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comparison sappDocker/fasta2rdf.xml @ 31:957156367442 draft

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author jjkoehorst
date Wed, 29 Jun 2016 01:36:58 -0400
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30:0a947cb25a3d 31:957156367442
1 <tool id="DFASTA2RDF" name="FASTA to RDF" version="0.1">
2 <description></description>
3 <requirements>
4 <container type="docker">jjkoehorst/sappdocker:FASTA2RDF</container>
5 </requirements>
6 <command interpreter="docker">java -jar /fasta2rdf/target/FASTA2RDF-0.1-jar-with-dependencies.jar
7 '--type' '$source.fastaType' '--ignorestop' '$IgnoreStopCodon'
8 '--input' '$input' '--output' '$output' '-organism' '$organism'
9 '--ncbi_taxid' '$ncbi_taxid'
10 #if len(str($identification_tag))==0
11 '--idtag' ${input.name}
12 #else
13 '--idtag' '$identification_tag'
14 #end if
15 --source SAPP
16
17 #for $index, $id in enumerate( $ids )
18 '--id_alternative' '$id.id_tag'
19 #end for
20 '--id_alternative' '$input.name'
21 '--codon' '$table'
22 </command>
23 <inputs>
24 <param size="60" name="input" type="data" format="fasta" label="Fasta file for conversion" />
25
26 <conditional name="source">
27 <param name="fastaType" type="select"
28 label="Select if it is a Genome/Gene/Protein or program wont start!">
29 <option value="">To be chosen</option>
30 <option value="genome"> Genome </option>
31 <option value="gene"> Gene</option>
32 <option value="protein"> Protein </option>
33 <validator type="empty_field"
34 message="Please select if it is a Genome, Gene or Protein" />
35 </param>
36 </conditional>
37
38 <param name="table" type="select" label="Codon table">
39 <option value="1"> 1 - UNIVERSAL </option>
40 <option value="2"> 2 - VERTEBRATE_MITOCHONDRIAL </option>
41 <option value="3"> 3 - YEAST_MITOCHONDRIAL </option>
42 <option value="4"> 4 - MOLD_MITOCHONDRIAL </option>
43 <option value="5"> 5 - INVERTEBRATE_MITOCHONDRIAL </option>
44 <option value="6"> 6 - CILIATE_NUCLEAR </option>
45 <option value="9"> 9 - ECHINODERM_MITOCHONDRIAL </option>
46 <option value="10"> 10 - EUPLOTID_NUCLEAR </option>
47 <option value="11" selected="true"> 11 - BACTERIAL </option>
48 <option value="12"> 12 - ALTERNATIVE_YEAST_NUCLEAR </option>
49 <option value="13"> 13 - ASCIDIAN_MITOCHONDRIAL </option>
50 <option value="14"> 14 - FLATWORM_MITOCHONDRIAL </option>
51 <option value="15"> 15 - BLEPHARISMA_MACRONUCLEAR </option>
52 <option value="16"> 16 - 2CHLOROPHYCEAN_MITOCHONDRIAL </option>
53 <option value="21"> 21 - TREMATODE_MITOCHONDRIAL </option>
54 <option value="23"> 23 - SCENEDESMUS_MITOCHONDRIAL </option>
55 </param>
56 <param size="60" name="organism" type="text" format="text"
57 label="organism name" />
58 <param name='IgnoreStopCodon' type='boolean'
59 label='Ignore if stop codon within protein sequence' truevalue='true'
60 falsevalue='false' checked="false" help='' />
61
62 <param size="60" name="ncbi_taxid" type="integer" value="0"
63 label="NCBI taxonomy ID" optional="False">
64 <validator type="in_range" min="1"
65 message="Minimum taxonomy value is 1" />
66 </param>
67 <param size="60" name="identification_tag" type="text" format="text"
68 label="An identification tag used for RDF storage !Needs to be very unique!"
69 optional="True" />
70 <repeat name="ids" title="Identification tags">
71 <param size="60" name="id_tag" type="text" format="text"
72 label="An identification tag used by other consortiums" />
73 </repeat>
74 </inputs>
75 <outputs>
76 <data format="ttl" name="output" label="FASTA2RDF: ${input.name}" />
77 </outputs>
78 <help>
79 RDF creation from a multi (gene/protein/genome) fasta file
80 </help>
81 </tool>
82