Mercurial > repos > bgruening > openms

comparison DigestorMotif.xml @ 4:6ead64a594bd draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
author bgruening
date Wed, 27 Jan 2016 10:06:49 -0500
parents 3d84209d3178
children
comparison
equal deleted inserted replaced
3:ec62782f6c68 4:6ead64a594bd
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="DigestorMotif" name="DigestorMotif" version="1.12.0"> 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 <description>digests a protein database in-silico</description> 3 <!--Proposed Tool Section: [Utilities]-->
4 <macros> 4 <tool id="DigestorMotif" name="DigestorMotif" version="2.0.0">
5 <token name="@EXECUTABLE@">DigestorMotif</token> 5 <description>digests a protein database in-silico</description>
6 <import>macros.xml</import> 6 <macros>
7 </macros> 7 <token name="@EXECUTABLE@">DigestorMotif</token>
8 <expand macro="stdio"/> 8 <import>macros.xml</import>
9 <expand macro="requirements"/> 9 </macros>
10 <command>DigestorMotif 10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>DigestorMotif
11 14
12 -in ${param_in} 15 #if $param_in:
13 -out ${param_out} 16 -in $param_in
14 -missed_cleavages ${param_missed_cleavages} 17 #end if
15 -mass_accuracy ${param_mass_accuracy} 18 #if $param_out:
16 -min_length ${param_min_length} 19 -out $param_out
17 -out_option ${param_out_option} 20 #end if
18 -enzyme ${param_enzyme} 21 #if $param_missed_cleavages:
19 -motif ${param_motif} 22 -missed_cleavages $param_missed_cleavages
20 -threads \${GALAXY_SLOTS:-24} 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 $param_enzyme:
34 -enzyme
35 #if &quot; &quot; in str($param_enzyme):
36 &quot;$param_enzyme&quot;
37 #else
38 $param_enzyme
39 #end if
40 #end if
41 #if $param_motif:
42 -motif &quot;$param_motif&quot;
43 #end if
44 -threads \${GALAXY_SLOTS:-24}
45 #if $adv_opts.adv_opts_selector=='advanced':
46 #if $adv_opts.param_force:
47 -force
48 #end if
49 #end if
21 </command> 50 </command>
22 <inputs> 51 <inputs>
23 <param name="param_in" type="data" format="fasta" optional="False" label="FASTA input file" help="(-in)"/> 52 <param format="fasta" help="(-in) " label="FASTA input file" name="param_in" optional="False" type="data"/>
24 <param name="param_missed_cleavages" type="integer" min="0" optional="True" value="1" label="the number of allowed missed cleavages" help="(-missed_cleavages)"/> 53 <param help="(-missed_cleavages) " label="the number of allowed missed cleavages" min="0" name="param_missed_cleavages" optional="True" type="integer" value="1"/>
25 <param name="param_mass_accuracy" type="integer" value="1000" label="give your mass accuracy in ppb" help="(-mass_accuracy)"/> 54 <param help="(-mass_accuracy) " label="give your mass accuracy in pp" name="param_mass_accuracy" type="integer" value="1000"/>
26 <param name="param_min_length" type="integer" value="6" label="minimum length of peptide" help="(-min_length)"/> 55 <param help="(-min_length) " label="minimum length of peptide" name="param_min_length" type="integer" value="6"/>
27 <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)"/> 56 <param help="(-out_option) " label="indicate 1 (peptide table only), 2 (statistics only) or (both peptide table + statistics)" name="param_out_option" type="integer" value="1"/>
28 <param name="param_enzyme" type="text" size="20" value="Trypsin" label="the digestion enzyme" help="(-enzyme)"/> 57 <param help="(-enzyme) " label="The enzyme used for peptide digestion" name="param_enzyme" optional="True" type="select" value="Trypsin">
29 <param name="param_motif" type="text" size="20" value="M" label="the motif for the restricted peptidome" help="(-motif)"/> 58 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
30 </inputs> 59 <option value="Asp-N">Asp-N</option>
31 <outputs> 60 <option value="Trypsin">Trypsin</option>
32 <data name="param_out" label="output file (peptides)#br#" format="idXML"/> 61 <option value="leukocyte elastase">leukocyte elastase</option>
33 </outputs> 62 <option value="no cleavage">no cleavage</option>
34 <help>**What it does** 63 <option value="unspecific cleavage">unspecific cleavage</option>
35 64 <option value="TrypChymo">TrypChymo</option>
36 digests a protein database in-silico 65 <option value="V8-E">V8-E</option>
66 <option value="Formic_acid">Formic_acid</option>
67 <option value="Lys-C/P">Lys-C/P</option>
68 <option value="Chymotrypsin">Chymotrypsin</option>
69 <option value="2-iodobenzoate">2-iodobenzoate</option>
70 <option value="CNBr">CNBr</option>
71 <option value="Lys-C">Lys-C</option>
72 <option value="Trypsin/P">Trypsin/P</option>
73 <option value="Asp-N_ambic">Asp-N_ambic</option>
74 <option value="PepsinA">PepsinA</option>
75 <option value="proline endopeptidase">proline endopeptidase</option>
76 <option value="V8-DE">V8-DE</option>
77 <option value="Arg-C">Arg-C</option>
78 </param>
79 <param help="(-motif) " label="the motif for the restricted peptidome" name="param_motif" size="30" type="text" value="M">
80 <sanitizer>
81 <valid initial="string.printable">
82 <remove value="'"/>
83 <remove value="&quot;"/>
84 </valid>
85 </sanitizer>
86 </param>
87 <expand macro="advanced_options">
88 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
89 </expand>
90 </inputs>
91 <outputs>
92 <data format="xml" name="param_out"/>
93 </outputs>
94 <help>digests a protein database in-silico
37 95
38 96
39 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_DigestorMotif.html 97 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_DigestorMotif.html</help>
40 98 </tool>
41 @REFERENCES@
42 </help>
43 </tool>