Mercurial > repos > jjkoehorst > sapp
comparison sappDocker/rdf2embl.xml @ 31:957156367442 draft
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| author | jjkoehorst |
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| date | Wed, 29 Jun 2016 01:36:58 -0400 |
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| 30:0a947cb25a3d | 31:957156367442 |
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| 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/target/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> |