Mercurial > repos > pieterlukasse > prims_masscomb
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 |
| rev | line source |
|---|---|
| 6 | 1 <tool name="File Splitter" id="masscomb_filesplitter" version="0.0.1"> |
| 2 <description>Basic file splitting</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 <command interpreter="java -jar"> | |
| 8 MassComb.jar | |
| 9 -action FILESPLITTER | |
| 10 -inputFile $inputFile | |
| 11 -outputFile $outputFile | |
| 12 -splitExpression $splitExpression | |
| 13 -nameExpression $nameExpression | |
| 7 | 14 -extension $extension |
| 6 | 15 </command> |
| 16 <inputs> | |
| 17 <param name="inputFile" type="data" format="" label="Input file to split"/> | |
| 18 | |
| 19 <param name="splitExpression" type="select" label="(regular)Expression to split on" help=""> | |
| 7 | 20 <option value="^>.+">line start with >alphanumeric (^>.+)</option> |
|
8
153e9eb5f2ff
new option in file splitter; small fix in xtandem form
pieter.lukasse@wur.nl
parents:
7
diff
changeset
|
21 <option value=".*<peak_listSLASHW+.*">APML peak_list tag (.*<peak_list\W+.*)</option> |
| 6 | 22 </param> |
| 23 <param name="nameExpression" type="select" label="(regular)Expression for file name" help=""> | |
| 7 | 24 <option value="SLASHw+">alphanumeric part (\w)</option> |
|
8
153e9eb5f2ff
new option in file splitter; small fix in xtandem form
pieter.lukasse@wur.nl
parents:
7
diff
changeset
|
25 <option value="SLASHw+SLASH.raw">APML peak_list raw source file name (\w+\.raw)</option> |
| 6 | 26 </param> |
| 27 | |
| 7 | 28 <param name="extension" type="text" size="30" label="File extension for the 'sub-files'" value=".txt" help=""/> |
| 6 | 29 |
| 30 </inputs> | |
| 31 <outputs> | |
| 32 <data format="prims.fileset.zip" name="outputFile" /> | |
| 33 </outputs> | |
| 34 <tests> | |
| 35 <test> | |
| 36 </test> | |
| 37 </tests> | |
| 38 <help> | |
|
8
153e9eb5f2ff
new option in file splitter; small fix in xtandem form
pieter.lukasse@wur.nl
parents:
7
diff
changeset
|
39 This tool splits files of mainly custom formats. The lists of "Expression to split on" and |
|
153e9eb5f2ff
new option in file splitter; small fix in xtandem form
pieter.lukasse@wur.nl
parents:
7
diff
changeset
|
40 "Expression for file name" are populated based on feedback from users. Users don't need |
|
153e9eb5f2ff
new option in file splitter; small fix in xtandem form
pieter.lukasse@wur.nl
parents:
7
diff
changeset
|
41 to learn the regular expressions but can select options based on descriptions. |
|
153e9eb5f2ff
new option in file splitter; small fix in xtandem form
pieter.lukasse@wur.nl
parents:
7
diff
changeset
|
42 A free input text box for the expressions is not supported for a number of reasons, |
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153e9eb5f2ff
new option in file splitter; small fix in xtandem form
pieter.lukasse@wur.nl
parents:
7
diff
changeset
|
43 one of them being the performance impact small errors could have. |
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153e9eb5f2ff
new option in file splitter; small fix in xtandem form
pieter.lukasse@wur.nl
parents:
7
diff
changeset
|
44 <!-- furthermore galaxy is not escaping all special characters correctly, so |
|
153e9eb5f2ff
new option in file splitter; small fix in xtandem form
pieter.lukasse@wur.nl
parents:
7
diff
changeset
|
45 having a text input box where advanced users can type in their expressions is |
|
153e9eb5f2ff
new option in file splitter; small fix in xtandem form
pieter.lukasse@wur.nl
parents:
7
diff
changeset
|
46 not supported. --> |
| 6 | 47 </help> |
| 48 </tool> |