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comparison scaffold.xml @ 0:e9981e6af666 draft

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Improved some datatype handling
author galaxyp
date Thu, 20 Jun 2013 11:07:47 -0400
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children 0d0cbb69a03f
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-1:000000000000 0:e9981e6af666
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:
10 #if $sample.category.specify
11 #set $category = $sample.category.name
12 #else
13 #set $category = $sample.sample_name
14 #end if
15 sample:$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
50 --output_driver $output_drirver \
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>
90 </repeat>
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>
117 <data format="xml" name="output_drirver" label="Scaffold Driver for ${on_string}">
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
137 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-scaffold
138 </help>
139 </tool>