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comparison protxml_to_gff.xml @ 0:956bfab63005 draft default tip

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planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
author iracooke
date Tue, 20 Oct 2015 20:36:03 -0400
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-1:000000000000 0:956bfab63005
1 <tool id="protxml_to_gff" name="Proteomics to GFF" version="1.1.0">
2 <description>Export Proteomics Data to GFF</description>
3 <requirements>
4 <container type="docker">iracooke/protk-1.4.3</container>
5 <requirement type="package" version="1.4.3">protk</requirement>
6 <requirement type="package" version="2.2.29">blast+</requirement>
7 </requirements>
8 <stdio>
9 <exit_code range="1:" level="fatal" description="Failure" />
10 </stdio>
11 <command>
12 protxml_to_gff.rb $protxml_file
13 #if $database.source_select=="built_in":
14 -d $database.dbkey
15 #else
16 -d $database.fasta_file
17 #end if
18 -c $gene_file
19 #if str( $gffidpattern ):
20 --gff-idregex='$gffidpattern'
21 #end if
22
23 #if str( $genomeidpattern ):
24 --genome-idregex='$genomeidpattern'
25 #end if
26
27 #if str( $ignorepattern ):
28 --ignore-regex='$ignorepattern'
29 #end if
30
31 --threshold=$peptide_threshold
32 --prot-threshold=$prot_threshold
33 $stack_charges
34 -o $output
35 </command>
36 <inputs>
37 <conditional name="database">
38 <param name="source_select" type="select" label="Database source used for Proteomics Searches" help="Database should be an amino acid fasta file with entry id's that can be parsed to obtain contig or scaffold ids referenced in your gff file">
39 <option value="input_ref">Your Upload File</option>
40 <option value="built_in">Built-In</option>
41 </param>
42 <when value="built_in">
43 <param name="dbkey" type="select" format="text" >
44 <label>Database</label>
45 <options from_file="pepxml_databases.loc">
46 <column name="name" index="0" />
47 <column name="value" index="2" />
48 </options>
49 </param>
50 </when>
51 <when value="input_ref">
52 <param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" />
53 </when>
54 </conditional>
55 <param name="protxml_file" type="data" format="protxml" multiple="false" label="Proteomics Search Results" help="A ProtXML file produced by Protein Prophet"/>
56 <param name="gene_file" type="data" format="gff3" multiple="false" label="Protein coordinates" help="A gff3 file with coordinates for all protein entries used for proteomics searches. Coordinates should correspond to entries in the genome fasta file"/>
57 <param name="peptide_threshold" label="Peptide Probability Threshold" type="float" value="0.95" min="0" max="1" help="Only peptides within accepted proteins and passing this threshold will appear in the output"/>
58 <param name="prot_threshold" label="Protein Probability Threshold" type="float" value="0.99" min="0" max="1" help="Only peptides within proteins passing this threshold will appear in the output"/>
59 <param name="stack_charges" value="false" type="boolean" label="Peptides with different charges get separate gff entries" help="" truevalue="--stack-charge-states" falsevalue="" />
60 <param name="gffidpattern" size="40" type="text" value="lcl\|([^ ]*)" label="gff id regex" help="Regex with capture group for parsing gff ids from protein ids">
61 <sanitizer>
62 <valid initial="string.printable">
63 <remove value="&apos;"/>
64 </valid>
65 <mapping initial="none">
66 <add source="&apos;" target="__sq__"/>
67 </mapping>
68 </sanitizer>
69 </param>
70
71 <param name="genomeidpattern" size="40" type="text" label="genome id regex" help="Regex with capture group for parsing genomic ids from protein ids">
72 <sanitizer>
73 <valid initial="string.printable">
74 <remove value="&apos;"/>
75 </valid>
76 <mapping initial="none">
77 <add source="&apos;" target="__sq__"/>
78 </mapping>
79 </sanitizer>
80 </param>
81
82 <param name="ignorepattern" size="40" type="text" label="ignore regex" help="Regex to match protein ids that we should ignore completely">
83 <sanitizer>
84 <valid initial="string.printable">
85 <remove value="&apos;"/>
86 </valid>
87 <mapping initial="none">
88 <add source="&apos;" target="__sq__"/>
89 </mapping>
90 </sanitizer>
91 </param>
92
93
94
95 </inputs>
96 <outputs>
97 <data format="gff3" name="output" />
98 </outputs>
99 <tests>
100 <test>
101 <param name="source_select" value="input_ref"/>
102 <param name="fasta_file" value="small_prot.fasta" format="fasta"/>
103
104 <param name="protxml_file" value="small.prot.xml" format="protxml"/>
105 <param name="gene_file" value="small_combined.gff" format="gff3"/>
106 <output name="output" format="gff3">
107 <assert_contents>
108 <has_text text="polypeptide" />
109 </assert_contents>
110 </output>
111 </test>
112 </tests>
113 <help>
114
115 **What it does**
116
117 Exports peptides and proteins to gff
118
119 </help>
120 </tool>