--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/final/create_annotation_sqlite.xml	Tue Mar 01 12:40:17 2022 +0000
@@ -0,0 +1,85 @@
+<tool id="create_annotation_sqlite" name="create annotation in sqlite for trips-viz" version="0.1.4">
+    <requirements>
+		  <container type="docker">triasteran/trips_create_annotation:latest</container>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+	    create_annotation_sqlite $annotation $fasta $pseudo_utr_len $transcript $gene $output
+    ]]></command>
+    <inputs>
+     <param format="gtf,gff" name="annotation" type="data" label="GTF/GFF3 File"/>
+    <param format="fasta" name="fasta" type="data" label="Transcriptome FASTA file"/>
+    <param name="pseudo_utr_len" type="text" label="Pseudo UTR length"/>
+    <param name="transcript" type="text" label="Example transcript"/>
+    <param name="gene" type="text" label="Example gene"/>
+    </inputs>
+    <outputs>
+         <data format="sqlite" name="output" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="fasta" value="sacCer3_transcripts.fasta"/>
+			<param name="annotation" value="saccharomyces_cerevisiae.R64-1-1.84.gtf"/>
+			<param name="pseudo_utr_len" value="300"/>
+			<param name="transcript" value="YDL248W"/>
+			<param name="gene" value="COS7"/>
+            <output name="output" file="output"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+        **GTF/GFF3 File**
+
+GFF lines have nine required fields that must be tab-separated.
+The GFF3 format addresses the most common extensions to GFF, while preserving backward compatibility with previous formats.
+
+Both transcript ids and gene names should be listed in the file.
+
+-----
+
+**Transcriptome FASTA file**
+
+A FASTA file with an entry for every transcript. The headers should be the transcript id's as they appear in the GTF/GFF3 file. 
+
+-----
+
+**Psuedo UTR length**
+An integer representing the length (in nucleotides) to be added to the 5' end and 3' end of every transcript with an annotated
+CDS. Useful for when an organism does not have any annotated UTR's, if it does use 0. If not 0, the extra nucleotides should
+already be present in the FASTA file. 
+
+-----
+
+**Example transcript**
+
+An example of a transcript id that appears in the FASTA/GTF/GFF3 file, e.g ENST00000123456
+
+-----
+
+**Example Gene**
+
+An example of a gene name as it appears in the GTF/GFF3 file, e.g BRCA1
+
+-----
+
+**Output**
+
+The output of the script can be downloaded and uploaded to Trips-viz_. by signing in and going to the uploads page, then selecting
+"Upload new transcriptome". When uploaded the new organism will appear on the home page of Trips-viz, or under the transcriptomes
+page if the organism name used is already present on Trips-viz.  
+
+
+
+.. _Trips-viz: http://trips.ucc.ie
+
+    ]]></help>
+    <citations>
+        <citation type="bibtex">
+@misc{githubTrips-Viz,
+  author = {LastTODO, FirstTODO},
+  year = {TODO},
+  title = {Trips-Viz},
+  publisher = {GitHub},
+  journal = {GitHub repository},
+  url = {https://github.com/skiniry/Trips-Viz},
+}</citation>
+    </citations>
+</tool>