--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sRbowtie.xml	Tue May 26 18:36:09 2015 -0400
@@ -0,0 +1,216 @@
+<tool id="bowtieForSmallRNA" name="sRbowtie" version="1.1.0">
+    <description>for FASTA small reads</description>
+    <requirements>
+        <requirement type="package" version="0.12.7">bowtie</requirement>
+        <requirement type="package" version="0.1.18">samtools</requirement>
+    </requirements>
+    <command interpreter="python"> sRbowtie.py --input $input
+                                             --input-format $input.extension
+                                             --method $method
+                                             --v-mismatches $v_mismatches
+                                             --output-format $output_format
+                                             --output $output
+                                             --index-from $refGenomeSource.genomeSource
+                                             ## the very source of the index (indexed or fasta file)
+                                             --index-source
+                                             #if $refGenomeSource.genomeSource == "history":
+                                                 $refGenomeSource.ownFile
+                                             #else:
+                                                 $refGenomeSource.index.fields.path
+                                             #end if
+                                             --aligned $aligned
+                                             --unaligned $unaligned
+                                             --num-threads \${GALAXY_SLOTS:-4} ## number of processors to be handled by bowtie
+  </command>
+    <inputs>
+        <param format="fasta, fastq" help="Only with clipped, raw fasta files" label="Input fasta file: reads clipped from their adapter" name="input" type="data" />
+        <param help="bowtie parameters adjusted to the type of matching. RNA option match to only one strand" label="What kind of matching do you want to do?" name="method" type="select">
+            <option value="RNA">Match on sense strand RNA reference index, multiple mappers randomly matched at a single position</option>
+            <option value="unique">Match unique mappers on DNA reference index</option>
+            <option selected="true" value="multiple">Match on DNA, multiple mappers randomly matched at a single position</option>
+            <option value="k_option">Match on DNA as fast as possible, without taking care of mapping issues (for raw annotation of reads)</option>
+            <option value="n_option">Match on DNA - RNAseq mode (-n bowtie option)</option>
+            <option value="a_option">Match and report all valid alignments</option>
+        </param>
+        <param help="specify the -v bowtie option" label="Number of mismatches allowed" name="v_mismatches" type="select">
+            <option value="0">0</option>
+            <option selected="true" value="1">1</option>
+            <option value="2">2</option>
+            <option value="3">3</option>
+        </param>
+        <conditional name="refGenomeSource">
+            <param help="Built-ins were indexed using default options" label="Will you select a reference genome from your history or use a built-in index?" name="genomeSource" type="select">
+                <option value="indexed">Use a built-in index</option>
+                <option value="history">Use one from the history</option>
+            </param>
+            <when value="indexed">
+                <param help="if your genome of interest is not listed - contact instance administrator" label="Select a DNA reference index" name="index" type="select">
+                    <options from_data_table="bowtie_indexes">
+      
+          </options>
+                </param>
+            </when>
+            <when value="history">
+                <param format="fasta" label="Select a fasta file, to serve as index reference" name="ownFile" type="data" />
+            </when>
+        </conditional>
+        <param help="Note that the BAM will be viewable in trackster only if you choose a full genome referenced for Trackster usage. see the doc below" label="Select output format" name="output_format" type="select">
+            <option select="true" value="tabular">tabular</option>
+            <option value="sam">sam</option>
+            <option value="bam">bam</option>
+        </param>
+        <param help="to get aligned and unaligned reads in fasta format" label="additional fasta output" name="additional_fasta" type="select">
+            <option select="true" value="No">No</option>
+            <option value="al">aligned</option>
+            <option value="unal">unaligned</option>
+            <option value="al_and_unal">both aligned and unaligned</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data format="tabular" label="Bowtie Output" name="output">
+            <change_format>
+                <when format="sam" input="output_format" value="sam" />
+                <when format="bam" input="output_format" value="bam" />
+            </change_format>
+            <actions>
+                <conditional name="refGenomeSource.genomeSource">
+                    <when value="indexed">
+                        <action name="dbkey" type="metadata">
+                            <option column="1" name="bowtie_indexes" offset="0" type="from_data_table">
+                                <filter column="0" compare="startswith" keep="False" type="param_value" value="#" />
+                                <filter column="0" ref="refGenomeSource.index" type="param_value" />
+                            </option>
+                        </action>
+                    </when>
+                    <when value="history">
+                        <action name="dbkey" type="metadata">
+                            <option name="refGenomeSource.ownFile" param_attribute="dbkey" type="from_param" />
+                        </action>
+                    </when>
+                </conditional>
+            </actions>
+        </data>
+        <data format="fasta" label="Matched reads" name="aligned">
+            <filter>additional_fasta == "al" or additional_fasta == "al_and_unal"</filter>
+        </data>
+        <data format="fasta" label="Unmatched reads" name="unaligned">
+            <filter>additional_fasta == "unal" or additional_fasta == "al_and_unal"</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="genomeSource" value="history" />
+            <param ftype="fasta" name="ownFile" value="297_reference.fa" />
+            <param name="method" value="unique" />
+            <param ftype="fasta" name="input" value="input.fa" />
+            <param name="v_mismatches" value="1" />
+            <param name="output_format" value="bam" />
+            <output file="output.bam" ftype="bam" lines_diff="4" name="output" />
+        </test>
+        <test>
+            <param name="genomeSource" value="history" />
+            <param ftype="fasta" name="ownFile" value="297_reference.fa" />
+            <param name="method" value="unique" />
+            <param ftype="fastq" name="input" value="input.fastq" />
+            <param name="v_mismatches" value="1" />
+            <param name="output_format" value="bam" />
+            <output file="output2.bam" ftype="bam" lines_diff="4" name="output" />
+        </test>
+    </tests>
+    <help>
+
+**What it does**
+
+Bowtie_ is a short read aligner designed to be ultrafast and memory-efficient. It is developed by Ben Langmead and Cole Trapnell. Please cite: Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25.
+
+.. _Bowtie: http://bowtie-bio.sourceforge.net/index.shtml
+
+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.
+
+The sRbowtie wrapper specifically works with short reads FASTA inputs (-v bowtie mode)
+
+------
+
+**OPTIONS**
+
+.. class:: infomark
+
+This script uses Bowtie to match reads on a reference index.
+
+Depending on the type of matching, different bowtie options are used:
+
+**Match on sense strand RNA reference index, multiple mappers randomly matched at a single position**
+
+Match on RNA reference, SENSE strand, randomly attributing multiple mapper to target with least mismatches, the polarity column is suppressed in the bowtie tabular report:
+
+*-v [0,1,2,3] -M 1 --best --strata -p 12 --norc --suppress 2,6,7,8*
+
+**Match unique mappers on DNA reference index**
+
+Match ONLY unique mappers on DNA reference index
+
+*-v [0,1,2,3] -m 1 -p 12 --suppress 6,7,8*
+
+Note that using this option with -v values other than 0 is questionnable...
+
+**Match on DNA, multiple mappers randomly matched at a single position**
+
+Match multiple mappers, randomly attributing multiple mapper to target with least mismatches, number of mismatch allowed specified by -v option:
+
+*-v [0,1,2,3] -M 1 --best --strata -p 12 --suppress 6,7,8*
+
+**Match on DNA as fast as possible, without taking care of mapping issues (for raw annotation of reads)**
+
+Match with highest speed, not guaranteeing best hit for speed gain:
+
+*-v [0,1,2,3] -k 1 --best -p 12 --suppress 6,7,8*
+
+
+-----
+
+**Input formats**
+
+.. class:: warningmark
+
+*The only accepted format for the script is a raw fasta list of reads, clipped from their adapter*
+
+-----
+
+**OUTPUTS**
+
+If you choose tabular as the output format, you will obtain the matched reads in standard bowtie output format, having the following columns::
+
+    Column    Description
+  --------    --------------------------------------------------------
+   1 FastaID  fasta identifier
+   2 polarity + or - depending whether the match was reported on the forward or reverse strand
+   3 target     name of the matched target
+   4 Offset   O-based coordinate of the miR on the miRBase pre-miR sequence
+   5 Seq      sequence of the matched Read
+
+If you choose SAM, you will get the output in unordered SAM format.
+
+.. class:: warningmark
+
+if you choose BAM, the output will be in sorted BAM format.
+To be viewable in Trackster, several condition must be fulfilled:
+
+.. class:: infomark
+
+Reads must have been matched to a genome whose chromosome names are compatible with Trackster genome indexes
+
+.. class:: infomark
+
+the database/Build (dbkey) which is indicated for the dataset (Pencil - Database/Build field) must match a Trackster genome index.
+
+Please contact the Galaxy instance administrator if your genome is not referenced
+
+**Matched and unmatched fasta reads can be retrieved, for further analyses**
+
+  </help>
+    <citations>
+        <citation type="doi">10.1186/gb-2009-10-3-r25</citation>
+    </citations>
+</tool>