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1 <tool name="Csv2Apml" id="csv2apml" version="1.0.2">
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2 <description>Converts MS/MS data in CSV format to APML format</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 -->
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8 <command interpreter="java -jar ">
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9 Csv2Apml.jar
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10 -peptideAndProteinMatchListCSV $peptideAndProteinMatchListCSV
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11 -attributesMappingCSV $attributesMappingCSV
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12 -apmlFile $apmlFile
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13 </command>
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14
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15 <inputs>
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16
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17 <param name="peptideAndProteinMatchListCSV" type="data"
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18 format="csv" label="MS/MS CSV file"
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19 help="MS/MS CSV file containing peptide identifications and protein matches" />
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20
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21 <param name="mz" type="text" optional="false" size="30"
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22 label="Column name for precursor m/z" />
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23
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24 <param name="rt" type="text" optional="false" size="30"
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25 label="Column name for precursor rt" />
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26
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27 <param name="charge" type="text" optional="false" size="30"
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28 label="Column name for precursor charge (z)" />
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29
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30 <param name="pepSequence" type="text" optional="false" size="30"
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31 label="Column name for peptide sequence" />
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32
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33 <param name="ppidScore" type="text" optional="false" size="30"
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34 label="Column name for peptide identification score" />
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35
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36 <param name="scoringSchemeName" type="text" optional="true" size="30"
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37 label="(Optional) Column name containing scoring scheme name" />
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38
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39 <param name="statisticalMeasure" type="text" optional="true" size="30"
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40 label="(Optional) Column name for reported statistical measure values"
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41 help="(e.g. column containing p-values or e-values)" />
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42
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43 <param name="ppidTheoreticalMz" type="text" optional="true" size="30"
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44 label="(Optional) Column name for peptide theoretical m/z" />
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45
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46 <param name="modifications" type="text" optional="true" size="30"
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47 label="(Optional) Column name for reported modifications" />
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48
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49 <param name="proteinAccession" type="text" optional="false" size="30"
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50 label="Column name for protein accession code" />
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51
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52 <param name="protSequenceLength" type="text" optional="true" size="30"
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53 label="(Optional) Column name for protein sequence length" />
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54
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55 <param name="pepProtStart" type="text" optional="true" size="30"
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56 label="(Optional) Column name for protein match location start"
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57 help="Where peptide sequence starts in protein"/>
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58
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59 <param name="pepProtEnd" type="text" optional="true" size="30"
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60 label="(Optional) Column name for protein match location end"
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61 help="Where peptide sequence ends in protein"/>
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62
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63 <param name="sourceName" type="text" optional="true" size="30"
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64 label="(Optional) Column name for sample names" />
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65
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66 </inputs>
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67 <configfiles>
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68 <configfile name="attributesMappingCSV">Generic name,name in S1 table CSV
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69 mz,${mz}
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70 rt,${rt}
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71 charge,${charge}
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72 pepSequence,${pepSequence}
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73 ppidScore,${ppidScore}
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74 proteinAccession,${proteinAccession}
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75 #if $ppidTheoreticalMz != "None"
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76 ppidTheoreticalMz,${ppidTheoreticalMz}
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77 #end if
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78 #if $modifications != "None"
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79 modifications,${modifications}
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80 #end if
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81 #if $scoringSchemeName != "None"
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82 scoringSchemeName,${scoringSchemeName}
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83 #end if
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84 #if $statisticalMeasure != "None"
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85 statisticalMeasure,${statisticalMeasure}
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86 #end if
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87 #if $protSequenceLength != "None"
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88 protSequenceLength,${protSequenceLength}
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89 #end if
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90 #if $pepProtStart != "None"
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91 pepProtStart,${pepProtStart}
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92 #end if
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93 #if $pepProtEnd != "None"
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94 pepProtEnd,${pepProtEnd}
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95 #end if
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96 #if $sourceName != "None"
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97 sourceName,${sourceName}
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98 #end if</configfile>
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99 </configfiles>
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100
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101 <outputs>
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102 <data name="apmlFile" format="apml" label="${tool.name} on ${on_string}: APML" >
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103 </data>
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104 </outputs>
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105 <tests>
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106 </tests>
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107 <help>
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108
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109 .. class:: infomark
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110
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111 This tool converts a CSV file containing MS/MS peptide identifications and their respective protein matches
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112 to the APML xml format.
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113 The identifications in APML format can be used for example to annotate unidentified MS features via SEDMAT(*).
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114 This format is also compatible with what is expected by other post-processing tools like Quantifere (for
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115 protein inference).
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116
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117 (*)SEDMAT can use MS2 identification data
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118 and couple it to this MS1 data, thereby annotating the MS1 feature list with identifications.
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119
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120 -----
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121
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122 **Output**
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123
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124 This tools returns the input data in APML xml format.
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125
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126 </help>
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127 </tool>
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