Mercurial > repos > galaxyp > ms_wiff_loader

comparison ms_wiff_loader.xml @ 0:5bc64a2d5f91 draft default tip

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author galaxyp
date Tue, 10 Mar 2015 18:26:36 -0400
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1 <tool id="ms_wiff_upload" name="MS Wiff Upload" version="1.0.0">
2 <description>into a galaxy dataset</description>
3 <stdio>
4 <exit_code range="1:" err_level="fatal" />
5 </stdio>
6 <command interpreter="python">ms_wiff_loader.py -w "$wiff"
7 #if len(str($scan)) > 0:
8 -s "$scan"
9 #end if
10 #if len(str($mtd)) > 0:
11 -m "$mtd"
12 #end if
13 -f "$out_file"
14 -o "${out_file.extra_files_path}"
15 </command>
16 <inputs>
17 <param name="wiff" type="text" value="" size="120" label="URL to .wiff file">
18 <validator type="regex" message="Must be a URL">^(ftp://|http://|https://|file:/)?(\\d+\\.\\d+\\.\\d+\\.\\d+|localhost|[a-zA-Z][^/]+)(:\\d+)?/(.*)$</validator>
19 </param>
20 <param name="scan" type="text" value="" size="120" label="URL to .wiff.scan file (optional)" optional="true">
21 <validator type="regex" message="Must be a URL">^(ftp://|http://|https://|file:/)?(\\d+\\.\\d+\\.\\d+\\.\\d+|localhost|[a-zA-Z][^/]+)(:\\d+)?/(.*)$</validator>
22 </param>
23 <param name="mtd" type="text" value="" size="120" label="URL to .wiff.mtd file (optional)" optional="true">
24 <validator type="regex" message="Must be a URL">^(ftp://|http://|https://|file:/)?(\\d+\\.\\d+\\.\\d+\\.\\d+|localhost|[a-zA-Z][^/]+)(:\\d+)?/(.*)$</validator>
25 </param>
26 <param name="name" type="text" value="" size="40" label="Name for dataset (optional)" optional="true">
27 </param>
28 </inputs>
29 <outputs>
30 <data format="wiff" name="out_file" label="$name wiff"/>
31 </outputs>
32 <tests>
33 <test>
34 <param name="wiff" value="http://www.ebi.ac.uk/pride/data/archive/2015/01/PXD001010/nselevse_L120327_016.wiff"/>
35 <output name="out_file">
36 <assert_contents>
37 <has_text text="Wiff" />
38 </assert_contents>
39 </output>
40 </test>
41 </tests>
42 <help>
43 Loads AB SCIEX wiff files into a Galaxy Composite dataset.
44 </help>
45 </tool>