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comparison xtandem_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="xtandem_adapter" version="0.1.0" name="X! Tandem (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">tandem</requirement>
10 </expand>
11 <command interpreter="python">
12 openms_wrapper.py
13 --executable 'XTandemAdapter' --config $config
14 </command>
15 <configfiles>
16 <configfile name="config">[simple_options]
17 in=$input1
18 out=$out
19 database=$database
20 xtandem_executable=@WHICH(tandem)@
21 variable_modifications=${variable_modifications or ''}
22 fixed_modifications=${fixed_modifications or ''}
23 precursor_mass_tolerance=$precursor_mass_tolerance
24 precursor_error_units=$precursor_mass_tolerance_unit
25 fragment_mass_tolerance=$fragment_mass_tolerance
26 fragment_error_units=$fragment_mass_tolerance_unit
27 min_precursor_charge=$min_precursor_charge
28 max_precursor_charge=$max_precursor_charge
29 cleavage_site=$cleavage_site
30 minimum_fragment_mz=$minimum_fragment_mz
31 max_valid_expect=$max_valid_expect
32 refinement=$refinement
33 semi_cleavage=$semi_cleavage
34 </configfile>
35 </configfiles>
36 <inputs>
37 <expand macro="id_inputs" />
38 <expand macro="fixed_modifications_param" />
39 <expand macro="variable_modifications_param" />
40 <expand macro="precursor_mass_tolerance_param" />
41 <expand macro="precursor_mass_tolerance_unit_param" />
42 <expand macro="fragment_mass_tolerance_param" />
43 <expand macro="fragment_mass_tolerance_unit_param" />
44 <expand macro="precursor_charge_params" />
45 <param name="cleavage_site" label="Cleavage Site" type="select">
46 <option value="[R]|{P}">argc</option>
47 <option value="[X]|[D]">aspn</option>
48 <option value="[FMWY]|{P}">chymotrypsin</option>
49 <option value="[R]|[X]">clostripain</option>
50 <option value="[M]|{P}">cnbr</option>
51 <option value="[AGILV]|{P}">elastase</option>
52 <option value="[D]|{P}">formicacid</option>
53 <option value="[DE]|{P}">gluc</option>
54 <option value="[E]|{P}">gluc_bicarb</option>
55 <option value="[W]|[X]">iodosobenzoate</option>
56 <option value="[K]|[P]">lysc</option>
57 <option value="[K]|[X]">lysc-p</option>
58 <option value="[X]|[K]">lysn</option>
59 <option value="[X]|[AKRS]">lysn_promisc</option>
60 <option value="[X]|[X]">nonspecific</option>
61 <option value="[FL]|[X]">pepsina</option>
62 <option value="[P]|[X]">protein_endopeptidase</option>
63 <option value="[E]|[X]">staph_protease</option>
64 <option value="[KR]|{P}" selected="true">trypsin</option>
65 <option value="[DEKR]|{P}">trypsin_gluc</option>
66 <option value="[K]|{P}">trypsin_k</option>
67 <option value="[R]|{P}">trypsin_r</option>
68 <sanitizer>
69 <valid>
70 <add value="{"/>
71 <add value="}"/>
72 <add value="|"/>
73 <add value="["/>
74 <add value="]"/>
75 </valid>
76 </sanitizer>
77 </param>
78 <param name="minimum_fragment_mz" label="Minimum Fragment m/z" value="150" type="float" />
79 <param name="max_valid_expect" label="Maximum Valid E-Value to be Reported" value=".1" type="float" />
80 <param name="semi_cleavage" type="boolean" label="Enable Semi-Cleavage" checked="false" truevalue="true" falsevalue="false" help="If set, both termini must NOT follow the cutting rule. For most applications it is NOT recommended to set this flag." />
81 <param name="refinement" type="boolean" label="Enable Refinement" checked="false" truevalue="true" falsevalue="false" help="Enable the refinement. For most applications (especially when using FDR, PEP approaches) it is NOT recommended to set this flag." />
82 </inputs>
83 <expand macro="id_outputs" />
84 <help>
85 **What it does**
86
87
88 **Citation**
89
90 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.``.
91
92 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms
93 </help>
94 </tool>