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comparison mascot_to_pepxml.xml @ 10:b3427b77073e draft default tip

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planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/mascot/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
author iracooke
date Tue, 20 Oct 2015 19:50:46 -0400
parents f567d1818b84
children
comparison
equal deleted inserted replaced
9:54c7e3593aac 10:b3427b77073e
1 <tool id="mascot_to_pepxml_1" name="Mascot to pepXML" version="1.1.0"> 1 <tool id="mascot_to_pepxml_1" name="Mascot to pepXML" version="1.1.1">
2 <requirements> 2 <description>Converts a mascot results file to pepXML</description>
3 <container type="docker">iracooke/protk-1.4.1</container> 3 <requirements>
4 <requirement type="package" version="1.4">protk</requirement> 4 <container type="docker">iracooke/protk-1.4.3</container>
5 <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement> 5 <requirement type="package" version="1.4.3">protk</requirement>
6 </requirements> 6 <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement>
7 </requirements>
8 <command>mascot_to_pepxml.rb
9 $input_file
7 10
8 <description>Converts a mascot results file to pepXML</description> 11 -o $output
9 12
10 <command>mascot_to_pepxml.rb 13 #if $database.source_select=="built_in":
11 $input_file 14 -d $database.dbkey
15 #else
16 -d $database.fasta_file
17 #end if
12 18
13 -o $output 19 #if $explicit_enzyme.explicit_enzyme_use
20 --enzyme $explicit_enzyme.enzyme
21 #end if
14 22
15 #if $database.source_select=="built_in": 23 $shortid
16 -d $database.dbkey 24 </command>
17 #else 25 <inputs>
18 -d $database.fasta_file 26 <param name="input_file" type="data" format="mascotdat" multiple="false" label="Input File" help="Mascot results file"/>
19 #end if
20 27
21 #if $explicit_enzyme.explicit_enzyme_use 28 <conditional name="database">
22 --enzyme $explicit_enzyme.enzyme 29 <param name="source_select" type="select" label="Database source" help="A local copy of the database used in the Mascot search">
23 #end if 30 <option value="built_in">Built-In</option>
31 <option value="input_ref">Uploaded fasta file</option>
32 </param>
33 <when value="built_in">
34 <param name="dbkey" type="select" format="text" >
35 <label>Database</label>
36 <options from_file="pepxml_databases.loc">
37 <column name="name" index="0" />
38 <column name="value" index="2" />
39 </options>
40 </param>
41 </when>
42 <when value="input_ref">
43 <param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" />
44 </when>
45 </conditional>
24 46
25 $shortid 47 <param name="shortid" type="boolean" label="Short ID" help="Use protein id from the Mascot result file instead reading from the fasta database." truevalue="--shortid" falsevalue="" />
26 48
27 </command> 49 <conditional name="explicit_enzyme">
28 <inputs> 50 <param name="explicit_enzyme_use" type="boolean" label="Specify Enzyme" help="If left unchecked the Enzyme will be read from the input file" truevalue="true" falsevalue="false" />
51 <when value="false" />
52 <when value="true">
53 <param name="enzyme" type="text" label="Enzyme" size="80" value="trypsin" help="Semi-cleavage can be specified as semisample_enyzme eg semitrypsin"/>
54 </when>
55 </conditional>
29 56
30 57 </inputs>
31 <param name="input_file" type="data" format="mascotdat" multiple="false" label="Input File" help="Mascot results file"/> 58 <outputs>
32 59 <data format="raw_pepxml" metadata_source="input_file" name="output" label="${input_file.display_name}.pepXML" />
33 <conditional name="database"> 60 </outputs>
34 <param name="source_select" type="select" label="Database source" help="A local copy of the database used in the Mascot search"> 61 <tests>
35 <option value="built_in">Built-In</option> 62 <test>
36 <option value="input_ref">Uploaded fasta file</option> 63 <param name="source_select" value="input_ref"/>
37 </param> 64 <param name="fasta_file" value="bsa.fasta"/>
38 <when value="built_in"> 65 <param name="input_file" value="F002832.dat"/>
39 <param name="dbkey" type="select" format="text" > 66 <output name="output" file="bsa_mascot2xml.pep.xml" compare="sim_size" delta="600" />
40 <label>Database</label> 67 </test>
41 <options from_file="pepxml_databases.loc"> 68 </tests>
42 <column name="name" index="0" /> 69 <help>
43 <column name="value" index="2" /> 70 Convert mascot results from mascotdat to pepXML
44 </options> 71 </help>
45 </param>
46 </when>
47 <when value="input_ref">
48 <param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" />
49 </when>
50 </conditional>
51
52 <param name="shortid" type="boolean" label="Short ID" help="Use protein id from the Mascot result file instead reading from the fasta database." truevalue="--shortid" falsevalue="" />
53
54 <conditional name="explicit_enzyme">
55 <param name="explicit_enzyme_use" type="boolean" label="Specify Enzyme" help="If left unchecked the Enzyme will be read from the input file" truevalue="true" falsevalue="false" />
56 <when value="false" />
57 <when value="true">
58 <param name="enzyme" type="text" label="Enzyme" size="80" value="trypsin" help="Semi-cleavage can be specified as semisample_enyzme eg semitrypsin"/>
59 </when>
60 </conditional>
61
62
63
64 </inputs>
65 <outputs>
66 <data format="raw_pepxml" metadata_source="input_file" name="output" label="${input_file.display_name}.pepXML" />
67 </outputs>
68
69 <tests>
70 <test>
71 <param name="source_select" value="input_ref"/>
72 <param name="fasta_file" value="bsa.fasta"/>
73 <param name="input_file" value="F002832.dat"/>
74 <output name="output" file="bsa_mascot2xml.pep.xml" compare="sim_size" delta="600" />
75 </test>
76
77 </tests>
78
79 <help>
80 Convert mascot results from mascotdat to pepXML
81 </help>
82
83 </tool> 72 </tool>