--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/quantifier.xml	Tue Jan 27 09:06:15 2015 -0500
@@ -0,0 +1,145 @@
+<tool id="rbc_mirdeep2_quantifier" name="MiRDeep2 Quantifier" version="2.0.0">
+    <description>
+<![CDATA[
+fast quantitation of reads mapping to known miRBase precursors
+]]>
+    </description>
+    <requirements>
+        <requirement type="package" version="2.0">mirdeep2_quantifier</requirement>
+        <requirement type="package" version="0.12.7">bowtie</requirement>
+        <requirement type="package" version="5.18.1">perl</requirement>
+        <requirement type="package" version="1.8.5">vienna_rna</requirement>
+        <requirement type="package" version="2.023">pdf_api2</requirement>
+    </requirements>
+
+    <command>
+<![CDATA[
+    quantifier.pl 
+    
+    -p $precursors 
+    
+    -m $mature 
+    
+    -r $reads
+    
+    #if $species.value != 'all'
+        -t $species
+    #end if
+    
+    #if $star_sequences
+        -s $star_sequences
+    #end if
+    
+    $sortReadsInPDF
+    $flexibleIdMapping
+    $skipFileConversion
+    $wholePrecursAsMature
+    $discardReadMultiMap
+    
+    -e $upstreamNtides
+    -f $downstreamNtides
+    -g $allowedMismatches
+    -y galaxy
+    
+     ## html output
+    ;
+    cp expression_galaxy.html $html 2> /dev/null
+    
+    ## move pdf directory to be accessible from the new index.html
+    ;
+    mkdir -p $html.files_path 2> /dev/null
+    ;
+    cp -R pdfs_galaxy $html.files_path 2> /dev/null
+    
+]]>
+    </command>
+    <stdio>
+        <!-- Anything other than zero is an error -->
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+        <!-- In case the return code has not been set propery check stderr too -->
+        <regex match="Error:" />
+        <regex match="Exception:" />
+    </stdio>
+    <inputs>
+        <param name="reads" format="fasta" type="data" label="Collapsed deep sequencing reads" help="Reads in fasta format. (-r)"/>
+        <param name="precursors" format="fasta" type="data" label="Precursor sequences" help="miRNA precursor sequences from miRBase. (-p)"/>
+        <param name="mature" format="fasta" type="data" label="Mature miRNA sequences" help="Mature miRNA sequences from miRBase. (-m)"/>
+        <param name="species" type="select" label="Search in species" help="If not searching in a specific species all species in your files will be analyzed. (-t)">
+            <option value="all">All species</option>
+            <option value="tni">tetraodon</option>
+            <option value="dps">d.pseudoobscura</option>
+            <option value="dya">d.yakuba</option>
+            <option value="ame">a.mellifera</option>
+            <option value="dmo">d.mojavensis</option>
+            <option value="cel">worm</option>
+            <option value="aga">a.gambiae</option>
+            <option value="cbr">c.briggsae</option>
+            <option value="cin">c.intestinalis</option>
+            <option value="mmu">mouse</option>
+            <option value="xtr">x.tropicalis</option>
+            <option value="eca">horse</option>
+            <option value="cfa">dog</option>
+            <option value="fru">fugu</option>
+            <option value="bta">cow</option>
+            <option value="der">d.erecta</option>
+            <option value="dgr">d.grimshawi</option>
+            <option value="gga">chicken</option>
+            <option value="spu">s.purpuratus</option>
+            <option value="bfl">lancelet</option>
+            <option value="ptr">chimp</option>
+            <option value="dse">d.sechellia</option>
+            <option value="dpe">d.persimilis</option>
+            <option value="dvi">d.virilis</option>
+            <option value="rno">rat</option>
+            <option value="dme">d.melanogaster</option>
+            <option value="lca">cat</option>
+            <option value="sja">c.japonica</option>
+            <option value="dan">d.ananassae</option>
+            <option value="hsa">human</option>
+            <option value="dsi">d.simulans</option>
+        </param>
+        <param name="star_sequences" format="fasta" type="data" optional="true" label="Star sequences" help="From miRBase in fasta format (optional) (-s)"/>
+        
+       <!-- <param name="generatePDFs" type="boolean" checked="true" truevalue="" falsevalue="-d" label="Generate PDFs" help="(-d)"/> -->
+        <param name="sortReadsInPDF" type="boolean" checked="true" truevalue="" falsevalue="-o" label="Sort reads by sample in PDF" help="(-o)"/>
+        <param name="flexibleIdMapping" type="boolean" checked="false" truevalue="-k" falsevalue="" label="Include ID-flexible mapping" help="Also considers precursor-mature mappings that have different ids, eg let7c would be allowed to map to pre-let7a. (-k)"/>
+        <param name="skipFileConversion" type="boolean" checked="false" truevalue="-n" falsevalue="" label="Skip file conversion" help="(-n)"/>
+        <param name="skipPrecursMapping" type="boolean" checked="false" truevalue="-x" falsevalue="" label="Skip mapping against precursor" help="(-x)"/>
+        <!-- <param name="noMrdPDF" type="boolean" checked="false" truevalue="-j" falsevalue="" label="Do not create output.mrd file or PDFs" help="(-j)"/> -->
+        <param name="wholePrecursAsMature" type="boolean" checked="false" truevalue="-w" falsevalue="" label="Consider the whole precursor as the 'mature sequence'" help="(-w)"/>
+        <param name="discardReadMultiMap" type="boolean" checked="false" truevalue="-U" falsevalue="" label="Discard all read multimapper" help="(-U)"/>
+        
+        <param name="upstreamNtides" type="integer" value="2" minvalue="0" label="Upstream nucleotides" help="Number of nucleotides upstream of the mature sequence to consider. (-e)"/>
+        <param name="downstreamNtides" type="integer" value="5" minvalue="0" label="Downstream nucleotides" help="Number of nucleotides downstream of the mature sequence to consider. (-f)"/>
+        <param name="allowedMismatches" type="integer" value="1" minvalue="0" label="Allowed mismatches" help="Number of allowed mismatches when mapping reads to precursors. (-g)"/>
+    </inputs>
+    <outputs>
+        <data name="miRNAsExpressed" format="tabular" from_work_dir="miRNAs_expressed_all_samples_galaxy.csv" label="output of ${tool.name} on ${on_string}"/>
+        <data format="html" name="html" label="${tool.name} on ${on_string} (html report)"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="reads" value="reads_collapsed.fa"/>
+            <param name="precursors" value="precursors_ref_this_species.fa"/>
+            <param name="mature" value="mature_ref_this_species.fa"/>
+            <param name="species" value="cel"/>
+            <output name="miRNAsExpressed" file="miRNAs_expressed_all_samples.csv"/>
+            <output name="html" file="expression_galaxy.html"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+**What MiRDeep2 Quantifier does**
+
+The module maps the deep sequencing reads to predefined miRNA precursors and determines by that the expression of the corresponding miRNAs. 
+First, the predefined mature miRNA sequences are mapped to the predefined precursors. Optionally, predefined star sequences can be mapped to the precursors too. 
+By that the mature and star sequence in the precursors are determined. Second, the deep sequencing reads are mapped to the precursors. 
+The number of reads falling into an interval 2nt upstream and 5nt downstream of the mature/star sequence is determined.
+]]>
+    </help>
+    <citations>
+        <citation type="doi">10.1093/nar/gkr688</citation>
+        <citation type="doi">10.1002/0471250953.bi1210s36</citation>
+    </citations>
+</tool>