annotate masscomb_visual_mspicture.xml @ 9:c317e0f939df

Made converter more robust and added support for mzXML in xtandem interface
author pieter.lukasse@wur.nl
date Fri, 07 Feb 2014 11:41:58 +0100
parents d6001e8d7441
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
1 <tool name="MsPicture" id="masscomb_mspicture" version="1.0.1">
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
2 <description>MS data view</description>
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
3 <!--
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
4 For remote debugging start you listener on port 8000 and use the following as command interpreter:
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
5 java -jar -Xdebug -Xrunjdwp:transport=dt_socket,address=D0100564.wurnet.nl:8000
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
6 -->
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
7 <command interpreter="java -jar">
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
8 MassComb.jar -action MSPICTURE
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
9 -outputFile $html_file
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
10 -picturesPath $html_file.files_path
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
11 -fileGrouping $fileType.type
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
12 #if $fileType.type == "single"
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
13 -inputFile $fileType.inputFormatType.inputFile
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
14 -inputFormat $fileType.inputFormatType.inputFormat
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
15 #elif $fileType.type == "fileSet"
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
16 -inputFile $fileType.inputFile
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
17 #end if
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
18 -parametersFile $parametersFile
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
19
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
20 </command>
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
21 <inputs>
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
22 <conditional name="fileType">
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
23 <param name="type" type="select" label="select MS/MS input type">
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
24 <option value="single" selected="true">single-File</option>
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
25 <option value="fileSet">fileSet</option>
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
26 </param>
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
27 <when value="single">
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
28 <conditional name="inputFormatType">
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
29 <param name="inputFormat" type="select" label="inputFormat">
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
30 <option value="mzml" selected="true">mzml</option>
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
31 <option value="mzxml">mzxml</option>
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
32 <option value="apml">apml</option>
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
33 </param>
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
34 <when value="mzxml">
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
35 <param name="inputFile" type="data" format="mzxml" label="MS input file (mzXML)"/>
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
36 </when>
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
37 <when value="mzml">
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
38 <param name="inputFile" type="data" format="mzml" label="MS input file (mzml)"/>
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
39 </when>
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
40 <when value="apml">
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
41 <param name="inputFile" type="data" format="apml" label="MS or MS/MS input file (APML)"/>
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
42 </when>
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
43 </conditional>
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
44 </when>
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
45 <when value="fileSet">
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
46 <param name="inputFile" type="data" format="prims.fileset.zip" label="input file"/>
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
47 </when>
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
48 </conditional>
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
49
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
50 <param name="data_type" type="select" label="Data type" help="">
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
51 <option value="LC-MS">LC-MS</option>
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
52 <option value="LC-MS/MS">LC-MS/MS</option>
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
53 </param>
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
54
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
55 <param name="gray_scale" type="select" display="checkboxes" multiple="True" label="Use gray scale" help="">
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
56 <option value="Yes">Yes</option>
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
57 </param>
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
58
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
59 </inputs>
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
60 <configfiles>
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
61 <configfile name="parametersFile">&lt;?xml version="1.0" encoding="UTF-8"?&gt;
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
62 &lt;tns:Program xmlns:tns="http://masscomb.pri.com/toolparameters/" name="MsPictureWrapper" program="MsPictureWrapper"&gt;
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
63 &lt;Files/&gt;
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
64 &lt;Parameters&gt;
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
65 &lt;Attribute attributeName="toolLocation" value="/home/lukas007/bin/" type="Unknown" description=""/&gt;
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
66 &lt;Attribute attributeName="gray_scale" toolSpecificName="--grey" value="${gray_scale}" type="Unknown" description=""/&gt;
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
67 &lt;Attribute attributeName="data_type" value="${data_type}" type="Unknown" description=""/&gt;
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
68 &lt;/Parameters&gt;
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
69 &lt;/tns:Program&gt;
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
70 </configfile>
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
71 </configfiles>
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
72 <outputs>
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
73 <data format="html" name="html_file" />
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
74 </outputs>
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
75 <tests>
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
76 <test>
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
77 </test>
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
78 </tests>
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
79 <help>
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
80
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
81 .. class:: infomark
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
82
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
83 This tool displays the MS data using ProteoWizard's msPicture tool
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
84
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
85
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
86 </help>
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
87 </tool>