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1 <tool name="SedMat" id="sedmat1" version="1.0.2">
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2 <description>Matches MS and MS/MS results</description>
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3 <!--
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4 For remote debugging start you listener on port 8000 and use the following as command interpreter:
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5 java -jar -Xdebug -Xrunjdwp:transport=dt_socket,address=D0100564.wurnet.nl:8000
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6 -->
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7 <command interpreter="java -jar ">
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8 SedMat_cli.jar
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9 -pl $inputMS
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10 -plInputFormat apml
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11 -ppids $fileType.inputFormatType.ppidsFile
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12 -ppidsFileGrouping $fileType.type
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13 -ppidsInputFormat $fileType.inputFormatType.ppidsInputFormat
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14 -ppidsFileDescription $fileType.inputFormatType.ppidsFile.name
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15 #if $fileType.inputFormatType.ppidsInputFormat == "mzid"
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16 -spectraDataFile $fileType.inputFormatType.spectraDataFile
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17 #end if
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18 -out $outputData
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19 -outUnmatchedMS2 $outUnmatchedMS2
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20 -mtol $mtol
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21 -rttol $rttol
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22 -rtShiftDetectionWindow $rtShiftDetectionWindow
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23 -matchOnSameSourceOnly $matchOnSameSourceOnly
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24 -chargeStatesToGenerate $chargeStatesToGenerate
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25 -outReport $htmlReportFile
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26 -outReportPicturesPath $htmlReportFile.files_path
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27 #if $troubleshoot1.troubleshootPeakLocations == True
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28 -troubleshootPeakLocations YES
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29 -mStart $troubleshoot1.mStart
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30 -mEnd $troubleshoot1.mEnd
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31 -rtStart $troubleshoot1.rtStart
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32 -rtEnd $troubleshoot1.rtEnd
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33 -filterSourceName $troubleshoot1.filterSourceName
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34 #end if
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35 #if $matchOnNamingConvention.match == True
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36 -matchOnNamingConvention YES
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37 -namingConventionCodesForMatching $matchOnNamingConvention.namingConventionCodesForMatching
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38 #end if
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39
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40 </command>
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41
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42 <inputs>
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43
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44 <param name="inputMS" type="data" format="apml" label="MS data (APML format)" />
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45 <!-- possible option <validator type="metadata" check="base_name" message="Metadata missing, click the pencil icon in the history item and set base_name."/> -->
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46
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47 <conditional name="fileType">
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48 <param name="type" type="select" label="Peptide identification file grouping type">
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49 <option value="single" selected="true">single-File</option>
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50 <option value="fileSet">fileSet</option>
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51 </param>
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52 <when value="single">
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53 <conditional name="inputFormatType">
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54 <param name="ppidsInputFormat" type="select" label="MS/MS input format">
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55 <option value="mzid" selected="true">mzIdentML on mzML</option>
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56 <option value="apml">APML</option>
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57 </param>
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58 <when value="mzid">
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59 <param name="spectraDataFile" type="data" format="mzml" label="MS/MS spectra file (mzml)"/>
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60 <param name="ppidsFile" type="data" format="mzid" label="MS/MS peptide identifications file (mzidentml)"/>
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61 </when>
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62 <when value="apml">
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63 <param name="ppidsFile" type="data" format="apml" label="MS/MS peptide identifications file (apml)">
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64 <!-- TODO - find out how to use
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65 <validator type="expression" message="You already selected this file as the MS data file.">value.id == inputMS,{"inputMS":$inputMS},{}</validator>-->
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66 </param>
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67 </when>
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68 </conditional>
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69 </when>
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70 <when value="fileSet">
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71 <conditional name="inputFormatType">
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72 <param name="ppidsInputFormat" type="select" label="inputFormat">
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73 <option value="mzid" selected="true">mzIdentML on mzML</option>
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74 </param>
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75 <when value="mzid">
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76 <param name="spectraDataFile" type="data" format="prims.fileset.zip" label="MS/MS spectra fileSet (N mzml files)"/>
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77 <param name="ppidsFile" type="data" format="prims.fileset.zip" label="MS/MS peptide identifications fileSet (N mzidentml files)"/>
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78 </when>
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79 </conditional>
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80 </when>
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81 </conditional>
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82 <param name="mtol" type="integer" size="10" value="50" label="m/z tolerance (ppm) " />
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83 <param name="rttol" type="integer" size="10" value="150" label="Rention time tolerance (seconds) " />
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84 <param name="rtShiftDetectionWindow" type="integer" size="10" value="20" label="Rention time shift detection window (seconds) " help="Size of the window to use for average rt shift calculations"/>
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85
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86 <param name="matchOnSameSourceOnly" type="boolean" checked="false" label="Match peaks from same source only" help="If you want this, you might have to inform how to match the source files"/>
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87 <conditional name="matchOnNamingConvention">
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88 <param name="match" type="boolean" truevalue="Yes" falsevalue="No" checked="false" label="Match using naming convention" help="Use a list of codes that occur in the file names and that link them together."/>
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89 <when value="Yes">
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90 <param name="namingConventionCodesForMatching" type="text" size="100" value="" label="List of codes in naming convention" help="Add the CSV list of codes that occur in the file names and that link them together. E.g. '_F1,_F2,_F3,etc.'"/>
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91 </when>
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92 </conditional>
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93
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94 <param name="chargeStatesToGenerate" type="select" display="checkboxes" multiple="true" label="Generate extra charge states" help="The selected charge states will be generated for each MS2 feature ">
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95 <option value="1" selected="true">1</option>
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96 <option value="2" selected="true">2</option>
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97 <option value="3" selected="true">3</option>
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98 <option value="4" selected="true">4</option>
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99 <option value="5">5</option>
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100 </param>
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101
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102 <param name="summaryReport" type="boolean" checked="true" label="Generate summary report" help="NB: this will increase the processing time"/>
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103
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104 <conditional name="troubleshoot1">
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105 <param name="troubleshootPeakLocations" type="boolean" truevalue="Yes" falsevalue="No" checked="false" label="Troubleshoot ms1/ms2 peak locations" help="Small trial run to check if the MS and MS/MS peak lists in their current states can easily be matched "/>
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106 <when value="Yes">
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107 <param name="mStart" optional="false" type="integer" size="10" value="100" label="Set m/z start " />
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108 <param name="mEnd" optional="false" type="integer" size="10" value="1000" label="Set m/z end " />
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109 <param name="rtStart" optional="false" type="integer" size="10" value="10" label="Set rention time start (minutes) " />
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110 <param name="rtEnd" optional="false" type="integer" size="10" value="20" label="Set rention time end (minutes) " />
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111 <param name="filterSourceName" type="text" size="100" value="" label="Restrict matching to a specific subset of the files " help="Part of a file name that occurs in both a ms1 and ms2 file (e.g. 'RibO_1_msE1')"/>
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112 </when>
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113 </conditional>
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114
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115 </inputs>
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116 <outputs>
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117 <data name="outputData" format="apml" label="${inputMS.metadata.base_name} - ${tool.name} on ${on_string}: APML" metadata_source="inputMS"></data>
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118 <data name="outUnmatchedMS2" format="csv" label="${inputMS.metadata.base_name} - ${tool.name} on ${on_string}: unmatched MS2 features CSV" metadata_source="inputMS"></data>
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119 <data name="htmlReportFile" format="html" label="${tool.name} on ${on_string} - HTML report">
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120 <!-- If the expression is false, the file is not created -->
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121 <filter>( summaryReport == True )</filter>
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122 </data>
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123 </outputs>
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124 <tests>
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125 <!-- find out how to use -->
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126 <test>
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127 </test>
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128 </tests>
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129 <help>
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130
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131 .. class:: infomark
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132
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133 This tool matches MS and MS/MS results. SEDMAT stands for "Single Experiment Data Matching Tool".
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134 It can match peaks found in the MS spectra with the peptides found using the MS/MS spectra.
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135 The result is the list of MS peaks annotated with peptides and proteins.
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136
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137 -----
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138
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139 **Output example**
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140
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141 This tools returns APML output, a Cytoscape network (.xgmml) of the matches and Retention Time plots (.pdf).
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142
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143 </help>
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144 </tool>
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