<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>