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comparison omssa_adapter.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="omssa_adapter" version="0.1.0" name="OMSSA (OpenMS)">
2 <description>
3 </description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="stdio" />
8 <expand macro="requires">
9 <requirement type="package">omssa</requirement>
10 <!--<requirement type="package">blast</requirement> -->
11 </expand>
12 <command interpreter="python">
13 openms_wrapper.py
14 --executable '__SHELL__' --config $setup
15 --executable 'OMSSAAdapter' --config $config
16 </command>
17 <configfiles>
18 <configfile name="setup">
19 ln -s $database db.fasta; makeblastdb -dbtype prot -parse_seqids -in 'db.fasta'
20 </configfile>
21 <configfile name="config">[simple_options]
22 in=$input1
23 out=$out
24 database=db.fasta.psq
25 omssa_executable=@WHICH(omssacl)@
26 variable_modifications=${variable_modifications or ''}
27 fixed_modifications=${fixed_modifications or ''}
28 precursor_mass_tolerance=$precursor_mass_tolerance
29 #if $precursor_mass_tolerance_unit == "ppm"
30 precursor_mass_tolerance_unit_ppm=true
31 #end if
32 fragment_mass_tolerance=$fragment_mass_tolerance
33 min_precursor_charge=$min_precursor_charge
34 max_precursor_charge=$max_precursor_charge
35 v=$v
36 e=$e
37 hl=$hl
38 he=$he
39 threads=4
40 </configfile>
41 </configfiles>
42 <inputs>
43 <expand macro="id_inputs" />
44 <expand macro="fixed_modifications_param" />
45 <expand macro="variable_modifications_param" />
46 <expand macro="precursor_mass_tolerance_param" />
47 <expand macro="precursor_mass_tolerance_unit_param" />
48 <expand macro="fragment_mass_tolerance_param" />
49 <expand macro="precursor_charge_params" />
50 <param name="v" label="Maximum Number of Missed Cleavages" value="1" type="integer" />
51 <param name="e" label="Enzyme" type="select">
52 <option value="0" selected="true">Trypsin</option>
53 <option value="1">Arg-C</option>
54 <option value="2">CNBr</option>
55 <option value="3">Chymotrypsin (FYWL)</option>
56 <option value="4">Formic Acid</option>
57 <option value="5">Lys-C</option>
58 <option value="6">Lys-C, no P rule</option>
59 <option value="7">Pepsin A</option>
60 <option value="8">Trypsin+CNBr</option>
61 <option value="9">Trypsin+Chymotrypsin (FYWLKR)</option>
62 <option value="10">Trypsin, no P rule</option>
63 <option value="11">Whole protein</option>
64 <option value="12">Asp-N</option>
65 <option value="13">Glu-C</option>
66 <option value="14">Asp-N+Glu-C</option>
67 <option value="15">Top-Down</option>
68 <option value="16">Semi-Tryptic</option>
69 <option value="17">No Enzyme</option>
70 <option value="18">Chymotrypsin, no P rule (FYWL)</option>
71 <option value="19">Asp-N (DE)</option>
72 <option value="20">Glu-C (DE)</option>
73 <option value="21">Lys-N (K)</option>
74 <option value="22">Thermolysin, no P rule</option>
75 <option value="23">Semi-Chymotrypsin (FYWL)</option>
76 <option value="24">Semi-Glu-C</option>
77 </param>
78 <param name="hl" label="Maximum Hits Per Spectrum" type="integer" value="30" />
79 <param name="he" label="Maximum Hits Per Spectrum" type="float" value="1000" help="The maximum e-value allowed in the hit list. If you set this parameter too small (e.g., he=1), this will effectively introduce FDR filtering. Thus, allowing a less stringent FDR during post-processing will nevertheless return the (better) FDR introduced here, since mediocre hits are not even reported. " />
80 </inputs>
81 <expand macro="id_outputs" />
82 <help>
83 **What it does**
84
85
86 **Citation**
87
88 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.``.
89
90 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms
91 </help>
92 </tool>