--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/prepare.xml	Fri May 01 05:41:51 2015 -0400
@@ -0,0 +1,174 @@
+<tool id="riboseqr_prepare_input" name="Prepare riboSeqR input" version="0.4.0">
+    <description>
+        (Step 1) Prepare alignment file (SAM format, Ribo-Seq or RNA-Seq alignments)
+        for riboSeqR analysis.
+    </description>
+    <requirements>
+        <requirement type="R-module">riboSeqR</requirement>
+    </requirements>
+    <command interpreter="python">riboseqr/prepare.py
+        #set $files_ribo = []
+        #set $files_rna = []
+        #set $replicates = []
+
+        #for $i, $s in enumerate($rnaseq.datasets)
+            #silent $replicates.append($s.replicate_name.value)
+            #silent $files_ribo.append($s.ribo_files.file_name)
+            #try:
+                #silent $s.rna_files
+            #except:
+                #pass
+            #else:
+                #silent $files_rna.append($s.rna_files.file_name)
+            #end try
+        #end for
+
+        #set $ribofiles = ", ".join($files_ribo)
+        #set $rnafiles = ", ".join($files_rna)
+        #set $replicate_names = ", ".join($replicates)
+
+        --ribo_files "$ribofiles"
+        --rna_files "$rnafiles"
+        --replicate_names "$replicate_names"
+        --seqnames "$seqnames"
+        --rdata_save "$rdata_save"
+        --sam_format
+        --html_file "$html_file"
+        --output_path "$html_file.files_path"
+    </command>
+    <inputs>
+        <conditional name="rnaseq">
+            <param name="have-rnaseq" type="boolean" truevalue="checked"
+                   falsevalue="unchecked" label="Have RNA-Seq data?"/>
+            <when value="checked">
+                <repeat name="datasets" title="Ribo and RNA-Seq alignment"
+                        default="1">
+                    <param type="text" name="replicate_name" size="20"
+                           label="Provide a common name for each replicate group"
+                           value=""/>
+                    <param format="sam" name="ribo_files" type="data"
+                           label="Ribo-Seq alignment file (SAM)"
+                           multiple="false"/>
+                    <param format="sam" name="rna_files" type="data"
+                           label="RNA-Seq alignment file (SAM)"
+                           multiple="false"/>
+                </repeat>
+            </when>
+            <when value="unchecked">
+                <repeat name="datasets" title="Ribo-Seq alignment" default="1">
+                    <param type="text" name="replicate_name" size="20"
+                           label="Provide a common name for each replicate group"
+                           value=""/>
+                    <param format="sam" name="ribo_files" type="data"
+                           label="Ribo-Seq alignment file (SAM)"
+                           multiple="false">
+                    </param>
+                </repeat>
+            </when>
+        </conditional>
+        <param name="seqnames" type="text" area="True" label="Transcript (seqname)
+             names to be read" size="3x60"
+               help="[Optional] - only the mapped footprints for these transcripts will be
+             used in further riboSeqR analysis. Multiple transcript names should
+             be separated by commas. There should be no quotes around transcript names.">
+            <sanitizer>
+                <valid>
+                    <add value="|"/>
+                </valid>
+            </sanitizer>
+        </param>
+    </inputs>
+    <outputs>
+        <data format="rda" name="rdata_save"
+              label="Prepare riboSeqR input (R data file)"/>
+        <data format="html" name="html_file"
+              label="Prepare riboSeqR input (HTML report)"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="ribo_files" value="12hRPF.sam" />
+            <output name="html_file" file="Prepare_riboSeqR_input_(HTML_report).html">
+                <extra_files type="file" name="RiboSeq file 1" value="RiboSeq file 1"/>
+            </output>
+        </test>
+    </tests>
+    <help>
+About
+-----
+This tool can be used to prepare input data for riboSeqR from SAM
+format alignments of Ribo or RNA-Seq data to a reference transcriptome. You can
+do this alignment manually using bowtie or the
+"Transcriptome Mapping" -> "Align to transcriptome using Bowtie"
+tool on RiboGalaxy_
+
+The required input format for riboSeqR_ is mentioned in the
+**"Getting Data"** section of the documentation_.
+
+riboSeqR version: **1.0.4**.
+
+How to use?
+-----------
+Inputs
+......
+Select SAM format Ribo-Seq alignment files in the input section.
+
+If you have RNA-Seq data, these can be included if the **"Have RNA-Seq data"**
+option is checked.
+
+Outputs
+.......
+The following files will be generated on completion:
+
+#. Prepare riboSeqR input (HTML report) - A HTML file with links to all other
+   output files.
+
+   * Generated riboSeqR format input files of RiboSeq and RNASeq data(if provided).
+     These files are plain text and lines have the following information -
+     strand, transcript name, alignment position, sequence.
+
+     Please note the alignments are made **0-indexed**.
+
+   * R script used in this session.
+
+#. Prepare riboSeqR input (R data file) - used as input for the next step -
+   *Triplet Periodicity*.
+
+How are the SAM alignments processed?
+.....................................
+#. Lines starting with ``@`` are ignored.
+#. Lines having a ``FLAG=0`` are considered as successful alignments. These are
+   considered for the next step.
+#. Alignment start is located on ``column 4``. These are decremented by
+   1 as SAM alignments are 1-indexed.
+#. riboSeqR input file is written with the strand (``+``), transcript name,
+   alignment start and the aligned sequence.
+
+riboSeqR functions used
+.......................
+readRibodata.
+
+For detailed description of the functions and the options used, please consult
+the riboSeqR documentation.
+
+Links
+.....
+* `Bioconductor package information on riboSeqR`__
+* riboSeqR - `Reference manual`_
+* riboSeqR - `Introduction and workflow example`_
+
+.. _RiboGalaxy: http://ribogalaxy.ucc.ie
+
+.. _riboSeqR: http://bioconductor.org/packages/3.0/bioc/html/riboSeqR.html
+
+__ riboSeqR_
+
+.. _manual: http://bioconductor.org/packages/3.0/bioc/manuals/riboSeqR/man/riboSeqR.pdf
+
+.. _`Reference manual`: manual_
+
+.. _documentation: http://bioconductor.org/packages/3.0/bioc/vignettes/riboSeqR/inst/doc/riboSeqR.pdf
+
+.. _`Introduction and workflow example`: documentation_
+
+    </help>
+</tool>