annotate masscomb_file_splitter.xml @ 8:153e9eb5f2ff

new option in file splitter; small fix in xtandem form
author pieter.lukasse@wur.nl
date Fri, 31 Jan 2014 12:06:57 +0100
parents 33899d82fbc1
children
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1 <tool name="File Splitter" id="masscomb_filesplitter" version="0.0.1">
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2 <description>Basic file splitting</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 MassComb.jar
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9 -action FILESPLITTER
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10 -inputFile $inputFile
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11 -outputFile $outputFile
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12 -splitExpression $splitExpression
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13 -nameExpression $nameExpression
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14 -extension $extension
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15 </command>
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16 <inputs>
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17 <param name="inputFile" type="data" format="" label="Input file to split"/>
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19 <param name="splitExpression" type="select" label="(regular)Expression to split on" help="">
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20 <option value="^>.+">line start with &gt;alphanumeric (^&gt;.+)</option>
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21 <option value=".*&lt;peak_listSLASHW+.*">APML peak_list tag (.*&lt;peak_list\W+.*)</option>
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22 </param>
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23 <param name="nameExpression" type="select" label="(regular)Expression for file name" help="">
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24 <option value="SLASHw+">alphanumeric part (\w)</option>
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25 <option value="SLASHw+SLASH.raw">APML peak_list raw source file name (\w+\.raw)</option>
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26 </param>
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27
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28 <param name="extension" type="text" size="30" label="File extension for the 'sub-files'" value=".txt" help=""/>
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30 </inputs>
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31 <outputs>
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32 <data format="prims.fileset.zip" name="outputFile" />
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33 </outputs>
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34 <tests>
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35 <test>
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36 </test>
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37 </tests>
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38 <help>
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39 This tool splits files of mainly custom formats. The lists of "Expression to split on" and
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40 "Expression for file name" are populated based on feedback from users. Users don't need
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41 to learn the regular expressions but can select options based on descriptions.
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42 A free input text box for the expressions is not supported for a number of reasons,
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43 one of them being the performance impact small errors could have.
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44 <!-- furthermore galaxy is not escaping all special characters correctly, so
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45 having a text input box where advanced users can type in their expressions is
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46 not supported. -->
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47 </help>
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48 </tool>