--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/trips_create_new_organism/create_annotation_sqlite_.xml	Fri Feb 25 11:24:50 2022 +0000
@@ -0,0 +1,71 @@
+<tool id="create_annotation_sqlite" name="Trips-viz:" version="0.1.0">
+  <description>create new organism</description>
+  <command interpreter="python">create_annotation_sqlite.py $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="input" value="fa_gc_content_input.fa"/>
+      <output name="output" file="saccharomyces_cerevisiae.sqlite"/>
+    </test>
+  </tests>
+
+  <help>
+
+**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>
+</tool>