Mercurial > repos > galaxyp > openms_openswathchromatogramextractor

annotate OpenSwathChromatogramExtractor.xml @ 14:92ecd10e5c03 draft default tip

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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 21:41:20 +0000
parents f78d734b7c01
children
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ebe0e9442a29 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
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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: [Targeted Experiments and OpenSWATH]-->
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3 <tool id="OpenSwathChromatogramExtractor" name="OpenSwathChromatogramExtractor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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4 <description>Extract chromatograms (XIC) from a MS2 map file</description>
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5 <macros>
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6 <token name="@EXECUTABLE@">OpenSwathChromatogramExtractor</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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15 ## Preprocessing
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16 mkdir in_cond.in &&
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17 #if $in_cond.in_select == "no"
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18 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} &&
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19 ${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
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20 #else
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21 cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
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22 #end if
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23 mkdir tr &&
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24 cp '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' &&
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25 #if $rt_norm:
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26 mkdir rt_norm &&
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27 cp '$rt_norm' 'rt_norm/${re.sub("[^\w\-_]", "_", $rt_norm.element_identifier)}.$gxy2omsext($rt_norm.ext)' &&
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28 #end if
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29 mkdir out &&
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31 ## Main program call
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33 set -o pipefail &&
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34 @EXECUTABLE@ -write_ctd ./ &&
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35 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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36 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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37 -in
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38 #if $in_cond.in_select == "no"
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39 ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
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40 #else
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41 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)'
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42 #end if
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43 -tr
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44 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)'
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45 #if $rt_norm:
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46 -rt_norm
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47 'rt_norm/${re.sub("[^\w\-_]", "_", $rt_norm.element_identifier)}.$gxy2omsext($rt_norm.ext)'
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48 #end if
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49 -out
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50 'out/output.${gxy2omsext("mzml")}'
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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 "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 <conditional name="in_cond">
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63 <param name="in_select" type="select" label="Run tool in batch mode for -in">
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64 <option value="no">No: process all datasets jointly</option>
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65 <option value="yes">Yes: process each dataset in an independent job</option>
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66 </param>
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67 <when value="no">
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68 <param argument="-in" type="data" format="mzml" multiple="true" label="Input files separated by blank" help=" select mzml data sets(s)"/>
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69 </when>
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70 <when value="yes">
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71 <param argument="-in" type="data" format="mzml" label="Input files separated by blank" help=" select mzml data sets(s)"/>
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72 </when>
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73 </conditional>
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74 <param argument="-tr" type="data" format="csv,traml" label="transition file ('TraML' or 'csv')" help=" select csv,traml data sets(s)"/>
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75 <param argument="-rt_norm" type="data" format="trafoxml" optional="true" label="RT normalization file (how to map the RTs of this run to the ones stored in the library)" help=" select trafoxml data sets(s)"/>
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76 <param argument="-min_upper_edge_dist" type="float" value="0.0" label="Minimal distance to the edge to still consider a precursor, in Thomson" help=""/>
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77 <param argument="-rt_window" type="float" value="-1.0" label="Extraction window in RT dimension (-1 means extract over the whole range)" help="This is the full window size, e.g. a value of 1000 seconds would extract 500 seconds on either side"/>
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78 <param argument="-ion_mobility_window" type="float" value="-1.0" label="Extraction window in ion mobility dimension (in milliseconds)" help="This is the full window size, e.g. a value of 10 milliseconds would extract 5 milliseconds on either side"/>
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79 <param argument="-mz_window" type="float" min="0.0" value="0.05" label="Extraction window in m/z dimension (in Thomson, to use ppm see -ppm flag)" help="This is the full window size, e.g. 100 ppm would extract 50 ppm on either side"/>
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80 <param argument="-ppm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="m/z extraction_window is in ppm" help=""/>
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81 <param argument="-is_swath" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set this flag if the data is SWATH data" help=""/>
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82 <param argument="-extract_MS1" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Extract the MS1 transitions based on the precursor values in the TraML file (useful for extracting MS1 XIC)" help=""/>
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83 <section name="model" title="Options to control the modeling of retention time transformations from data" help="" expanded="false">
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84 <param name="type" argument="-model:type" type="select" label="Type of model" help="">
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85 <option value="linear" selected="true">linear</option>
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86 <option value="b_spline">b_spline</option>
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87 <option value="interpolated">interpolated</option>
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88 <option value="lowess">lowess</option>
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89 <expand macro="list_string_san" name="type"/>
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90 </param>
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91 <param name="symmetric_regression" argument="-model:symmetric_regression" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Only for 'linear' model: Perform linear regression on 'y - x' vs" help="'y + x', instead of on 'y' vs. 'x'"/>
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92 </section>
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93 <expand macro="adv_opts_macro">
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94 <param argument="-extraction_function" type="select" label="Function used to extract the signal" help="">
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95 <option value="tophat" selected="true">tophat</option>
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96 <option value="bartlett">bartlett</option>
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97 <expand macro="list_string_san" name="extraction_function"/>
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98 </param>
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99 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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100 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
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101 <expand macro="list_string_san" name="test"/>
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102 </param>
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103 </expand>
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104 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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105 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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106 </param>
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107 </inputs>
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108 <outputs>
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109 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/>
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110 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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111 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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112 </data>
0
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113 </outputs>
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114 <tests>
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115 <!-- TOPP_OpenSwathChromatogramExtractor_test_1 -->
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116 <test expect_num_outputs="2">
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117 <section name="adv_opts">
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118 <param name="extraction_function" value="tophat"/>
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119 <param name="force" value="false"/>
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120 <param name="test" value="true"/>
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121 </section>
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122 <conditional name="in_cond">
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123 <param name="in" value="OpenSwathChromatogramExtractor_input.mzML"/>
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124 </conditional>
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125 <param name="tr" value="OpenSwathChromatogramExtractor_input.TraML"/>
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126 <output name="out" value="OpenSwathChromatogramExtractor_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
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127 <param name="min_upper_edge_dist" value="0.0"/>
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128 <param name="rt_window" value="-1.0"/>
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129 <param name="ion_mobility_window" value="-1.0"/>
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130 <param name="mz_window" value="0.05"/>
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131 <param name="ppm" value="false"/>
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132 <param name="is_swath" value="false"/>
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133 <param name="extract_MS1" value="false"/>
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134 <section name="model">
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135 <param name="type" value="linear"/>
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136 <param name="symmetric_regression" value="false"/>
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137 </section>
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138 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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139 <output name="ctd_out" ftype="xml">
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140 <assert_contents>
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141 <is_valid_xml/>
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142 </assert_contents>
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143 </output>
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144 <assert_stdout>
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145 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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146 </assert_stdout>
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147 </test>
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148 <!-- TOPP_OpenSwathChromatogramExtractor_test_2 -->
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149 <test expect_num_outputs="2">
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150 <section name="adv_opts">
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151 <param name="extraction_function" value="tophat"/>
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152 <param name="force" value="false"/>
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153 <param name="test" value="true"/>
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154 </section>
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155 <conditional name="in_cond">
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156 <param name="in" value="OpenSwathChromatogramExtractor_input.mzML"/>
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157 </conditional>
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158 <param name="tr" value="OpenSwathChromatogramExtractor_input.TraML"/>
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159 <param name="rt_norm" value="OpenSwathChromatogramExtractor_input.trafoXML"/>
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160 <output name="out" value="OpenSwathChromatogramExtractor_output_2.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
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161 <param name="min_upper_edge_dist" value="0.0"/>
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162 <param name="rt_window" value="50.0"/>
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163 <param name="ion_mobility_window" value="-1.0"/>
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164 <param name="mz_window" value="0.05"/>
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165 <param name="ppm" value="false"/>
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166 <param name="is_swath" value="false"/>
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167 <param name="extract_MS1" value="false"/>
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168 <section name="model">
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169 <param name="type" value="linear"/>
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170 <param name="symmetric_regression" value="false"/>
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171 </section>
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172 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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173 <output name="ctd_out" ftype="xml">
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174 <assert_contents>
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175 <is_valid_xml/>
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176 </assert_contents>
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177 </output>
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178 <assert_stdout>
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179 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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180 </assert_stdout>
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181 </test>
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182 <!-- TOPP_OpenSwathChromatogramExtractor_test_3 -->
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183 <test expect_num_outputs="2">
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184 <section name="adv_opts">
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185 <param name="extraction_function" value="tophat"/>
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186 <param name="force" value="false"/>
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187 <param name="test" value="true"/>
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188 </section>
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189 <conditional name="in_cond">
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190 <param name="in" value="OpenSwathChromatogramExtractor_input.mzML"/>
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191 </conditional>
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192 <param name="tr" value="OpenSwathChromatogramExtractor_input.TraML"/>
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193 <output name="out" value="OpenSwathChromatogramExtractor_output_3.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
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194 <param name="min_upper_edge_dist" value="0.0"/>
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195 <param name="rt_window" value="-1.0"/>
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196 <param name="ion_mobility_window" value="-1.0"/>
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197 <param name="mz_window" value="0.05"/>
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198 <param name="ppm" value="false"/>
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199 <param name="is_swath" value="false"/>
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200 <param name="extract_MS1" value="true"/>
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201 <section name="model">
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202 <param name="type" value="linear"/>
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203 <param name="symmetric_regression" value="false"/>
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204 </section>
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205 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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206 <output name="ctd_out" ftype="xml">
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207 <assert_contents>
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208 <is_valid_xml/>
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209 </assert_contents>
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210 </output>
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211 <assert_stdout>
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212 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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213 </assert_stdout>
13
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214 </test>
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215 <!-- TOPP_OpenSwathChromatogramExtractor_test_4 -->
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216 <test expect_num_outputs="2">
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217 <section name="adv_opts">
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218 <param name="extraction_function" value="tophat"/>
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219 <param name="force" value="false"/>
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220 <param name="test" value="true"/>
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221 </section>
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222 <conditional name="in_cond">
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223 <param name="in" value="OpenSwathChromatogramExtractor_4_input.mzML"/>
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224 </conditional>
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225 <param name="tr" value="OpenSwathChromatogramExtractor_4_input.TraML"/>
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226 <output name="out" value="OpenSwathChromatogramExtractor_4_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
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227 <param name="min_upper_edge_dist" value="0.0"/>
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228 <param name="rt_window" value="-1.0"/>
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229 <param name="ion_mobility_window" value="0.05"/>
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230 <param name="mz_window" value="0.05"/>
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231 <param name="ppm" value="false"/>
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232 <param name="is_swath" value="true"/>
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233 <param name="extract_MS1" value="false"/>
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234 <section name="model">
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235 <param name="type" value="linear"/>
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236 <param name="symmetric_regression" value="false"/>
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237 </section>
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238 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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239 <output name="ctd_out" ftype="xml">
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240 <assert_contents>
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241 <is_valid_xml/>
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242 </assert_contents>
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243 </output>
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244 <assert_stdout>
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245 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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246 </assert_stdout>
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247 </test>
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248 <!-- TOPP_OpenSwathChromatogramExtractor_test_5 -->
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249 <test expect_num_outputs="2">
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250 <section name="adv_opts">
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251 <param name="extraction_function" value="tophat"/>
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252 <param name="force" value="false"/>
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253 <param name="test" value="true"/>
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254 </section>
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255 <conditional name="in_cond">
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256 <param name="in" value="OpenSwathChromatogramExtractor_input.mzML"/>
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257 </conditional>
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258 <param name="tr" value="OpenSwathChromatogramExtractor_5_input.TraML"/>
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259 <output name="out" value="OpenSwathChromatogramExtractor_5_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
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260 <param name="min_upper_edge_dist" value="0.0"/>
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261 <param name="rt_window" value="-1.0"/>
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262 <param name="ion_mobility_window" value="-1.0"/>
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263 <param name="mz_window" value="0.05"/>
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264 <param name="ppm" value="false"/>
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265 <param name="is_swath" value="false"/>
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266 <param name="extract_MS1" value="true"/>
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267 <section name="model">
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268 <param name="type" value="linear"/>
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269 <param name="symmetric_regression" value="false"/>
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270 </section>
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271 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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272 <output name="ctd_out" ftype="xml">
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273 <assert_contents>
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274 <is_valid_xml/>
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275 </assert_contents>
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276 </output>
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277 <assert_stdout>
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278 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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279 </assert_stdout>
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280 </test>
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281 </tests>
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282 <help><![CDATA[Extract chromatograms (XIC) from a MS2 map file.
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283
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284
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285 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_OpenSwathChromatogramExtractor.html]]></help>
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286 <expand macro="references"/>
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287 </tool>