--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ribotaper_part2_create_metaplots.xml	Tue Jun 07 17:49:46 2016 -0400
@@ -0,0 +1,93 @@
+<tool id="ribotaper_create_metaplots" name="ribotaper part 2: metagene analysis for P-sites definition" version="0.1.0">
+    <requirements>
+            <requirement type="package" version="1.3.1">ribotaper</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" />
+    </stdio>
+
+    <command><![CDATA[
+        create_metaplots.bash
+            "$ribo_bam"
+            "$start_stops_FAR"
+            "metagene"
+
+        &&
+
+        find "metaplots"
+            "-name"
+            "metagene*.pdf"
+            | sort | xargs gs
+            "-dAutoRotatePages=/None"
+            "-dBATCH"
+            "-dNOPAUSE"
+            "-q"
+            "-sDEVICE=pdfwrite"
+            "-sOutputFile=merged_metagene.pdf"
+
+    ]]></command>
+    <inputs>
+        <param name="ribo_bam" type="data" format="bam" label="ribo_bam" help="Ribo-seq alignment file in BAM format."/>
+        <param name="start_stops_FAR" type="data" format="bed" label="start_stops_FAR" help="Please run 'ribotaper part 1' to generate the table."/>
+    </inputs>
+    <outputs>
+        <data name="output1" type="data" format="pdf" from_work_dir="merged_metagene.pdf" label="Metagene analysis results for P-sites definition (figures)"/>
+        <data name="output2" type="data" format="tabular" from_work_dir="metagene" label="Metagene analysis results for P-sites definition (table)"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="ribo_bam" value="test_ribo.bam" ftype="bam"/>
+            <param name="start_stops_FAR" value="annotation_path/start_stops_FAR.bed"  ftype="bed"/>
+            <output name="output2" file="metagene"/>
+        </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 2``,
+metagene analysis for P-sites definition.
+
+Output
+--------
+
+``Ribotaper part 2`` generates two files:
+
+  - **Metagene analysis results for P-sites definition** in pdf format
+  - **Metagene analysis results for P-sites definition** in tablular format
+
+The outputs include the aggregate profiles around the start and stop codons for the 5'-end of different Ribo-seq read lengths.
+Deciding which Ribo-seq read length to use at which distance cutoff to define P-sites position is the critical decision for the whole RiboTaper pipeline.
+These plots should help you decide which read lengths to use and with which cutoff.
+Ideally, the user should pick up the read lengths which show a specific frame preference (same color preference for all the 4 subplots) and a peak around a specific distance on the start codon.
+Sometimes a peak at the stop codon is also visible, but often in a different frame. This may have biological relevance, but it is still not very well explained by the community.
+As seen in the example, taken from the Ribo-seq data of our publication, the 29 nt reads show a very nice frame preference and a peak of 12 nt distance from the annotated start codons. Which means the 29 nt reads with a 12 distance cutoff can be chosen.
+Usually reads around 29 nt with 12 nt distance cutoff are the outcome of many Ribo-seq experiments, however, despite biochemical constraint about the size of ribosome-protected fragments, the outcome of such analysis is heavily influenced by the experimental protocol used.
+More read lengths can be chosen, but they have to display a strong frame preference.
+
+From the output, user shall determine the appropriate
+read lengths and cutoffs which are required
+for running ``ribotaper part 3``, ribosome profiling.
+
+]]></help>
+    <citations>
+        <citation type="doi">10.1038/nmeth.3688</citation>
+    </citations>
+</tool>