Mercurial > repos > galaxyp > openms
comparison peak_file_filter.xml @ 0:ba86fd127f5a draft
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author | galaxyp |
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date | Wed, 19 Dec 2012 00:32:25 -0500 |
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children | cf0d72c7b482 |
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-1:000000000000 | 0:ba86fd127f5a |
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1 <tool id="openms_peak_file_filter" version="0.1.0" name="mzML File Filter"> | |
2 <description> | |
3 Extract portions of peak lists. | |
4 </description> | |
5 <requirements> | |
6 <requirement type="package">openms</requirement> | |
7 </requirements> | |
8 <command interpreter="python"> | |
9 openms_wrapper.py --executable 'FileFilter' --config $config | |
10 </command> | |
11 <configfiles> | |
12 <configfile name="config">[simple_options] | |
13 #if $mz.specify | |
14 mz=${mz.min}:${mz.max} | |
15 #end if | |
16 #if $rt.specify | |
17 rt=${rt.min}:${rt.max} | |
18 #end if | |
19 #if $intensity.specify | |
20 int=${intensity.min}:${intensity.max} | |
21 #end if | |
22 sn=${signal_to_noise} | |
23 in=${in} | |
24 in_type=mzML | |
25 out=${out} | |
26 out_type=mzML | |
27 </configfile> | |
28 </configfiles> | |
29 <inputs> | |
30 <param format="mzml" name="in" type="data" label="Input mzML File"/> | |
31 <param type="float" name="signal_to_noise" label="Minimum signal-to-noise ratio" value="0" /> | |
32 <conditional name="mz"> | |
33 <param type="boolean" name="specify" label="Filter by m/z" /> | |
34 <when value="true"> | |
35 <param type="float" name="min" label="Minimum m/z (optional)" optional="true" value="" /> | |
36 <param type="float" name="max" label="Maximum m/z (optional)" optional="true" value="" /> | |
37 </when> | |
38 </conditional> | |
39 <conditional name="rt"> | |
40 <param type="boolean" name="specify" label="Filter by retention time" /> | |
41 <when value="true"> | |
42 <param type="float" name="min" label="Minimum retention time (optional)" optional="true" value="" /> | |
43 <param type="float" name="max" label="Maximum retention (optional)" optional="true" value="" /> | |
44 </when> | |
45 </conditional> | |
46 <conditional name="intensity"> | |
47 <param type="boolean" name="specify" label="Filter by intensity" /> | |
48 <when value="true"> | |
49 <param type="float" name="min" label="Minimum intensity (optional)" optional="true" value="" /> | |
50 <param type="float" name="max" label="Maximum intensity (optional)" optional="true" value="" /> | |
51 </when> | |
52 </conditional> | |
53 </inputs> | |
54 <outputs> | |
55 <data format="mzml" name="out" /> | |
56 </outputs> | |
57 <help> | |
58 **What it does** | |
59 | |
60 Extracts portions of the data from an mzML. | |
61 | |
62 **Citation** | |
63 | |
64 For the underlying tool, please cite ``Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, and Oliver Kohlbacher, 2008. OpenMS – an Open-Source Software Framework for Mass Spectrometry. BMC Bioinformatics 9: 163. doi:10.1186/1471-2105-9-163.`` | |
65 | |
66 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms | |
67 </help> | |
68 </tool> |