <param name="max_trace" value="2"/>
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200 <param name="believe_charge" value="false"/>
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201 <param name="keep_original" value="false"/>
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202 <param name="assign_all_matching" value="false"/>
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203 </section>
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204 <section name="nearest_peak">
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205 <param name="mz_tolerance" value="0.0"/>
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206 <param name="mz_tolerance_unit" value="ppm"/>
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207 </section>
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208 <section name="highest_intensity_peak">
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209 <param name="mz_tolerance" value="0.0"/>
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210 <param name="mz_tolerance_unit" value="ppm"/>
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211 </section>
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212 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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213 <output name="ctd_out" ftype="xml">
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214 <assert_contents>
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215 <is_valid_xml/>
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216 </assert_contents>
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217 </output>
16
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218 <assert_stdout>
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219 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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220 </assert_stdout>
15
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221 </test>
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222 <!-- TOPP_HighResPrecursorMassCorrector_5 -->
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223 <test expect_num_outputs="2">
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224 <section name="adv_opts">
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225 <param name="force" value="false"/>
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226 <param name="test" value="true"/>
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227 </section>
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228 <param name="in" value="HighResPrecursorMassCorrector_3070_1191_3.mzML"/>
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229 <output name="out" value="HighResPrecursorMassCorrector_3070_1191_3_out.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
15
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230 <section name="feature">
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231 <param name="in" value="HighResPrecursorMassCorrector_3070_1191_3.featureXML"/>
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232 <param name="mz_tolerance" value="5.0"/>
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233 <param name="mz_tolerance_unit" value="ppm"/>
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234 <param name="rt_tolerance" value="0.0"/>
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235 <param name="max_trace" value="2"/>
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236 <param name="believe_charge" value="false"/>
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237 <param name="keep_original" value="false"/>
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238 <param name="assign_all_matching" value="false"/>
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239 </section>
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240 <section name="nearest_peak">
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241 <param name="mz_tolerance" value="0.0"/>
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242 <param name="mz_tolerance_unit" value="ppm"/>
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243 </section>
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244 <section name="highest_intensity_peak">
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245 <param name="mz_tolerance" value="0.0"/>
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246 <param name="mz_tolerance_unit" value="ppm"/>
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247 </section>
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248 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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249 <output name="ctd_out" ftype="xml">
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250 <assert_contents>
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251 <is_valid_xml/>
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252 </assert_contents>
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253 </output>
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254 <assert_stdout>
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255 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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256 </assert_stdout>
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257 </test>
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258 <!-- TOPP_HighResPrecursorMassCorrector_6 -->
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259 <test expect_num_outputs="2">
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260 <section name="adv_opts">
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261 <param name="force" value="false"/>
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262 <param name="test" value="true"/>
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263 </section>
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264 <param name="in" value="HighResPrecursorMassCorrector_6.mzML"/>
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265 <output name="out" value="HighResPrecursorMassCorrector_6_out.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
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266 <section name="feature">
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267 <param name="mz_tolerance" value="5.0"/>
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268 <param name="mz_tolerance_unit" value="ppm"/>
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269 <param name="rt_tolerance" value="0.0"/>
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270 <param name="max_trace" value="2"/>
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271 <param name="believe_charge" value="false"/>
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272 <param name="keep_original" value="false"/>
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273 <param name="assign_all_matching" value="false"/>
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274 </section>
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275 <section name="nearest_peak">
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276 <param name="mz_tolerance" value="0.0"/>
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277 <param name="mz_tolerance_unit" value="ppm"/>
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278 </section>
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279 <section name="highest_intensity_peak">
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280 <param name="mz_tolerance" value="0.2"/>
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281 <param name="mz_tolerance_unit" value="ppm"/>
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282 </section>
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283 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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284 <output name="ctd_out" ftype="xml">
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285 <assert_contents>
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286 <is_valid_xml/>
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287 </assert_contents>
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288 </output>
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289 <assert_stdout>
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290 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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291 </assert_stdout>
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292 </test>
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293 </tests>
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294 <help><![CDATA[Corrects the precursor mass and charge determined by the instrument software.
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295
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296
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297 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_HighResPrecursorMassCorrector.html]]></help>
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298 <expand macro="references"/>
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299 </tool>