annotate conversion/fasta2rdf/fastatordf.xml @ 16:74b8ba5e2d5b

aragorn addition
author jjkoehorst <jasperkoehorst@gmail.com>
date Sat, 21 Feb 2015 17:17:06 +0100
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
16
74b8ba5e2d5b aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
1 <tool id="SAPP_genome_to_ttl" name="FASTA to RDF" version="0.1">
74b8ba5e2d5b aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
2 <requirements>
74b8ba5e2d5b aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
3 <requirement type='package' version="3.4">python</requirement>
74b8ba5e2d5b aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
4 <requirement type='package' version="1.0">rdflib</requirement>
74b8ba5e2d5b aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
5 </requirements>
74b8ba5e2d5b aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
6 <description></description>
74b8ba5e2d5b aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
7 <command interpreter="python3">fastatordf.py '-input' '$input' '-output' '$output' '-organism' '$organism' '-ncbi_taxid' '$ncbi_taxid' '-idtag' '$identification_tag' -sourcedb SAPP
74b8ba5e2d5b aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
8 #for $index, $id in enumerate( $ids )
74b8ba5e2d5b aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
9 '-ids' '$id.id_tag'
74b8ba5e2d5b aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
10 #end for
74b8ba5e2d5b aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
11 '-id_alternative' '$input.name'
74b8ba5e2d5b aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
12 </command>
74b8ba5e2d5b aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
13 <inputs>
74b8ba5e2d5b aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
14 <param size="60" name="input" type="data" format="fasta,fa" label="File for annotation, file types used fasta,fa"/>
74b8ba5e2d5b aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
15 <param size="60" name="organism" type="text" format="text" label="organism name" optional="false"/>
74b8ba5e2d5b aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
16 <param size="60" name="ncbi_taxid" type="text" format="text" label="NCBI taxonomy ID"/>
74b8ba5e2d5b aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
17 <param size="60" name="identification_tag" type="text" format="text" label="An identification tag used for RDF storage !Needs to be very unique!" optional="false"/>
74b8ba5e2d5b aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
18 <repeat name="ids" title="Identification tags">
74b8ba5e2d5b aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
19 <param size="60" name="id_tag" type="text" format="text" label="An identification tag used by other consortiums"/>
74b8ba5e2d5b aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
20 </repeat>
74b8ba5e2d5b aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
21 </inputs>
74b8ba5e2d5b aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
22
74b8ba5e2d5b aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
23 <outputs>
74b8ba5e2d5b aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
24 <data format="rdf" name="output" label="genomeTTL: ${input.name}" />
74b8ba5e2d5b aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
25 </outputs>
74b8ba5e2d5b aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
26
74b8ba5e2d5b aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
27 <tests>
74b8ba5e2d5b aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
28 <test>
74b8ba5e2d5b aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
29 <param name="input" value="test-data/NC_017117.fna"/>
74b8ba5e2d5b aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
30 <output name="$output" file="NC_017117.rdf"/>
74b8ba5e2d5b aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
31 <output name="$ncbi_taxid" value="634455"/>
74b8ba5e2d5b aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
32 <output name="$idtag" value="Acetobacter pasteurianus IFO 3283-22"/>
74b8ba5e2d5b aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
33 <output name="$organism" value="Acetobacter pasteurianus IFO 3283-22"/>
74b8ba5e2d5b aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
34 </test>
74b8ba5e2d5b aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
35 </tests>
74b8ba5e2d5b aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
36
74b8ba5e2d5b aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
37 <help> Genome FASTA file to RDF</help>
74b8ba5e2d5b aragorn addition
jjkoehorst <jasperkoehorst@gmail.com>
parents:
diff changeset
38 </tool>