Mercurial > repos > bgruening > openms

comparison Digestor.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="Digestor" name="Digestor" 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="Digestor" name="Digestor" version="2.0.0">
5 <token name="@EXECUTABLE@">Digestor</token> 5 <description>Digests a protein database in-silico.</description>
6 <import>macros.xml</import> 6 <macros>
7 </macros> 7 <token name="@EXECUTABLE@">Digestor</token>
8 <expand macro="stdio"/> 8 <import>macros.xml</import>
9 <expand macro="requirements"/> 9 </macros>
10 <command>Digestor 10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>Digestor
11 14
12 -in ${param_in} 15 #if $param_in:
13 -out ${param_out} 16 -in $param_in
14 -out_type ${param_out_type} 17 #end if
15 -missed_cleavages ${param_missed_cleavages} 18 #if $param_out:
16 -min_length ${param_min_length} 19 -out $param_out
17 -max_length ${param_max_length} 20 #end if
18 -enzyme ${param_enzyme} 21 #if $param_out_type:
19 -threads \${GALAXY_SLOTS:-24} 22 -out_type
23 #if &quot; &quot; in str($param_out_type):
24 &quot;$param_out_type&quot;
25 #else
26 $param_out_type
27 #end if
28 #end if
29 #if $param_missed_cleavages:
30 -missed_cleavages $param_missed_cleavages
31 #end if
32 #if $param_min_length:
33 -min_length $param_min_length
34 #end if
35 #if $param_max_length:
36 -max_length $param_max_length
37 #end if
38 #if $param_enzyme:
39 -enzyme
40 #if &quot; &quot; in str($param_enzyme):
41 &quot;$param_enzyme&quot;
42 #else
43 $param_enzyme
44 #end if
45 #end if
46 -threads \${GALAXY_SLOTS:-24}
47 #if $adv_opts.adv_opts_selector=='advanced':
48 #if $adv_opts.param_force:
49 -force
50 #end if
51 #end if
20 </command> 52 </command>
21 <inputs> 53 <inputs>
22 <param name="param_in" type="data" format="fasta" optional="False" label="input file" help="(-in)"/> 54 <param format="fasta" help="(-in) " label="input file" name="param_in" optional="False" type="data"/>
23 <param name="param_out_type" type="select" optional="True" label="Set this if you cannot control the filename of 'out', e.g., in TOPPAS." help="(-out_type)"> 55 <param help="(-out_type) e.g., in TOPPAS" label="Set this if you cannot control the filename of 'out'," name="param_out_type" optional="True" type="select">
24 <option value="idXML">idXML</option> 56 <option value="idXML">idXML</option>
25 <option value="fasta">fasta</option> 57 <option value="fasta">fasta</option>
26 </param> 58 </param>
27 <param name="param_missed_cleavages" type="integer" min="0" optional="True" value="1" label="The number of allowed missed cleavages" help="(-missed_cleavages)"/> 59 <param help="(-missed_cleavages) " label="The number of allowed missed cleavages" min="0" name="param_missed_cleavages" optional="True" type="integer" value="1"/>
28 <param name="param_min_length" type="integer" value="6" label="Minimum length of peptide" help="(-min_length)"/> 60 <param help="(-min_length) " label="Minimum length of peptide" name="param_min_length" type="integer" value="6"/>
29 <param name="param_max_length" type="integer" value="40" label="Maximum length of peptide" help="(-max_length)"/> 61 <param help="(-max_length) " label="Maximum length of peptide" name="param_max_length" type="integer" value="40"/>
30 <param name="param_enzyme" type="select" optional="True" value="Trypsin" label="The type of digestion enzyme" help="(-enzyme)"> 62 <param help="(-enzyme) " label="The type of digestion enzyme" name="param_enzyme" optional="True" type="select" value="Trypsin">
31 <option value="Trypsin">Trypsin</option> 63 <option value="no cleavage">no cleavage</option>
32 <option value="none">none</option> 64 <option value="Arg-C">Arg-C</option>
33 </param> 65 <option value="Lys-C">Lys-C</option>
34 </inputs> 66 <option value="PepsinA">PepsinA</option>
35 <outputs> 67 <option value="leukocyte elastase">leukocyte elastase</option>
36 <data name="param_out" label="Output file (peptides)" format="fasta"> 68 <option value="unspecific cleavage">unspecific cleavage</option>
37 <change_format> 69 <option value="V8-DE">V8-DE</option>
38 <when input="param_out_type" value="idXML" format="idXML"/> 70 <option value="CNBr">CNBr</option>
39 </change_format> 71 <option value="Chymotrypsin">Chymotrypsin</option>
40 </data> 72 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
41 </outputs> 73 <option value="Asp-N_ambic">Asp-N_ambic</option>
42 <help>**What it does** 74 <option value="2-iodobenzoate">2-iodobenzoate</option>
43 75 <option value="proline endopeptidase">proline endopeptidase</option>
44 Digests a protein database in-silico. 76 <option value="Formic_acid">Formic_acid</option>
77 <option value="TrypChymo">TrypChymo</option>
78 <option value="Asp-N">Asp-N</option>
79 <option value="Trypsin/P">Trypsin/P</option>
80 <option value="Lys-C/P">Lys-C/P</option>
81 <option value="V8-E">V8-E</option>
82 <option value="Trypsin">Trypsin</option>
83 </param>
84 <expand macro="advanced_options">
85 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
86 </expand>
87 </inputs>
88 <outputs>
89 <data format="xml" name="param_out"/>
90 </outputs>
91 <help>Digests a protein database in-silico.
45 92
46 93
47 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_Digestor.html 94 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_Digestor.html</help>
48 95 </tool>
49 @REFERENCES@
50 </help>
51 </tool>