|
0
|
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>
|
