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comparison trips_create_annotation/trips_create_annotation.xml @ 2:d70696d3341e draft

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author jackcurragh
date Sun, 17 Apr 2022 08:45:11 +0000
parents f089034be679
children f1c72ed4b32c
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1:f089034be679 2:d70696d3341e
1 <tool id="trips_create_annotation" name="Create TRIPS-Viz annotation" version="1.1"> 1 <tool id="trips_create_annotation" name="Create TRIPS-Viz annotation" version="1.0">
2 <description>Covert GFF3/GTF and transcriptome FASTA to custom annotation sqlite</description> 2 <description>Covert GFF3/GTF and transcriptome FASTA to custom annotation sqlite</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.19.0">pysam</requirement> 4 <requirement type="package" version="0.19.0">pysam</requirement>
5 <requirement type="package" version="2.0.0">sqlitedict</requirement> 5 <requirement type="package" version="2.0.0">sqlitedict</requirement>
6 <requirement type="package" version="3.37.1">sqlite</requirement> 6 <requirement type="package" version="3.37.1">sqlite</requirement>
7 <requirement type="package" version="3.0.2">python-intervaltree</requirement> 7 <requirement type="package" version="3.0.2">intervaltree</requirement>
8 8
9 </requirements> 9 </requirements>
10 <command><![CDATA[ 10 <command><![CDATA[
11 python $__tool_directory__/create_annotation_sqlite.py ${input1} ${input2} ${input3} ${input4} ${input5} ${input6} 11 python $__tool_directory__/create_annotation_sqlite.py ${input1} ${input2} ${input3} ${input4} ${input5} ${input6}
12 ]]></command> 12 ]]></command>
21 <outputs> 21 <outputs>
22 <data name="output1" format="sqlite"/> 22 <data name="output1" format="sqlite"/>
23 </outputs> 23 </outputs>
24 <tests> 24 <tests>
25 <test> 25 <test>
26 <param name="input1" value="test_organism" ftype="text"/> 26 <param name="input1" value="test_org" ftype="text"/>
27 <param name="input2" value="test.gtf" ftype="gff"/> 27 <param name="input2" value="test.gtf" ftype="gff"/>
28 <param name="input3" value="test.fasta" ftype="fasta"/> 28 <param name="input3" value="test.fasta" ftype="fasta"/>
29 <param name="input4" value="0" ftype="integer"/> 29 <param name="input4" value="0" ftype="integer"/>
30 <param name="input5" value="YAL012W" ftype="text"/> 30 <param name="input5" value="YDL248W" ftype="text"/>
31 <param name="input6" value="YDL248W" ftype="text"/> 31 <param name="input6" value="YDL248W" ftype="text"/>
32 <output name="output1" file="test_organism.sqlite" ftype="sqlite" lines_diff="4" /> 32 <output name="output1" file="test_org.sqlite" ftype="sqlite" lines_diff="4" />
33 </test> 33 </test>
34 </tests> 34 </tests>
35 <help> 35 <help>
36 **What it does** 36 **What it does**
37 37