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comparison compnovo.xml @ 2:cf0d72c7b482 draft

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author galaxyp
date Fri, 10 May 2013 17:31:05 -0400
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1:5c65f8116244 2:cf0d72c7b482
1 <tool id="compnovo" version="0.1.0" name="CompNovo (OpenMS)">
2 <description>
3 Performs a de novo peptide identification using the CompNovo engine.
4 </description>
5 <macros>
6 <import>macros.xml</import>
7 </macros>
8 <expand macro="stdio" />
9 <expand macro="requires" />
10 <command interpreter="python">
11 #if str($mode) == "cid"
12 #set $executable = "CompNovoCID"
13 #else
14 #set $executable = "CompNovo"
15 #end if
16 openms_wrapper.py --executable '$executable' --config $config
17 </command>
18 <configfiles>
19 <configfile name="config">[simple_options]
20 in=${input1}
21 out=${out}
22 #set $fixed_mods_str=",".join([str($fixed_mod.fixed_mod) for $fixed_mod in $fixed_mods])
23 #if $fixed_mods_str
24 algorithm!fixed_modifications=$fixed_mods_str
25 #end if
26 #set $variable_mods_str=",".join([str($variable_mod.fixed_mod) for $variable_mod in $variable_mods])
27 #if $variable_mods_str
28 algorithm!variable_modifications=$variable_mods_str
29 #end if
30 </configfile>
31 </configfiles>
32 <inputs>
33 <param name="input1" type="data" format="mzml" label="Input peak list" />
34 <param name="mode" type="select" label="Mode">
35 <option value="cid">CID-only</option>
36 <option value="cidetd">CID/ETD</option>
37 </param>
38 <repeat name="fixed_mods" title="Fixed Modification">
39 <param name="fixed_mod" type="select" label="Fixed Modification">
40 <options from_file="openms_mods.loc">
41 <column name="name" index="0" />
42 <column name="value" index="0" />
43 </options>
44 </param>
45 </repeat>
46 <repeat name="variable_mods" title="Variable Modification">
47 <param name="variable_mod" type="select" label="Variable Modification">
48 <options from_file="openms_mods.loc">
49 <column name="name" index="0"/>
50 <column name="value" index="0" />
51 </options>
52 </param>
53 </repeat>
54 </inputs>
55 <outputs>
56 <data format="idxml" name="out" />
57 </outputs>
58 <help>
59 **What it does**
60
61 De novo peptide sequencing of mass spectrometry data.
62
63 **Citation**
64
65 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.`` and ``Bertsch A, Leinenbach A, Pervukhin A, Lubeck M, Hartmer R, Baessmann C, et al.: De novo peptide sequencing by tandem MS using complementary CID and electron transfer dissociation. Electrophoresis 2009, 30:3736-3747.``
66
67 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms
68 </help>
69 </tool>