diff trips_create_annotation/trips_create_annotation.xml @ 0:f24aed7a5cc7 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/trips_create_annotation/trips_create_annotation.xml	Mon Apr 04 09:30:51 2022 +0000
@@ -0,0 +1,42 @@
+<tool id="trips_create_annotation" name="Create TRIPS-Viz annotation" version="1.0">
+    <description>Covert GFF3/GTF and transcriptome FASTA to custom annotation sqlite</description>
+    <requirements>
+        <requirement type="package" version="0.19.0">pysam</requirement>
+        <requirement type="package" version="2.0.0">sqlitedict</requirement>
+        <requirement type="package" version="3.37.1">sqlite</requirement>
+        <requirement type="package" version="3.0.2">intervaltree</requirement>
+
+    </requirements>
+    <command><![CDATA[
+        python $__tool_directory__/create_annotation_sqlite.py ${input1} ${input2} ${input3} ${input4} ${input5} ${input6}
+    ]]></command>
+    <inputs>
+        <param name="input1" type="text" label="Transcriptome name" />
+        <param name="input2" type="data" format="gff" label="Transcriptome Annotation file (GFF/GTF)" />
+        <param name="input3" type="data" format="fasta" label="Transcriptome FASTA File" />
+        <param name="input4" type="integer" value="0" label="Psuedo UTR length" help="This value will be added used to create UTRs of this length. This is useful when looking at transcriptomes without annotated UTRs"/>
+        <param name="input5" type="text" label="Transcript ID" help="An example of a transcript_id from the annotation file, e.g ENST000000123456.1"/>
+        <param name="input6" type="text" label="Gene Name" help="An example of a gene name from the annotation file" />
+    </inputs>
+    <outputs>
+       <data name="output1" format="sqlite"/>
+    </outputs>
+    <tests>
+        <test>
+        <param name="input1" value="test_organism" ftype="text"/>
+        <param name="input2" value="test.gtf" ftype="gff"/>
+        <param name="input3" value="test.fasta" ftype="fasta"/>
+        <param name="input4" value="0" ftype="integer"/>
+        <param name="input5" value="YAL012W" ftype="text"/>
+        <param name="input6" value="YDL248W" ftype="text"/>
+        <output name="output1" file="test_organism.sqlite" ftype="sqlite" lines_diff="4" />
+        </test>
+    </tests>
+    <help>
+    **What it does**
+
+    Builds a custom transcirptome annoatation stored in sqlite format for you organism.
+    </help>
+    <citations/>
+</tool>
+