--- a/sRbowtie_wrapper.xml	Mon May 12 12:24:28 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,183 +0,0 @@
-<tool id="sRbowtie" name="GED bowtie" version="1.0.0">
-  <description>small RNA oriented</description>
-  <requirements><requirement type='package'>bowtie</requirement></requirements>
-  <parallelism method="basic"></parallelism>
-  <command interpreter="python"> sRbowtie_wrapper.py $input
-                                                    $method
-                                                    $v_mismatches
-                                                    $output_type
-                                                    $refGenomeSource.genomeSource
-                                                    ## the very source of the index (indexed or fasta file)
-                                                    #if $refGenomeSource.genomeSource == "history":
-                                                        $refGenomeSource.ownFile
-                                                    #else:
-                                                        $refGenomeSource.index
-                                                    #end if
-                                                    ##
-                                                    $output
-                                                    $aligned
-                                                    $unaligned
-  </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"/>
-<!-- which method will be used --> 
-      <param name="method" type="select" label="What kind of matching do you want to do?" help="bowtie parameters adjusted to the type of matching. RNA option match to only one strand">
-        <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 value="multiple" selected="true">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>
-
-<!-- END of which method will be used -->
-
-    <param name="v_mismatches" type="select" label="Number of mismatches allowed" help="specify the -v bowtie option">
-        <option value="0">0</option>
-        <option value="1" selected="true">1</option>
-        <option value="2">2</option>
-        <option value="3">3</option>
-    </param>
-
-
-<!-- nouvel index in dev below -->
-    <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="ged_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>
-<!-- nouvel index input FIN -->
-       <param name="output_type" type="select" label="Select output format" 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">
-          <option value="tabular" select="true">tabular</option>
-          <option value="sam">sam</option>
-          <option value="bam">bam</option>
-       </param>
-      
-     <param name="additional_fasta" type="select" label="additional fasta output" help="to get aligned and unaligned reads in fasta format">
-        <option value="No" select="true">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" name="output" label="Bowtie Output">
-        <change_format>
-            <when input="output_type" value="sam" format="sam" />
-            <when input="output_type" value="bam" format="bam" />
-        </change_format>
-   </data>
-
-   <data format="fasta" name="aligned" label="Matched reads">
-	<filter>additional_fasta == "al" or additional_fasta == "al_and_unal"</filter>
-   </data>
-   <data format="fasta" name="unaligned" label ="Unmatched reads">
-        <filter>additional_fasta == "unal" or additional_fasta == "al_and_unal"</filter>
-   </data>
-   </outputs>
-
-  <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 useful Bowtie wrapper tool only takes as inputs FASTQ files.
-
-Our sRbowtie wrapper is intented to work specifically with short reads FASTA inputs and to serve downstream small RNA sequencing analyses
-
-------
-
-**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 FULL 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 GED galaxy team is your reference genome is not referenced properly in GED galaxy
-
-**Optionnal matched and unmatched fasta reads can be obtained, for further annotations**
-
-  </help>
-</tool>