Mercurial > repos > pieterlukasse > prims_proteomics

comparison csv2apml.xml @ 0:d50f079096ee

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Push to main toolshed
author pieter.lukasse@wur.nl
date Wed, 08 Jan 2014 11:39:16 +0100
parents
children 40ec8770780d
comparison
equal deleted inserted replaced
-1:000000000000 0:d50f079096ee
1 <tool name="Csv2Apml" id="csv2apml" version="1.0.2">
2 <description>Converts MS/MS data in CSV format to APML format</description>
3 <!--
4 For remote debugging start you listener on port 8000 and use the following as command interpreter:
5 java -jar -Xdebug -Xrunjdwp:transport=dt_socket,address=D0100564.wurnet.nl:8000
6 //////////////////////////
7 -->
8 <command interpreter="java -jar ">
9 Csv2Apml.jar
10 -peptideAndProteinMatchListCSV $peptideAndProteinMatchListCSV
11 -attributesMappingCSV $attributesMappingCSV
12 -apmlFile $apmlFile
13 </command>
14
15 <inputs>
16
17 <param name="peptideAndProteinMatchListCSV" type="data"
18 format="csv" label="MS/MS CSV file"
19 help="MS/MS CSV file containing peptide identifications and protein matches" />
20
21 <param name="mz" type="text" optional="false" size="30"
22 label="Column name for precursor m/z" />
23
24 <param name="rt" type="text" optional="false" size="30"
25 label="Column name for precursor rt" />
26
27 <param name="charge" type="text" optional="false" size="30"
28 label="Column name for precursor charge (z)" />
29
30 <param name="pepSequence" type="text" optional="false" size="30"
31 label="Column name for peptide sequence" />
32
33 <param name="ppidScore" type="text" optional="false" size="30"
34 label="Column name for peptide identification score" />
35
36 <param name="scoringSchemeName" type="text" optional="true" size="30"
37 label="(Optional) Column name containing scoring scheme name" />
38
39 <param name="statisticalMeasure" type="text" optional="true" size="30"
40 label="(Optional) Column name for reported statistical measure values"
41 help="(e.g. column containing p-values or e-values)" />
42
43 <param name="ppidTheoreticalMz" type="text" optional="true" size="30"
44 label="(Optional) Column name for peptide theoretical m/z" />
45
46 <param name="modifications" type="text" optional="true" size="30"
47 label="(Optional) Column name for reported modifications" />
48
49 <param name="proteinAccession" type="text" optional="false" size="30"
50 label="Column name for protein accession code" />
51
52 <param name="protSequenceLength" type="text" optional="true" size="30"
53 label="(Optional) Column name for protein sequence length" />
54
55 <param name="pepProtStart" type="text" optional="true" size="30"
56 label="(Optional) Column name for protein match location start"
57 help="Where peptide sequence starts in protein"/>
58
59 <param name="pepProtEnd" type="text" optional="true" size="30"
60 label="(Optional) Column name for protein match location end"
61 help="Where peptide sequence ends in protein"/>
62
63 <param name="sourceName" type="text" optional="true" size="30"
64 label="(Optional) Column name for sample names" />
65
66 </inputs>
67 <configfiles>
68 <configfile name="attributesMappingCSV">Generic name,name in S1 table CSV
69 mz,${mz}
70 rt,${rt}
71 charge,${charge}
72 pepSequence,${pepSequence}
73 ppidScore,${ppidScore}
74 proteinAccession,${proteinAccession}
75 #if $ppidTheoreticalMz != "None"
76 ppidTheoreticalMz,${ppidTheoreticalMz}
77 #end if
78 #if $modifications != "None"
79 modifications,${modifications}
80 #end if
81 #if $scoringSchemeName != "None"
82 scoringSchemeName,${scoringSchemeName}
83 #end if
84 #if $statisticalMeasure != "None"
85 statisticalMeasure,${statisticalMeasure}
86 #end if
87 #if $protSequenceLength != "None"
88 protSequenceLength,${protSequenceLength}
89 #end if
90 #if $pepProtStart != "None"
91 pepProtStart,${pepProtStart}
92 #end if
93 #if $pepProtEnd != "None"
94 pepProtEnd,${pepProtEnd}
95 #end if
96 #if $sourceName != "None"
97 sourceName,${sourceName}
98 #end if</configfile>
99 </configfiles>
100
101 <outputs>
102 <data name="apmlFile" format="apml" label="${tool.name} on ${on_string}: APML" >
103 </data>
104 </outputs>
105 <tests>
106 </tests>
107 <help>
108
109 .. class:: infomark
110
111 This tool converts a CSV file containing MS/MS peptide identifications and their respective protein matches
112 to the APML xml format.
113 The identifications in APML format can be used for example to annotate unidentified MS features via SEDMAT(*).
114 This format is also compatible with what is expected by other post-processing tools like Quantifere (for
115 protein inference).
116
117 (*)SEDMAT can use MS2 identification data
118 and couple it to this MS1 data, thereby annotating the MS1 feature list with identifications.
119
120 -----
121
122 **Output**
123
124 This tools returns the input data in APML xml format.
125
126 </help>
127 </tool>