annotate gbk2rdf.xml @ 36:2201c5d61f16 draft default tip

planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
author jjkoehorst
date Mon, 04 Jul 2016 10:53:52 -0400
parents fa736576c7ed
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
35
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
1 <tool id="DGBK2RDF" name="EMBL/GBK to RDF" version="0.1">
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
2 <description>Converts GenBank/EMBL files to RDF</description>
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
3 <requirements>
36
2201c5d61f16 planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents: 35
diff changeset
4 <container>jjkoehorst/sappdocker:GBK2RDF</container>
35
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
5 </requirements>
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
6 <command>java -jar /genbank2rdf/GenBank2RDF-0.0.1-SNAPSHOT-jar-with-dependencies.jar '-input' '$input' -output '$output' -source "$source" -format "$format" -identifier "${input.name}" -codon "$codon" </command>
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
7 <inputs>
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
8 <param format="gbk,gb,genbank" label="Genbank file" name="input" type="data"/>
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
9 <param label="EMBL/GBK" name="format" type="select">
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
10 <option value="gbk">Genbank</option>
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
11 <option selected="true" value="embl">EMBL</option>
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
12 </param>
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
13 <param label="11/4" name="codon" type="select">
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
14 <option selected="true" value="11">11</option>
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
15 <option value="4">4</option>
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
16 </param>
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
17 <param label="Source of annotation eg. RAST/NCBI/EBI" name="source" optional="false" type="text"/>
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
18 </inputs>
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
19 <outputs>
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
20 <data format="ttl" label="GBKttl: ${input.name}" name="output"/>
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
21 </outputs>
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
22 <help>Java Genbank or EMBL to RDF conversion
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
23 </help>
fa736576c7ed planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
jjkoehorst
parents:
diff changeset
24 </tool>