--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ribotaper_part1_create_annotation_files.xml	Wed Nov 30 16:44:53 2016 -0500
@@ -0,0 +1,94 @@
+<tool id="ribotaper_create_annotation" name="ribotaper part 1: creation of annotation files" version="0.1.0">
+    <requirements>
+            <requirement type="package" version="1.3.1a">ribotaper</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" />
+    </stdio>
+
+    <command><![CDATA[
+        create_annotations_files.bash
+            "$gtf"
+            "$fa"
+            "$ccdsid"
+            "$appris"
+            "annotation_path"
+        &&
+        tar
+            "czvf"
+            "$output2"
+            "annotation_path"
+
+    ]]></command>
+    <inputs>
+        <param name="gtf" type="data" format="GTF" label="GTF"
+               help="GTF should contain:
+               1) coding and non-coding genes, 2) a 'transcript_id' and a 'gene_id' field for each 'exon' and 'CDS' row.
+               "/>
+        <param name="fa" type="data" format="fasta" label="Genome fasta file" help="FASTA-format, indexed and not repeat masked."/>
+        <param name="ccdsid" type="boolean" falsevalue="false" truevalue="true" checked="true" label="Use ccdsid? (valid for Human Gencode 19 and Mouse Gencode M3 )"
+               help="If yes, only exons/transcripts with the CCDS tag will be used as CCDS exons/transcripts, otherwise all exons/transcripts with a CDS region are going to be annotated as CCDS.
+                    "/>
+        <param name="appris" type="boolean" falsevalue="false" truevalue="true" checked="true" label="Use appris? (valid for Human Gencode 19 and Mouse Gencode M3 )"
+               help=" If yes, only exons/transcripts with the appris tag will be used, using only 1 transcript per appris gene (the appris_principal transcript or other appris transcript). If a               gene does not have appris transcript, all the annotated transcript structures are used.
+               "/>
+    </inputs>
+    <outputs>
+        <data name="output1" format="bed" from_work_dir="annotation_path/start_stops_FAR.bed" label="start_stops_FAR"/>
+        <data name="output2" format="tar" label="annotation_path"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="gtf" value="test.gtf"/>
+            <param name="fa" value="test.fa"/>
+            <param name="ccdsid" value="true"/>
+            <param name="appris" value="true"/>
+            <output name="output1" file="annotation_path/start_stops_FAR.bed"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+Overview
+--------
+
+RiboTaper is an analysis pipeline for Ribosome Profiling
+(Ribo-seq) experiments,
+which exploits the triplet periodicity of
+ribosomal footprints to call translated regions.
+See
+https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/ for details.
+
+
+The Ribotaper Galaxy tool set consists of three tools:
+
+  - ``ribotaper part 1``: creation of annotation files
+  - ``ribotaper part 2``: metagene analysis for P-sites definition
+  - ``ribotaper part 3``: ribosome profiling
+
+The order of execution should follow:
+``ribotaper part 1, part 2 and part 3``.
+
+The current tool is ``ribotaper part 1``,
+creation of annotation files.
+
+Output
+------
+
+``Ribotaper part 1`` builds a list of exon coordinates,
+exon sequences and transcript structures.
+
+``Ribotaper part 1`` generates two files:
+
+  - **start_stops_FAR** in BED format
+  - **annotation_path**  in format of tar
+
+*Start_stops_FAR*
+is used as an input for ``ribotaper part 2``.
+*Annotation_path*
+is used as an input for ``ribotaper part 3``.
+
+
+]]></help>
+    <citations>
+        <citation type="doi">10.1038/nmeth.3688</citation>
+    </citations>
+</tool>