annotate thermo_converter.xml @ 9:92ac8e086317 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser commit 9bb883e027809047684fd6c45e9a6f1f3bf69351"
author galaxyp
date Wed, 17 Feb 2021 09:50:26 +0000
parents 26c6706bfb07
children b9b385097f13
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1 <tool id="thermo_raw_file_converter" name="Thermo" version="@TOOL_VERSION@+galaxy0" profile="20.05">
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2 <description>RAW file converter</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">1.3.2</token>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="@TOOL_VERSION@">thermorawfileparser</requirement>
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8 </requirements>
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9 <stdio>
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10 <regex match="ERROR" source="both" level="fatal" description="Fatal error"/>
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11 </stdio>
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12 <version_command><![CDATA[ThermoRawFileParser.sh --version]]></version_command>
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13 <command>
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14 <![CDATA[
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15 #import re
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16
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17 #set $input_name = re.sub('[^\w\-\.]', '_', $input_file.element_identifier.replace(".raw", "") + ".raw")
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18 ln -s -f '$input_file' '$input_name' &&
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19
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20 ThermoRawFileParser.sh
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21 --input='$input_name'
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22 --output_file='$output'
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23 -f=$format_cond.output_format
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24 #if $output_metadata_selector != "off":
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25 --metadata="$output_metadata_selector"
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26 --metadata_output_file='$output_metadata'
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27 #end if
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28 #if $format_cond.output_format == "0"
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29 $format_cond.mgfPrecursor
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30 #end if
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31 #if $format_cond.output_format in ['1', '2']
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32 $format_cond.zlib_boolean
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33 $format_cond.peakpicking_boolean
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34 #end if
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35 $ignore_instrument_errors_boolean
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36 $allDetectors
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37 $includeExceptionData
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38 #if $msLevel != ''
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39 --msLevel="$msLevel"
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40 #end if
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41 ]]>
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42 </command>
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43 <inputs>
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44 <param argument="--input" name="input_file" type="data" format="thermo.raw" label="Thermo RAW file" help="" optional="False"/>
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45 <conditional name="format_cond">
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46 <param argument="--format" name="output_format" type="select" label="Output format">
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47 <option value="0">mgf</option>
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48 <option value="1" selected="True">mzml</option>
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49 <option value="2">Indexed mzml</option>
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50 <!-- <option value="3">Parquet</option> -->
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51 </param>
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52 <when value="0">
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53 <param argument="--mgfPrecursor" type="boolean" truevalue="--mgfPrecursor" falsevalue="" label="Include precursor scan number in MGF file" help=""/>
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54 </when>
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55 <when value="1">
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56 <param argument="--noZlibCompression" name="zlib_boolean" type="boolean" truevalue="" falsevalue="-z" checked="true"
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57 label="Use zlib compression for the m/z ratios and intensities" help=""/>
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58 <param argument="--noPeakPicking" name="peakpicking_boolean" type="boolean" truevalue="" falsevalue="-p" checked="true"
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59 label="Use the peak picking provided by the native thermo library" help=""/>
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60 </when>
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61 <when value="2">
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62 <param argument="--noZlibCompression" name="zlib_boolean" type="boolean" truevalue="" falsevalue="-z" checked="true"
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63 label="Use zlib compression for the m/z ratios and intensities" help=""/>
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64 <param argument="--noPeakPicking" name="peakpicking_boolean" type="boolean" truevalue="" falsevalue="-p" checked="true"
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65 label="Use the peak picking provided by the native thermo library" help=""/>
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66 </when>
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67 <when value="3"/>
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68 </conditional>
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69 <param argument="--metadata" name="output_metadata_selector" type="select" label="Output metadata">
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70 <option value="off" selected="True">No</option>
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71 <option value="0">json</option>
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72 <option value="1">txt</option>
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73 </param>
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74 <param argument="--ignoreInstrumentErrors" name="ignore_instrument_errors_boolean" type="boolean" truevalue="-e" falsevalue="" checked="true"
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75 label="Ignore missing instrument properties" help="If false, it stops the conversion if instrument properties are missing"/>
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76 <param argument="--allDetectors" type="boolean" truevalue="--allDetectors" falsevalue="" checked="false" label="Extract additional detector data" help="UV/PDA etc"/>
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77 <param argument="--includeExceptionData" type="boolean" truevalue="--includeExceptionData" falsevalue="" label="Include reference and exception data"/>
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78 <param argument="--msLevel" type="text" value="" label="Select MS levels " help="(MS1, MS2, etc) included in the output, should be a comma-separated list of integers ( 1,2,3 ) and/or intervals ( 1-3 ), open-end intervals ( 1- ) are allowed">
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79 <sanitizer invalid_char="">
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80 <valid initial="string.digits">
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81 <add value="-"/>
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82 <add value=","/>
92ac8e086317 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser commit 9bb883e027809047684fd6c45e9a6f1f3bf69351"
galaxyp
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83 </valid>
92ac8e086317 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser commit 9bb883e027809047684fd6c45e9a6f1f3bf69351"
galaxyp
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diff changeset
84 </sanitizer>
92ac8e086317 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser commit 9bb883e027809047684fd6c45e9a6f1f3bf69351"
galaxyp
parents: 8
diff changeset
85 </param>
0
00c4b28150bd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit f211dc8467604ef106cc85b4c68aec5707a24c6d
galaxyp
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86 </inputs>
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87 <outputs>
9
92ac8e086317 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser commit 9bb883e027809047684fd6c45e9a6f1f3bf69351"
galaxyp
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88 <data name="output" format="mzml" label="${tool.name} on ${on_string}">
92ac8e086317 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser commit 9bb883e027809047684fd6c45e9a6f1f3bf69351"
galaxyp
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89 <change_format>
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galaxyp
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90 <when input="format_cond.output_format" value="0" format="mgf"/>
92ac8e086317 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser commit 9bb883e027809047684fd6c45e9a6f1f3bf69351"
galaxyp
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91 <!-- <when input="format_cond.output_format" value="3" format="parquet"/> -->
92ac8e086317 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser commit 9bb883e027809047684fd6c45e9a6f1f3bf69351"
galaxyp
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92 </change_format>
92ac8e086317 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser commit 9bb883e027809047684fd6c45e9a6f1f3bf69351"
galaxyp
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diff changeset
93 </data>
92ac8e086317 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser commit 9bb883e027809047684fd6c45e9a6f1f3bf69351"
galaxyp
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94 <data name="output_metadata" format="txt" label="${tool.name} on ${on_string}: metadata">
5
77a18a61aeed "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
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diff changeset
95 <filter>output_metadata_selector != "off"</filter>
9
92ac8e086317 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser commit 9bb883e027809047684fd6c45e9a6f1f3bf69351"
galaxyp
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96 <change_format>
92ac8e086317 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser commit 9bb883e027809047684fd6c45e9a6f1f3bf69351"
galaxyp
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97 <when input="output_metadata_selector" value="0" format="json"/>
92ac8e086317 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser commit 9bb883e027809047684fd6c45e9a6f1f3bf69351"
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98 </change_format>
92ac8e086317 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser commit 9bb883e027809047684fd6c45e9a6f1f3bf69351"
galaxyp
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diff changeset
99 </data>
0
00c4b28150bd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit f211dc8467604ef106cc85b4c68aec5707a24c6d
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100 </outputs>
5
77a18a61aeed "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
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101
0
00c4b28150bd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit f211dc8467604ef106cc85b4c68aec5707a24c6d
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102 <tests>
9
92ac8e086317 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser commit 9bb883e027809047684fd6c45e9a6f1f3bf69351"
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103 <!-- mgf test, no metadata -->
5
77a18a61aeed "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
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diff changeset
104 <test expect_num_outputs="1">
9
92ac8e086317 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser commit 9bb883e027809047684fd6c45e9a6f1f3bf69351"
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105 <param name="input_file" value="really_small.raw" ftype="thermo.raw"/>
92ac8e086317 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser commit 9bb883e027809047684fd6c45e9a6f1f3bf69351"
galaxyp
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diff changeset
106 <conditional name="format_cond">
92ac8e086317 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser commit 9bb883e027809047684fd6c45e9a6f1f3bf69351"
galaxyp
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diff changeset
107 <param name="output_format" value="0"/>
92ac8e086317 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser commit 9bb883e027809047684fd6c45e9a6f1f3bf69351"
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108 <param name="mgfPrecursor" value="true"/>
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109 </conditional>
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diff changeset
110 <output name="output" ftype="mgf" value="really_small.mgf">
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galaxyp
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111 <assert_contents>
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galaxyp
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diff changeset
112 <has_text text="SCANS=36"/>
92ac8e086317 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser commit 9bb883e027809047684fd6c45e9a6f1f3bf69351"
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diff changeset
113 <has_text text="RTINSECONDS=73.863181104"/>
92ac8e086317 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser commit 9bb883e027809047684fd6c45e9a6f1f3bf69351"
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diff changeset
114 <has_text text="PEPMASS=675.248779296875"/>
92ac8e086317 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser commit 9bb883e027809047684fd6c45e9a6f1f3bf69351"
galaxyp
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diff changeset
115 <has_text text="CHARGE=2+"/>
92ac8e086317 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser commit 9bb883e027809047684fd6c45e9a6f1f3bf69351"
galaxyp
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diff changeset
116 <has_text text="121.3116455 920.2367553711"/>
92ac8e086317 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser commit 9bb883e027809047684fd6c45e9a6f1f3bf69351"
galaxyp
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diff changeset
117 <has_text text="229.2241211 1137.6958007813"/>
92ac8e086317 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser commit 9bb883e027809047684fd6c45e9a6f1f3bf69351"
galaxyp
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diff changeset
118 <has_text text="1577.8967285 1487.9519042969"/>
92ac8e086317 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser commit 9bb883e027809047684fd6c45e9a6f1f3bf69351"
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diff changeset
119 </assert_contents>
92ac8e086317 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser commit 9bb883e027809047684fd6c45e9a6f1f3bf69351"
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120 </output>
92ac8e086317 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser commit 9bb883e027809047684fd6c45e9a6f1f3bf69351"
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121 <assert_command>
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122 <has_text text="--mgfPrecursor"></has_text>
92ac8e086317 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser commit 9bb883e027809047684fd6c45e9a6f1f3bf69351"
galaxyp
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123 </assert_command>
8
26c6706bfb07 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit a502d3fbf1f1ecfca1c9b115beab9d9c0e358fb5"
galaxyp
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124 </test>
26c6706bfb07 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit a502d3fbf1f1ecfca1c9b115beab9d9c0e358fb5"
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diff changeset
125
9
92ac8e086317 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser commit 9bb883e027809047684fd6c45e9a6f1f3bf69351"
galaxyp
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diff changeset
126 <!-- mzml test and json metadata -->
92ac8e086317 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser commit 9bb883e027809047684fd6c45e9a6f1f3bf69351"
galaxyp
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diff changeset
127 <test expect_num_outputs="2">
92ac8e086317 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser commit 9bb883e027809047684fd6c45e9a6f1f3bf69351"
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128 <param name="input_file" value="really_small.raw" ftype="thermo.raw"/>
92ac8e086317 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser commit 9bb883e027809047684fd6c45e9a6f1f3bf69351"
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diff changeset
129 <conditional name="format_cond">
92ac8e086317 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser commit 9bb883e027809047684fd6c45e9a6f1f3bf69351"
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diff changeset
130 <param name="output_format" value="1"/>
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diff changeset
131 </conditional>
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diff changeset
132 <param name="output_metadata_selector" value="0"/>
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galaxyp
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diff changeset
133 <output name="output" file="really_small.mzml" ftype="mzml"/>
92ac8e086317 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser commit 9bb883e027809047684fd6c45e9a6f1f3bf69351"
galaxyp
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diff changeset
134 <output name="output_metadata" value="really_small.json" ftype="json"/>
92ac8e086317 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser commit 9bb883e027809047684fd6c45e9a6f1f3bf69351"
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diff changeset
135 <assert_command>
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galaxyp
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diff changeset
136 <not_has_text text="--mgfPrecursor"></not_has_text>
92ac8e086317 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser commit 9bb883e027809047684fd6c45e9a6f1f3bf69351"
galaxyp
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diff changeset
137 </assert_command>
0
00c4b28150bd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit f211dc8467604ef106cc85b4c68aec5707a24c6d
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138 </test>
5
77a18a61aeed "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
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139
9
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140 <!-- mzml test (wo zlib compression and peak picking) and json metadata -->
5
77a18a61aeed "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
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141 <test expect_num_outputs="2">
9
92ac8e086317 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser commit 9bb883e027809047684fd6c45e9a6f1f3bf69351"
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diff changeset
142 <param name="input_file" value="really_small.raw" ftype="thermo.raw"/>
92ac8e086317 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser commit 9bb883e027809047684fd6c45e9a6f1f3bf69351"
galaxyp
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diff changeset
143 <conditional name="format_cond">
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diff changeset
144 <param name="output_format" value="1"/>
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diff changeset
145 <param name="zlib_boolean" value="false"/>
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diff changeset
146 <param name="peakpicking_boolean" value="false"/>
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diff changeset
147 </conditional>
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diff changeset
148 <param name="output_metadata_selector" value="0"/>
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galaxyp
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diff changeset
149 <output name="output" file="really_small_ext.mzml" ftype="mzml"/>
92ac8e086317 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser commit 9bb883e027809047684fd6c45e9a6f1f3bf69351"
galaxyp
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diff changeset
150 <output name="output_metadata" value="really_small.json" ftype="json"/>
92ac8e086317 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser commit 9bb883e027809047684fd6c45e9a6f1f3bf69351"
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diff changeset
151 <assert_command>
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galaxyp
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diff changeset
152 <not_has_text text="--mgfPrecursor"></not_has_text>
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galaxyp
parents: 8
diff changeset
153 <has_text text="-z "></has_text>
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galaxyp
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diff changeset
154 <has_text text="-p "></has_text>
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diff changeset
155 </assert_command>
5
77a18a61aeed "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
parents: 4
diff changeset
156 </test>
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galaxyp
parents: 4
diff changeset
157
9
92ac8e086317 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser commit 9bb883e027809047684fd6c45e9a6f1f3bf69351"
galaxyp
parents: 8
diff changeset
158 <!-- indexed mzml, txt metadata (+ extra options) -->
5
77a18a61aeed "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"
galaxyp
parents: 4
diff changeset
159 <test expect_num_outputs="2">
9
92ac8e086317 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser commit 9bb883e027809047684fd6c45e9a6f1f3bf69351"
galaxyp
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diff changeset
160 <param name="input_file" value="really_small.raw" ftype="thermo.raw"/>
92ac8e086317 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser commit 9bb883e027809047684fd6c45e9a6f1f3bf69351"
galaxyp
parents: 8
diff changeset
161 <conditional name="format_cond">
92ac8e086317 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser commit 9bb883e027809047684fd6c45e9a6f1f3bf69351"
galaxyp
parents: 8
diff changeset
162 <param name="output_format" value="2"/>
92ac8e086317 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser commit 9bb883e027809047684fd6c45e9a6f1f3bf69351"
galaxyp
parents: 8
diff changeset
163 </conditional>
92ac8e086317 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser commit 9bb883e027809047684fd6c45e9a6f1f3bf69351"
galaxyp
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diff changeset
164 <param name="output_metadata_selector" value="1"/>
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diff changeset
165 <param name="ignore_instrument_errors_boolean" value="true"/>
92ac8e086317 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser commit 9bb883e027809047684fd6c45e9a6f1f3bf69351"
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diff changeset
166 <param name="allDetectors" value="true"/>
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galaxyp
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167 <param name="includeExceptionData" value="--includeExceptionData"/>
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168 <param name="msLevel" value="1"/>
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169 <output name="output" value="really_small.indexed_mzML" ftype="mzml"/>
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170 <output name="output_metadata" ftype="txt">
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171 <assert_contents>
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172 <has_text text="Instrument model=[MS, MS:1000494, Thermo Scientific instrument model, Orbitrap Fusion]"/>
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173 <has_text text="Instrument name=Orbitrap Fusion"/>
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174 <has_text text="Instrument serial number=[MS, MS:1000529, instrument serial number, FSN10188]"/>
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175 <has_text text="Software version=[NCIT, NCIT:C111093, Software Version, 3.1.2412.17]"/>
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176 <has_text text="Mass resolution=[MS, MS:1000011, mass resolution, 0.500]"/>
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177 <has_text text="Number of scans=101"/>
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178 <has_text text="Scan range=1;101"/>
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179 <has_text text="Scan start time=[MS, MS:1000016, scan start time, 0.89]"/>
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180 <has_text text="Time range=0.89;1.59"/>
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181 <has_text text="Mass range=120.0000;2000.0000"/>
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182 </assert_contents>
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183 </output>
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184 <assert_command>
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185 <not_has_text text="--mgfPrecursor"></not_has_text>
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186 <has_text text="-e "/>
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187 <has_text text="--allDetectors"/>
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188 <has_text text="--includeExceptionData"/>
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189 <has_text text="--msLevel=&quot;1&quot;"/>
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190 </assert_command>
1
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191 </test>
9
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192 <!-- parquet test, no metadata
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193 <test expect_num_outputs="1">
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194 <param name="input_file" value="really_small.raw" ftype="thermo.raw"/>
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195 <conditional name="format_cond">
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196 <param name="output_format" value="3"/>
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197 </conditional>
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198 <output name="output" ftype="parquet" value="really_small.parquet"/>
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199 </test> -->
0
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200 </tests>
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201 <help>
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202 <![CDATA[
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203
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204 Thermo RAW file converter based on the great `ThermoRawFileParser <https://github.com/compomics/ThermoRawFileParser>`_ project.
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205
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206 ]]>
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207 </help>
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208 <citations>
9
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209 <citation type="doi">10.1021/acs.jproteome.9b00328</citation>
0
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210 </citations>
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211 </tool>