Mercurial > repos > galaxyp > openms_eicextractor

annotate EICExtractor.xml @ 16:c0f39306c687 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 21:40:11 +0000
parents f253d41d9170
children
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72e0bc55a462 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: [Quantitation]-->
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3 <tool id="EICExtractor" name="EICExtractor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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4 <description>Extracts intensities from dedicates positions in a LC/MS map</description>
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5 <macros>
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6 <token name="@EXECUTABLE@">EICExtractor</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_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 #if $in_header_cond.in_header:
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24 mkdir in_header_cond.in_header &&
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25 #if $in_header_cond.in_header_select == "no"
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26 mkdir ${' '.join(["'in_header_cond.in_header/%s'" % (i) for i, f in enumerate($in_header_cond.in_header) if f])} &&
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27 ${' '.join(["cp '%s' 'in_header_cond.in_header/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_header_cond.in_header) if f])}
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28 #else
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29 cp '$in_header_cond.in_header' 'in_header_cond.in_header/${re.sub("[^\w\-_]", "_", $in_header_cond.in_header.element_identifier)}.$gxy2omsext($in_header_cond.in_header.ext)' &&
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30 #end if
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31 #end if
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32 mkdir pos &&
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33 cp '$pos' 'pos/${re.sub("[^\w\-_]", "_", $pos.element_identifier)}.$gxy2omsext($pos.ext)' &&
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34 mkdir out &&
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35 #if "out_debug_TIC_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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36 mkdir auto_rt_out_debug_TIC &&
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37 #end if
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38
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39 ## Main program call
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40
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41 set -o pipefail &&
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42 @EXECUTABLE@ -write_ctd ./ &&
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43 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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44 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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45 -in
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46 #if $in_cond.in_select == "no"
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47 ${' '.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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48 #else
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49 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)'
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50 #end if
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51 #if $in_header_cond.in_header:
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52 -in_header
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53 #if $in_header_cond.in_header_select == "no"
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54 ${' '.join(["'in_header_cond.in_header/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_header_cond.in_header) if f])}
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55 #else
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56 'in_header_cond.in_header/${re.sub("[^\w\-_]", "_", $in_header_cond.in_header.element_identifier)}.$gxy2omsext($in_header_cond.in_header.ext)'
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57 #end if
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58 #end if
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59 -pos
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60 'pos/${re.sub("[^\w\-_]", "_", $pos.element_identifier)}.$gxy2omsext($pos.ext)'
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61 -out
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62 'out/output.${gxy2omsext("csv")}'
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63 #if "out_debug_TIC_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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64 -auto_rt:out_debug_TIC
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65 'auto_rt_out_debug_TIC/output.${gxy2omsext("mzml")}'
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66 #end if
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67 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
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68 | tee '$stdout'
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69 #end if
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70
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71 ## Postprocessing
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72 && mv 'out/output.${gxy2omsext("csv")}' '$out'
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73 #if "out_debug_TIC_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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74 && mv 'auto_rt_out_debug_TIC/output.${gxy2omsext("mzml")}' '$auto_rt_out_debug_TIC'
0
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75 #end if
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76 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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77 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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78 #end if]]></command>
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79 <configfiles>
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80 <inputs name="args_json" data_style="paths"/>
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81 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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82 </configfiles>
0
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83 <inputs>
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84 <conditional name="in_cond">
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85 <param name="in_select" type="select" label="Run tool in batch mode for -in">
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86 <option value="no">No: process all datasets jointly</option>
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87 <option value="yes">Yes: process each dataset in an independent job</option>
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88 </param>
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89 <when value="no">
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90 <param argument="-in" type="data" format="mzml" multiple="true" label="Input raw data file" help=" select mzml data sets(s)"/>
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91 </when>
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92 <when value="yes">
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93 <param argument="-in" type="data" format="mzml" label="Input raw data file" help=" select mzml data sets(s)"/>
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94 </when>
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95 </conditional>
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96 <conditional name="in_header_cond">
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97 <param name="in_header_select" type="select" label="Run tool in batch mode for -in_header">
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98 <option value="no">No: process all datasets jointly</option>
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99 <option value="yes">Yes: process each dataset in an independent job</option>
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100 </param>
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101 <when value="no">
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102 <param argument="-in_header" type="data" format="txt" multiple="true" optional="true" label="[for Waters data only] Read additional information from _HEADER.TXT" help="Provide one for each raw input file select txt data sets(s)"/>
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103 </when>
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104 <when value="yes">
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105 <param argument="-in_header" type="data" format="txt" optional="true" label="[for Waters data only] Read additional information from _HEADER.TXT" help="Provide one for each raw input file select txt data sets(s)"/>
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106 </when>
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107 </conditional>
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108 <param argument="-pos" type="data" format="edta" label="Input config file stating where to find signal" help=" select edta data sets(s)"/>
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109 <param argument="-rt_tol" type="float" value="3.0" label="RT tolerance in [s] for finding max peak (whole RT range around RT middle)" help=""/>
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110 <param argument="-mz_tol" type="float" value="10.0" label="m/z tolerance in [ppm] for finding a peak" help=""/>
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111 <param argument="-rt_collect" type="integer" value="1" label="# of scans up &amp; down in RT from highest point for ppm estimation in result" help=""/>
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112 <section name="auto_rt" title="Parameters for automatic detection of injection RT peaks (no need to specify them in 'pos' input file)" help="" expanded="false">
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113 <param name="enabled" argument="-auto_rt:enabled" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Automatically detect injection peaks from TIC and quantify all m/z x RT combinations" help=""/>
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114 <param name="FHWM" argument="-auto_rt:FHWM" type="float" value="5.0" label="Expected full width at half-maximum of each raw RT peak in [s]" help="Gaussian smoothing filter with this width is applied to TIC"/>
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115 <param name="SNThreshold" argument="-auto_rt:SNThreshold" type="float" value="5.0" label="S/N threshold for a smoothed raw peak to pass peak picking" help="Higher thesholds will result in less peaks"/>
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116 </section>
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117 <expand macro="adv_opts_macro">
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118 <param argument="-out_separator" type="text" value="," label="Separator character for output CSV file" help="">
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119 <expand macro="list_string_san" name="out_separator"/>
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120 </param>
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121 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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122 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
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123 <expand macro="list_string_san" name="test"/>
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124 </param>
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125 </expand>
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126 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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127 <option value="out_debug_TIC_FLAG">out_debug_TIC (Optional output file (for first input) containing the smoothed TIC, S/N levels and picked RT positions)</option>
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128 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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129 </param>
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130 </inputs>
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131 <outputs>
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132 <data name="out" label="${tool.name} on ${on_string}: out" format="csv"/>
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133 <data name="auto_rt_out_debug_TIC" label="${tool.name} on ${on_string}: auto_rt:out_debug_TIC" format="mzml">
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134 <filter>OPTIONAL_OUTPUTS is not None and "out_debug_TIC_FLAG" in OPTIONAL_OUTPUTS</filter>
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135 </data>
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136 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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137 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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138 </data>
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139 </outputs>
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140 <tests>
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141 <test expect_num_outputs="1">
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142 <!-- just using some random test data -->
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143 <param name="adv_opts|test" value="true"/>
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144 <param name="in" value="spectra.mzML"/>
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145 <param name="pos" ftype="edta" value="FileConverter_10_input.edta"/>
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146 <output name="out" ftype="csv" value="EICExtractor.csv" lines_diff="2"/>
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147 </test>
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148 </tests>
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149 <help><![CDATA[Extracts intensities from dedicates positions in a LC/MS map
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150
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151
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152 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_EICExtractor.html]]></help>
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153 <expand macro="references"/>
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154 </tool>