comparison rdf2embl.xml @ 35:fa736576c7ed draft

planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
author jjkoehorst
date Mon, 04 Jul 2016 10:37:59 -0400
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34:f2cbf1230026 35:fa736576c7ed
1 <tool id="DRDF2EMBL" name="EMBL/GenBank creation" version="0.1">
2 <description/>
3 <requirements>
4 <container type="docker">jjkoehorst/sappdocker:RDF2EMBL</container>
5 </requirements>
6 <command interpreter="docker">java -jar /rdf2embl/rdf2embl-0.0.1-SNAPSHOT-jar-with-dependencies.jar
7 '-input' '$input' -output '$output' -format 'TURTLE' '-organism'
8 '$organism' '-strain' '$strain' '-substrain' '$substrain' '-keywords'
9 '$keywords' '-taxon' '$taxon' -codon '$codon'
10 -locus '$prefix' '-title'
11 '$title' '-authors' '$authors' '-consortium' '$consortium' '-journal'
12 '$journal' '-dataclass' '$dataclass' '-writer' '$writer' '-projectid'
13 '$projectid' '$pathwaytools' '-note' '$note' '-scaffold' '$scaffold'
14 '$gapprotein'
15 </command>
16 <inputs>
17 <param format="ttl" label="TTL / RDF file" multiple="False" name="input" type="data"/>
18 <param label="Organism name" name="organism" optional="false" type="text"/>
19 <param label="Strain name" name="strain" optional="false" type="text"/>
20 <param label="Substrain name" name="substrain" optional="false" type="text"/>
21 <param label="Keywords" name="keywords" optional="false" type="text"/>
22 <param label="Project identifier" name="projectid" optional="false" type="text"/>
23 <param label="Taxon number" name="taxon" optional="false" type="text"/>
24 <param label="Locus prefix (FZH_)" name="prefix" optional="false" type="text"/>
25 <param label="Scaffold prefix (SCAF_)" name="scaffold" optional="false" type="text"/>
26 <param label="Journal" name="journal" optional="false" type="text" value="journal vol:pp-pp(year)"/>
27 <param label="Authors" name="authors" optional="false" type="text"/>
28 <param label="Title" name="title" optional="false" type="text"/>
29 <param label="Consortium" name="consortium" optional="false" type="text"/>
30 <param area="True" label="Note for each record" name="note" optional="false" size="10" type="text" value="Annotation was performed using the Semantic Annotation Platform for Prokaryotes (SAPP) and the sha384 key is $shakey and the FASTA header name is: $header"/>
31 <param label="codon table selection" name="codon" type="select">
32 <option value="11">The Bacterial, Archaeal and Plant Plastid Code
33 (transl_table=11)
34 </option>
35 <option value="4">The Mold, Protozoan, Coelenterate Mitochondrial
36 and Mycoplasma/Spiroplasma Code (transl_table=4)
37 </option>
38 </param>
39 <param label="Output format" name="writer" type="select">
40 <option selected="true" value="embl">EMBL format</option>
41 <option value="genbank">Genbank format</option>
42 </param>
43 <param label="Data class selection" name="dataclass" type="select">
44 <option value="PAT">Patent</option>
45 <option value="EST">Expressed Sequence Tag</option>
46 <option value="GSS">Genome Survey Sequence</option>
47 <option value="HTC">High Thoughput CDNA sequencing</option>
48 <option value="HTG">High Thoughput Genome sequencing</option>
49 <option value="MGA">Mass Genome Annotation</option>
50 <option selected="true" value="WGS">Whole Genome Shotgun</option>
51 <option value="TSA">Transcriptome Shotgun Assembly</option>
52 <option value="STS">Sequence Tagged Site</option>
53 <option value="STD">Standard (all entries not classified as above)
54 </option>
55 </param>
56 <param label="Remove gap spanning proteins (contains more than 50% of XXX in sequence)" name="gapprotein" type="select">
57 <option selected="true" value="">No</option>
58 <option selected="false" value="-gapprotein">Yes</option>
59 </param>
60 <param label="Pathway tools compatible? WARNING: Each contig needs to be loaded individually into Pathway tools (V19.0)" name="pathwaytools" type="select">
61 <option selected="true" value="">No</option>
62 <option selected="false" value="-pathwaytools">Yes</option>
63 </param>
64 </inputs>
65 <outputs>
66 <data format="embl" label="EMBL: ${input.name}" name="output"/>
67 </outputs>
68 <help>RDF to EMBL conversion. Locus tags are automatically generated unless locus tags have been inferred or generated through the locus module.
69 </help>
70 </tool>