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comparison Digestor.xml @ 0:3070d71e0e5c draft

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author bgruening
date Thu, 16 Apr 2015 08:37:04 -0400
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-1:000000000000 0:3070d71e0e5c
1 <?xml version='1.0' encoding='UTF-8'?>
2 <tool id="Digestor" name="Digestor" version="2.0.0">
3 <description>Digests a protein database in-silico.</description>
4 <macros>
5 <token name="@EXECUTABLE@">Digestor</token>
6 <import>macros.xml</import>
7 </macros>
8 <expand macro="stdio"/>
9 <expand macro="requirements"/>
10 <command>Digestor
11
12 #if $param_in:
13 -in $param_in
14 #end if
15 #if $param_out:
16 -out $param_out
17 #end if
18 #if $param_out_type:
19 -out_type
20 #if " " in str($param_out_type):
21 "$param_out_type"
22 #else
23 $param_out_type
24 #end if
25 #end if
26 #if $param_missed_cleavages:
27 -missed_cleavages $param_missed_cleavages
28 #end if
29 #if $param_min_length:
30 -min_length $param_min_length
31 #end if
32 #if $param_max_length:
33 -max_length $param_max_length
34 #end if
35 #if $param_enzyme:
36 -enzyme
37 #if " " in str($param_enzyme):
38 "$param_enzyme"
39 #else
40 $param_enzyme
41 #end if
42 #end if
43 -threads \${GALAXY_SLOTS:-24}
44 #if $adv_opts.adv_opts_selector=='advanced':
45 #if $adv_opts.param_force:
46 -force
47 #end if
48 #end if
49 </command>
50 <inputs>
51 <param name="param_in" type="data" format="fasta" optional="False" label="input file" help="(-in) "/>
52 <param name="param_out_type" type="select" optional="True" label="Set this if you cannot control the filename of 'out'," help="(-out_type) e.g., in TOPPAS">
53 <option value="idXML">idXML</option>
54 <option value="fasta">fasta</option>
55 </param>
56 <param name="param_missed_cleavages" type="integer" min="0" optional="True" value="1" label="The number of allowed missed cleavages" help="(-missed_cleavages) "/>
57 <param name="param_min_length" type="integer" value="6" label="Minimum length of peptide" help="(-min_length) "/>
58 <param name="param_max_length" type="integer" value="40" label="Maximum length of peptide" help="(-max_length) "/>
59 <param name="param_enzyme" type="select" optional="True" value="Trypsin" label="The type of digestion enzyme" help="(-enzyme) ">
60 <option value="Trypsin">Trypsin</option>
61 <option value="none">none</option>
62 </param>
63 <expand macro="advanced_options">
64 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
65 </expand>
66 </inputs>
67 <outputs>
68 <data name="param_out" format="fasta"/>
69 </outputs>
70 <help>**What it does**
71
72 Digests a protein database in-silico.
73
74
75 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_Digestor.html</help>
76 <expand macro="references"/>
77 </tool>