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comparison DigestorMotif.xml @ 0:d2ba97751d56 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
author galaxyp
date Wed, 01 Mar 2017 12:43:51 -0500
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-1:000000000000 0:d2ba97751d56
1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
3 <!--Proposed Tool Section: [Utilities]-->
4 <tool id="DigestorMotif" name="DigestorMotif" version="2.1.0">
5 <description>digests a protein database in-silico</description>
6 <macros>
7 <token name="@EXECUTABLE@">DigestorMotif</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>DigestorMotif
14
15 #if $param_in:
16 -in $param_in
17 #end if
18 #if $param_out:
19 -out $param_out
20 #end if
21 #if $param_missed_cleavages:
22 -missed_cleavages $param_missed_cleavages
23 #end if
24 #if $param_mass_accuracy:
25 -mass_accuracy $param_mass_accuracy
26 #end if
27 #if $param_min_length:
28 -min_length $param_min_length
29 #end if
30 #if $param_out_option:
31 -out_option $param_out_option
32 #end if
33 #if $param_enzyme:
34 -enzyme $param_enzyme
35 #end if
36 #if $param_motif:
37 -motif "$param_motif"
38 #end if
39 #if $adv_opts.adv_opts_selector=='advanced':
40 #if $adv_opts.param_force:
41 -force
42 #end if
43 #end if
44 </command>
45 <inputs>
46 <param name="param_in" type="data" format="fasta" optional="False" label="FASTA input file" help="(-in) "/>
47 <param name="param_missed_cleavages" type="integer" min="0" optional="True" value="1" label="the number of allowed missed cleavages" help="(-missed_cleavages) "/>
48 <param name="param_mass_accuracy" type="integer" value="1000" label="give your mass accuracy in pp" help="(-mass_accuracy) "/>
49 <param name="param_min_length" type="integer" value="6" label="minimum length of peptide" help="(-min_length) "/>
50 <param name="param_out_option" type="integer" value="1" label="indicate 1 (peptide table only), 2 (statistics only) or (both peptide table + statistics)" help="(-out_option) "/>
51 <param name="param_enzyme" type="select" optional="False" value="Trypsin" label="The enzyme used for peptide digestion" help="(-enzyme) ">
52 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
53 <option value="unspecific cleavage">unspecific cleavage</option>
54 <option value="Formic_acid">Formic_acid</option>
55 <option value="CNBr">CNBr</option>
56 <option value="Lys-C">Lys-C</option>
57 <option value="Trypsin" selected="true">Trypsin</option>
58 <option value="Arg-C">Arg-C</option>
59 <option value="proline endopeptidase">proline endopeptidase</option>
60 <option value="2-iodobenzoate">2-iodobenzoate</option>
61 <option value="Lys-C/P">Lys-C/P</option>
62 <option value="V8-DE">V8-DE</option>
63 <option value="leukocyte elastase">leukocyte elastase</option>
64 <option value="Trypsin/P">Trypsin/P</option>
65 <option value="Chymotrypsin">Chymotrypsin</option>
66 <option value="V8-E">V8-E</option>
67 <option value="Asp-N">Asp-N</option>
68 <option value="PepsinA">PepsinA</option>
69 <option value="no cleavage">no cleavage</option>
70 <option value="Asp-N_ambic">Asp-N_ambic</option>
71 <option value="TrypChymo">TrypChymo</option>
72 </param>
73 <param name="param_motif" type="text" size="30" value="M" label="the motif for the restricted peptidome" help="(-motif) ">
74 <sanitizer>
75 <valid initial="string.printable">
76 <remove value="'"/>
77 <remove value="&quot;"/>
78 </valid>
79 </sanitizer>
80 </param>
81 <expand macro="advanced_options">
82 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
83 </expand>
84 </inputs>
85 <outputs>
86 <data name="param_out" format="idxml"/>
87 </outputs>
88 <help>digests a protein database in-silico
89
90
91 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_DigestorMotif.html</help>
92 </tool>