--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/small_rna_clusters.xml	Mon Oct 07 12:51:25 2019 -0400
@@ -0,0 +1,181 @@
+<tool id="small_rna_clusters" name="small_rna_clusters" version="1.0.0">
+  <description></description>
+  <requirements>
+        <requirement type="package" version="0.15.3=py27hda2845c_1">pysam</requirement>
+        <requirement type="package" version="1.6.4=r36h6115d3f_0">r-optparse</requirement>
+        <requirement type="package" version="0.6_28=r36h6115d3f_1002">r-latticeextra</requirement>
+        <requirement type="package" version="2.3=r36h6115d3f_1002">r-gridextra</requirement>
+        <requirement type="package" version="1.4.3=r36h29659fb_0">r-reshape2</requirement>
+        <requirement type="package" version="0.6.6">sambamba</requirement>
+        <requirement type="package" version="1.9=h10a08f8_12">samtools</requirement>
+        <requirement type="package" version="64.2=he1b5a44_1">icu</requirement>
+  </requirements>
+  <stdio>
+      <exit_code range="1:" level="fatal" description="Tool exception" />
+  </stdio>
+  <command detect_errors="exit_code"><![CDATA[
+          #import json
+          #import os
+          #for $file in $inputs
+              sambamba view -t \${GALAXY_SLOTS} -F "not unmapped and sequence_length >= ${minsize} and sequence_length <= ${maxsize}" -f bam '$file' -o '$file.element_identifier' &&
+              samtools index '$file.element_identifier' &&
+          #end for
+
+          python '$__tool_directory__'/small_rna_clusters.py
+              --inputs ${ ' '.join(['"%s"' % x.element_identifier for x in $inputs]) }
+              #set $labels = list()
+              #for $file in $inputs:
+                  $labels.append(str($file.element_identifier))
+              #end for
+              --sample_names ${ ' '.join(['"%s"' % x for x in $labels]) }
+              --minsize $minsize
+              --maxsize $maxsize
+              --outputs '$output_tab'
+              --cluster $cluster
+              --bed '$output_bed'
+              --bed_skipsize $skip_size
+              --bed_skipcounts $skip_counts
+              --bed_skipdensity $skip_density
+              $strandness &&
+
+          Rscript '$__tool_directory__'/small_rna_clusters.r
+              --first_dataframe '$output_tab'
+              --first_plot_method 'Counts'
+              --output_pdf '$output_pdf'
+  ]]></command>
+ <inputs>
+    <param name="inputs" type="data" format="bam" label="Select a alignment files to parse" multiple="true"
+           help="maps from these bam inputs will be collected in a single pdf output" />
+    <param name="minsize" type="integer" label="Minimal size of reads for inclusion in analysis"
+           value="19" help="default value: 19" />
+    <param name="maxsize" type="integer" label="Maximal size of reads for inclusion in analysis"
+           value="29" help="default value: 29" />
+    <param name="first_plot" type="hidden" value="Counts"/>
+    <param name="cluster" type="integer" label="Clustering distance in nucleotides" value="1"
+           help="Sets the distance (in nt) below which reads are clustered to a single median position" />
+    <param name="strandness" argument="--nostrand" type="boolean" truevalue="--nostrand" falsevalue="" checked="false"
+           label="Ignore polarity of reads ?" help="Set if you wish to cluster reads regardless of whether they are forward or reverse"/>
+    <param name="skip_size" type="integer" label="do not report clusters whose size is less than the specified value" value="1"
+           help="Cluster size threshod (in nucleotides) for reporting. Set to 1 (default) reports all clusters, including singlets" />
+    <param name="skip_counts" type="integer" label="do not report cluster with a number of reads lower than the specified value" value="1"
+           help="Number-of-reads threshod (in nucleotides) for cluster reporting. Set to 1 (default) reports all clusters, irrespective of their counts" />
+     <param name="skip_density" type="float" label="do not report cluster with density equal or less than the specified value" value="0"
+           help="Density threshod (in reads per nucleotides) for reporting. Set to 0 (default) reports all cluster densities" />
+ </inputs>
+
+ <outputs>
+    <data format="tabular" name="output_tab" label="Counts Dataframe" />
+    <data format="bed" name="output_bed" label="bed file for clusters" />
+    <data format="pdf" name="output_pdf" label="small RNA maps" />
+</outputs>
+
+    <tests>
+        <test> <!-- 0 -->
+            <param name="inputs" value="input1.bam,input2.bam" ftype="bam" />
+            <param name="cluster" value="500" />
+            <param name="skip_size" value="1" />
+            <param name="strandness" value="false" />
+            <output file="clustering_0.tab" name="output_tab" />
+            <output file="clustering_0.pdf" name="output_pdf" />
+            <output file="bed_0.bed" name="output_bed" />
+        </test>
+        <test> <!-- 1 -->
+            <param name="inputs" value="input1.bam,input2.bam" ftype="bam" />
+            <param name="cluster" value="500" />
+            <param name="skip_size" value="1" />
+            <param name="strandness" value="true" />
+            <output file="clustering_1.tab" name="output_tab" />
+            <output file="clustering_1.pdf" name="output_pdf" />
+            <output file="bed_1.bed" name="output_bed" />
+        </test>
+        <test> <!-- 2 -->
+            <param name="inputs" value="input1.bam,input2.bam" ftype="bam" />
+            <param name="cluster" value="500" />
+            <param name="skip_size" value="1000" />
+            <param name="strandness" value="false" />
+            <output file="clustering_2.tab" name="output_tab" />
+            <output file="clustering_2.pdf" name="output_pdf" />
+            <output file="bed_2.bed" name="output_bed" />
+        </test>
+        <test> <!-- 3 -->
+            <param name="inputs" value="input1.bam,input2.bam" ftype="bam" />
+            <param name="cluster" value="500" />
+            <param name="skip_size" value="1000" />
+            <param name="skip_counts" value="200" />
+            <param name="skip_density" value="0.1" />
+            <param name="strandness" value="false" />
+            <output file="clustering_3.tab" name="output_tab" />
+            <output file="clustering_3.pdf" name="output_pdf" />
+            <output file="bed_3.bed" name="output_bed" />
+        </test>
+        <test> <!-- 4 -->
+            <param name="inputs" value="input1.bam,input2.bam" ftype="bam" />
+            <param name="cluster" value="2000" />
+            <param name="skip_size" value="2000" />
+            <param name="skip_counts" value="100" />
+            <param name="skip_density" value="0.1" />
+            <param name="strandness" value="true" />
+            <output file="clustering_4.tab" name="output_tab" />
+            <output file="clustering_4.pdf" name="output_pdf" />
+            <output file="bed_4.bed" name="output_bed" />
+        </test>
+    </tests>
+<help>
+**What it does**
+
+Clusters of read alignments (provided as bam files) are aggregated along regions of
+*variable* lengths. The Clustering algorithm works as follows:
+
+A read is clustered with the next read on the genomic reference if the two reads are
+separated by *at maximum* the clustering distance (set in nucleotides). If clustered, the
+step is repeated with the following read until clustering fails. A new cluster is then
+searched.
+
+For clustering procedure, one has the possibility to consider the polarity of reads
+(default setting, only forward reads or reverse reads can be clustered, separately), or to
+ignore this polarity.
+
+Clusters of reads are plotted as single bars, their coordinates being the medians of
+the flanking coordinates of the clusters.
+
+In addition, cluster are reported in a bed file. There, clusters can be filtered out upon
+various parameters: cluster size, cluster read number or cluster read density (number of
+reads divided by the length of the cluster).
+
+Note that bed filtering options only affect the number of reported line in the bed file.
+All clusters are shown in the plot. **i.e. the only parameter that affects the number of
+found clusters is the clustering distance.**
+
+**Inputs**
+
+bam alignment files that must be
+
+  - single-read
+  - sorted
+  - mapped to the same reference
+
+.. class:: warningmark
+
+This tools follows a "map-reduce" procedure: multiple inputs, which can be arranged in a
+data collection, are visualised side by side in a single pdf file and are reported in a
+single bed file.
+ 
+**Output**
+
+A pdf file generated by the R package lattice, a dataframe used to plot the clusters, and
+a bed file that reports significant clusters.
+</help>
+
+<citations>
+    <citation type="doi">10.1093/bioinformatics/btp352</citation>
+     <citation type="bibtex">@Book{,
+    title = {Lattice: Multivariate Data Visualization with R},
+    author = {Deepayan Sarkar},
+    publisher = {Springer},
+    address = {New York},
+    year = {2008},
+    note = {ISBN 978-0-387-75968-5},
+    url = {http://lmdvr.r-forge.r-project.org},
+  }</citation>
+</citations>
+</tool>