annotate peak_file_filter.xml @ 5:9816d9abb501 draft

Added repo dependencies
author galaxyp
date Thu, 20 Jun 2013 16:12:09 -0400
parents cf0d72c7b482
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
1 <tool id="openms_peak_file_filter" version="0.1.0" name="mzML File Filter">
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
2 <description>
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
3 Extract portions of peak lists.
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
4 </description>
2
cf0d72c7b482 Update.
galaxyp
parents: 0
diff changeset
5 <macros>
cf0d72c7b482 Update.
galaxyp
parents: 0
diff changeset
6 <import>macros.xml</import>
cf0d72c7b482 Update.
galaxyp
parents: 0
diff changeset
7 </macros>
cf0d72c7b482 Update.
galaxyp
parents: 0
diff changeset
8 <expand macro="stdio" />
cf0d72c7b482 Update.
galaxyp
parents: 0
diff changeset
9 <expand macro="requires" />
0
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
10 <command interpreter="python">
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
11 openms_wrapper.py --executable 'FileFilter' --config $config
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
12 </command>
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
13 <configfiles>
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
14 <configfile name="config">[simple_options]
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
15 #if $mz.specify
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
16 mz=${mz.min}:${mz.max}
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
17 #end if
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
18 #if $rt.specify
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
19 rt=${rt.min}:${rt.max}
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
20 #end if
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
21 #if $intensity.specify
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
22 int=${intensity.min}:${intensity.max}
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
23 #end if
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
24 sn=${signal_to_noise}
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
25 in=${in}
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
26 in_type=mzML
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
27 out=${out}
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
28 out_type=mzML
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
29 </configfile>
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
30 </configfiles>
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
31 <inputs>
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
32 <param format="mzml" name="in" type="data" label="Input mzML File"/>
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
33 <param type="float" name="signal_to_noise" label="Minimum signal-to-noise ratio" value="0" />
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
34 <conditional name="mz">
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
35 <param type="boolean" name="specify" label="Filter by m/z" />
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
36 <when value="true">
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
37 <param type="float" name="min" label="Minimum m/z (optional)" optional="true" value="" />
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
38 <param type="float" name="max" label="Maximum m/z (optional)" optional="true" value="" />
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
39 </when>
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
40 </conditional>
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
41 <conditional name="rt">
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
42 <param type="boolean" name="specify" label="Filter by retention time" />
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
43 <when value="true">
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
44 <param type="float" name="min" label="Minimum retention time (optional)" optional="true" value="" />
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
45 <param type="float" name="max" label="Maximum retention (optional)" optional="true" value="" />
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
46 </when>
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
47 </conditional>
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
48 <conditional name="intensity">
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
49 <param type="boolean" name="specify" label="Filter by intensity" />
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
50 <when value="true">
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
51 <param type="float" name="min" label="Minimum intensity (optional)" optional="true" value="" />
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
52 <param type="float" name="max" label="Maximum intensity (optional)" optional="true" value="" />
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
53 </when>
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
54 </conditional>
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
55 </inputs>
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
56 <outputs>
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
57 <data format="mzml" name="out" />
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
58 </outputs>
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
59 <help>
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
60 **What it does**
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
61
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
62 Extracts portions of the data from an mzML.
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
63
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
64 **Citation**
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
65
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
66 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.``
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
67
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
68 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
69 </help>
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
70 </tool>