|
0
|
1 <tool id="scaffold" name="Scaffold" version="0.1.0">
|
|
|
2 <description>
|
|
|
3 Visualize and Validate Complex MS/MS Proteomics Experiments
|
|
|
4 </description>
|
|
|
5 <configfiles>
|
|
|
6 <configfile name="sample_config"># Simple format group:group_name followed by pairs of name:name and path:path lines
|
|
|
7 #if $sample_mode.mode == "full"
|
|
|
8 #set $samples = $sample_mode.samples
|
|
|
9 #for $sample in $samples:
|
|
1
|
10 #if $sample.category.specify
|
|
0
|
11 #set $category = $sample.category.name
|
|
|
12 #else
|
|
1
|
13 #set $category = $sample.sample_name
|
|
0
|
14 #end if
|
|
|
15 sample:$sample.sample_name
|
|
|
16 mudpit:$sample.mudpit
|
|
|
17 category:$category
|
|
|
18 #for $sample_input in $sample.sample_inputs:
|
|
|
19 name:${sample_input.display_name}
|
|
|
20 path:${sample_input}
|
|
|
21 ext:${sample_input.ext}
|
|
|
22 #end for
|
|
|
23 #end for
|
|
|
24 #elif $sample_mode.mode == "sample_per_file":
|
|
|
25 #for $sample_input in $sample_mode.sample_inputs:
|
|
|
26 sample:${sample_input.display_name}
|
|
|
27 mudpit:false
|
|
|
28 category:${sample_input.display_name}
|
|
|
29 name:${sample_input.display_name}
|
|
|
30 path:${sample_input}
|
|
|
31 ext:${sample_input.ext}
|
|
|
32 #end for
|
|
|
33 #end if
|
|
|
34 </configfile>
|
|
|
35 </configfiles>
|
|
|
36 <command interpreter="python">
|
|
|
37 scaffold_wrapper.py run \
|
|
|
38 --samples $sample_config \
|
|
|
39 --database $database \
|
|
|
40 --database_name '$database.display_name'\
|
|
|
41 --output $output \
|
|
|
42 --database_type $database_type \
|
|
|
43 --database_decoy_regex '$database_decoy_regex' \
|
|
|
44 #if $thresholds.specify
|
|
|
45 --protein_probability '$thresholds.protein_probability' \
|
|
|
46 --peptide_probability '$thresholds.peptide_probability' \
|
|
|
47 #end if
|
|
|
48 #if $advanced.specify
|
|
|
49 #if $advanced.output_driver
|
|
1
|
50 --output_driver $output_driver \
|
|
0
|
51 #end if
|
|
|
52 #end if
|
|
|
53 </command>
|
|
|
54 <inputs>
|
|
|
55 <param format="fasta" name="database" type="data" label="Search Database" />
|
|
|
56 <param type="select" name="database_type" label="Database Type">
|
|
|
57 <option value="GENERIC">Generic</option>
|
|
|
58 <option value="ESTNR">EST/NR (NCBI)</option>
|
|
|
59 <option value="IPI">IPI (EBI)</option>
|
|
|
60 <option value="SWISSPROT">Swiss-Prot (SIB/EBI)</option>
|
|
|
61 <option value="UNIPROT">UniProt/Swiss-Prot (UniProtKB)</option>
|
|
|
62 <option value="UNIREF">UniRef/NREF (UniProt)</option>
|
|
|
63 <option value="ENSEMBL">Ensembl (EMBL/EBI)</option>
|
|
|
64 <option value="MSDB">MSDB (Proteomics Group)</option>
|
|
|
65 </param>
|
|
|
66 <param name="database_decoy_regex" type="text" label="Database Decoy Prefix" help="Regular expression describing decoys in specified FASTA databse." value="REV|RRR">
|
|
|
67 <sanitizer>
|
|
|
68 <valid initial="string.printable">
|
|
|
69 <add value="|"/>
|
|
|
70 </valid>
|
|
|
71 </sanitizer>
|
|
|
72 </param>
|
|
|
73 <conditional name="sample_mode">
|
|
|
74 <param name="mode" type="select" label="How should samples be created">
|
|
|
75 <option value="full">Create Samples Manually</option>
|
|
|
76 <option value="sample_per_file">Create Sample per File</option>
|
|
|
77 </param>
|
|
|
78 <when value="full">
|
|
|
79 <repeat name="samples" title="Biological Sample">
|
|
|
80 <param name="sample_name" type="text" label="Sample Name" help="Name for the scample (use only letters and numbers)." />
|
|
|
81 <param format="t.xml,omx" name="sample_inputs" type="data" multiple="true" label="Sample Input Files" />
|
|
|
82 <param name="mudpit" type="boolean" label="Mudpit" help="" truevalue="true" falsevalue="false" />
|
|
|
83 <conditional name="category">
|
|
|
84 <param name="specify" type="boolean" label="Specify Custom Category" help="" truevalue="true" falsevalue="false" />
|
|
|
85 <when value="false" />
|
|
|
86 <when value="true">
|
|
|
87 <param name="name" type="text" label="Category Name" help="" />
|
|
|
88 </when>
|
|
|
89 </conditional>
|
|
1
|
90 </repeat>
|
|
0
|
91 </when>
|
|
|
92 <when value="sample_per_file">
|
|
|
93 <param format="t.xml,omx" name="sample_inputs" type="data" multiple="true" label="Input Files" />
|
|
|
94 </when>
|
|
|
95 </conditional>
|
|
|
96 <conditional name="thresholds">
|
|
|
97 <param name="specify" type="boolean" label="Specify Reporting Thresholds" help="" truevalue="true" falsevalue="false" />
|
|
|
98 <when value="false" />
|
|
|
99 <when value="true">
|
|
|
100 <param name="protein_probability" type="float" label="Minimum Protein Probility" help="Optional value between 0.0 and 1.0." optional="true" />
|
|
|
101 <param name="peptide_probability" type="float" label="Minimum Peptide Probility" help="Optional value between 0.0 and 1.0." optional="true" />
|
|
|
102 </when>
|
|
|
103 </conditional>
|
|
|
104 <conditional name="advanced">
|
|
|
105 <param name="specify" type="boolean" label="Specify Advanced Options" help="" truevalue="true" falsevalue="false" />
|
|
|
106 <when value="false" />
|
|
|
107 <when value="true">
|
|
|
108 <param name="output_driver" type="boolean" label="Include Scaffold Driver File in Output" truevalue="true" falsevalue="false" />
|
|
|
109 <!--
|
|
|
110 <param name="ncbi_annotate" type="boolean" label="" truevalue="true" falsevalue="false" />
|
|
|
111 <param name="go_annotate" type="boolean" label="" truevalue="true" falsevalue="false" />
|
|
|
112 -->
|
|
|
113 </when>
|
|
|
114 </conditional>
|
|
|
115 </inputs>
|
|
|
116 <outputs>
|
|
1
|
117 <data format="xml" name="output_driver" label="Scaffold Driver for ${on_string}">
|
|
0
|
118 <filter>(advanced['specify'] and advanced["output_driver"])</filter>
|
|
|
119 </data>
|
|
|
120 <data format="sf3" name="output" />
|
|
|
121 </outputs>
|
|
|
122 <requirements>
|
|
|
123 <requirement type="package">scaffold</requirement>
|
|
|
124 </requirements>
|
|
|
125 <help>
|
|
|
126 **What it does**
|
|
|
127
|
|
|
128 Merges multiple protein identification search results together into a single SF3 file for viewing. A free viewer for Scaffold SF3 files can be obtained from Proteome software at http://www.proteomesoftware.com/Scaffold/Scaffold_viewer.htm.
|
|
|
129
|
|
|
130 ------
|
|
|
131
|
|
|
132
|
|
|
133 **Citation**
|
|
|
134
|
|
|
135 For the underlying tool, please cite `TODO`
|
|
|
136
|
|
1
|
137 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/scaffold
|
|
0
|
138 </help>
|
|
1
|
139 </tool>
|
