# HG changeset patch
# User drosofff
# Date 1403456936 14400
# Node ID 6f25e1dac784d974db6aba48129ddb232083bf7a

Uploaded

diff -r 000000000000 -r 6f25e1dac784 sRbowtieCascade.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sRbowtieCascade.xml	Sun Jun 22 13:08:56 2014 -0400
@@ -0,0 +1,142 @@
+<tool id="sRbowtie_cascade" name="Annotate smRNA datasets" version="0.9.0">
+  <description>Using iterative sRbowtie Alignments</description>
+  <requirements>
+	<requirement type='package'>bowtie</requirement>
+  </requirements>
+  <parallelism method="basic"></parallelism>
+  <command interpreter="python"> sRbowtieCascade.py --output $output
+                                                    --num-threads \${GALAXY_SLOTS:-4} ## number of processors to be handled by bowtie
+                                                    --mismatch $mismatches
+                                                    --input
+						    #for $i in $input:
+						      $i
+						    #end for
+                                                   --label
+                                                    #for $i in $input:
+                                                      "$i.name"
+                                                    #end for
+                                                   --index
+                                                    #if $refGenomeSource1.genomeSource == "history":
+                                                      $refGenomeSource1.ownFile
+                                                    #else:
+                                                      $refGenomeSource1.index.fields.path
+                                                    #end if
+                                                    #for $i in $AdditionalQueries:
+						      #if $i.refGenomeSource.genomeSource == "history":
+						        $i.refGenomeSource.ownFile
+                                                      #else:
+                                                        $i.refGenomeSource.index.fields.path
+                                                      #end if
+                                                    #end for
+                                                   --indexing-flags
+						    $refGenomeSource1.genomeSource
+                                                    #for $i in $AdditionalQueries:
+						      $i.refGenomeSource.genomeSource
+                                                    #end for
+                                                   --indexName
+                                                    #if $refGenomeSource1.genomeSource == "history":
+                                                      "$refGenomeSource1.ownFile.name"
+                                                    #else:
+                                                      "$refGenomeSource1.index.fields.name"
+                                                    #end if
+                                                    #for $i in $AdditionalQueries:
+                                                      #if $i.refGenomeSource.genomeSource == "history":
+                                                        "$i.refGenomeSource.ownFile.name"
+                                                      #else:
+                                                        "$i.refGenomeSource.index.fields.name"
+                                                      #end if
+                                                    #end for
+  </command>
+  <inputs>
+      <param name="input" type="data" format="fasta" label="Input fasta file: reads clipped from their adapter" help="Only with clipped, raw fasta files" multiple="true"/>
+    <param name="mismatches" type="select" label="Number of mismatches allowed" help="specify the number of mismatches allowed during alignments">
+        <option value="0">0</option>
+        <option value="1" selected="true">1</option>
+        <option value="2">2</option>
+        <option value="3">3</option>
+    </param>
+<!-- First bowtie index selection -->
+    <conditional name="refGenomeSource1">
+      <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
+        <option value="indexed">Use a built-in index</option>
+        <option value="history">Use one from the history</option>
+      </param>
+      <when value="indexed">
+        <param name="index" type="select" label="Select a DNA reference index" help="if your genome of interest is not listed - contact GED team">
+          <options from_data_table="bowtie_indexes"/>
+        </param>
+      </when>
+      <when value="history">
+        <param name="ownFile" type="data" format="fasta" label="Select a fasta file, to serve as index reference" />
+      </when>
+    </conditional>
+<!-- End of first bowtie index selection -->
+<!-- other  bowtie index selections -->
+    <repeat name="AdditionalQueries" title="Additional Alignment Step">
+	<conditional name="refGenomeSource">
+      		<param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
+			<option value="indexed">Use a built-in index</option>
+			<option value="history">Use one from the history</option>
+		</param>
+		<when value="indexed">
+			<param name="index" type="select" label="Select a DNA reference index" help="if your genome of interest is not listed - contact GED team">
+				<options from_data_table="bowtie_indexes"/>
+			</param>
+		</when>
+		<when value="history">
+			<param name="ownFile" type="data" format="fasta" label="Select a fasta file, to serve as index reference" />
+		</when>
+        </conditional>
+    </repeat>
+<!-- End of other bowtie index selections -->
+   </inputs>
+   <outputs>
+   <data format="tabular" name="output" label="Cascade Annotation Analysis"/>
+   </outputs>
+
+    <test>
+    </test>
+
+  <help>
+
+**Intro**
+
+Bowtie_ is a short read aligner designed to be ultrafast and memory-efficient.
+A generic "Map with Bowtie for Illumina" Galaxy tool is available in the main Galaxy distribution.
+However, this Bowtie wrapper tool only takes FASTQ files as inputs.
+
+Here The sRbowtie wrapper specifically works with short reads FASTA inputs (-v bowtie mode, with -k 1)
+
+.. _Bowtie: http://bowtie-bio.sourceforge.net/index.shtml
+
+
+------
+
+**What it does**
+
+.. class:: infomark
+
+This script uses the sRbowtie wrapper to iteratively match reads on a reference indexes.
+
+Reads are Matched on DNA references as fast as possible, without taking care of mapping issues
+
+*-v [0,1,2,3] -k 1 --best -p 12 --suppress 6,7,8*
+
+unaligned reads at step N are used input for sRbowtie at step N+1
+
+-----
+
+**Input formats**
+
+.. class:: warningmark
+
+*The only accepted format for the script is a raw fasta list of reads, clipped from their adapter*
+
+-----
+
+**OUTPUTS**
+
+**Annotation table**
+
+  </help>
+</tool>