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comparison pepnovo_adapter.xml @ 0:ba86fd127f5a draft

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author galaxyp
date Wed, 19 Dec 2012 00:32:25 -0500
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1 <tool id="pepnovo_adapter" version="0.1.0" name="PepNovo (OpenMS)">
2 <description>
3
4 </description>
5 <requirements>
6 <requirement type="package">openms</requirement>
7 <requirement type="package">pepnovo</requirement>
8 </requirements>
9 <command interpreter="python">
10 openms_wrapper.py
11 #if $input_block.do_clean
12 --executable 'FileConverter' --config $inputConfig
13 #end if
14 --executable 'PepNovoAdapter' --config $config
15 </command>
16 <configfiles>
17 <configfile name="config">[simple_options]
18 #if $input_block.do_clean
19 in=input.mzXML
20 #else
21 in=${input_block.input1}
22 #end if
23 out=${out}
24 model_directory=@PEPNOVO_MODELS_PATH@
25 pepnovo_executable=@PEPNOVO_EXECUTABLE_PATH@
26 temp_data_directory=.
27 model=${model}
28 digest=${digest}
29 #if $corrections != "none"
30 correct_pm=true
31 #end if
32 #if $corrections == "mass"
33 use_spectrum_charge=true
34 #end if
35 #if $corrections == "mz"
36 use_spectrum_mz=true
37 #end if
38 $quality_filter
39 #if $override_pm.do_override
40 pm_tolerance=${override_pm.percursor_tolerance}
41 #end if
42 #if $override_fragment.do_override
43 fragment_tolerance=${override_fragment.fragment_tolerance}
44 #end if
45 </configfile>
46 <configfile name="inputConfig">[simple_options]
47 in=${input_block.input1}
48 in_type=${input_block.input1.ext}
49 out=input.mzXML
50 out_type=mzXML
51 </configfile>
52 </configfiles>
53 <inputs>
54 <conditional name="input_block">
55 <param name="do_clean" type="boolean" label="Process input peak list" description="The version of PepNovo used by this tool takes only mzXML files and even then fails to parse many valid such files. Enabling this option will run the input peak list (mzXML or otherwise) through the OpenMS FileConverter application to hopefully produce an mzXML file suiteable for PepNovo." />
56 <when value="true">
57 <param name="input1" type="data" format="mzxml,mzml,mgf,ms2" label="Input peak list" />
58 </when>
59 <when value="false">
60 <param name="input1" type="data" format="mzxml" label="Input peak list" />
61 </when>
62 </conditional>
63 <param name="model" type="select" label="Model">
64 <options from_file="pepnovo_models.loc">
65 <column name="name" index="0" />
66 <column name="value" index="0" />
67 </options>
68 </param>
69 <param name="digest" type="select" label="Digest">
70 <option value="TRYPSIN">Trypsin</option>
71 <option value="NON_SPECIFIC">Non-specific</option>
72 </param>
73 <param name="corrections" type="select" label="Spectrum adjustments">
74 <option value="none">None.</option>
75 <option value="both">Find optimal precursor m/z and charge values.</option>
76 <option value="mz">Find optimal precursor m/z values.</option>
77 <option value="charge">Find optimal charge values.</option>
78 </param>
79 <param name="quality_filter" type="boolean" checked="true" label="Filter low quality spectra" truevalue="no_quality_filter=true" falsevalue=""/>
80 <conditional name="override_pm">
81 <param name="do_override" type="boolean" label="Override model's percursor mass tolerance" />
82 <when value="true">
83 <param name="percursor_tolerance" type="float" label="Precursor mass tolerance (Daltons)" help="Must between 0 and 5.0. Set to -1.0 to use model default." value="-1.0">
84 <validator type="in_range" min="-1.0" max="5.0" />
85 </param>
86 </when>
87 <when value="false">
88 </when>
89 </conditional>
90 <conditional name="override_fragment">
91 <param name="do_override" type="boolean" label="Override model's fragment tolerance" />
92 <when value="true">
93 <param name="fragment_tolerance" type="float" label="Fragment tolerance (Daltons)" help="Must between 0 and 0.75. Set to -1.0 to use model default." value="-1.0">
94 <validator type="in_range" min="-1.0" max="0.75" />
95 </param>
96 </when>
97 <when value="false">
98 </when>
99 </conditional>
100 </inputs>
101 <outputs>
102 <data format="idxml" name="out" />
103 </outputs>
104 <help>
105 **What it does**
106
107 De novo peptide sequencing of mass spectrometry data.
108
109 More information and publications on PepNovo can be found at the following site: http://proteomics.ucsd.edu/Software/PepNovo.html.
110
111 **Citation**
112
113 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 ``PepNovo: De Novo Peptide Sequencing via Probabilistic Network Modeling. Frank, A. and Pevzner, P. Analytical Chemistry 77:964-973, 2005.``.
114
115 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms
116 </help>
117 </tool>