--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/discosnp_RAD.xml	Fri Nov 24 12:48:46 2017 -0500
@@ -0,0 +1,86 @@
+<?xml version='1.0' encoding='utf-8'?>
+<tool profile="16.04" id="discosnp_rad" name="DiscoSnpRAD" version="@DISCOSNP_VERSION@">
+    <description>discovering polymorphism from raw unassembled RADSeq NGS reads.</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="discosnp_requirements" />
+    <command><![CDATA[
+        ## simple option
+        #if str( $input_type_options.input_type) == "single"
+            @discosnp_single_reads@
+        ## paired option
+        #else if str( $input_type_options.input_type) == "paired"
+            @discosnp_paired_reads@
+        ## mix option
+        #else
+            @discosnp_single_reads@
+            @discosnp_paired_reads@
+        #end if
+
+        ## get the absolute path for short_reads_connector
+        CONNECTOR_PATH=`which short_read_connector.sh` &&
+        CONNECTOR_DIR=`dirname \$CONNECTOR_PATH` &&
+
+        run_discoSnpRad.sh
+        @discosnp_inputs@
+        -S "\$CONNECTOR_DIR"
+        -a ${a}
+
+  ]]></command>
+
+  <inputs>
+
+      <expand macro="discosnp_inputs" />
+
+      <param argument="-b" type="select" label="Branching strategy">
+          <option value="1">forbid SNPs for wich the two paths are branching</option>
+          <option value="2">No limitation on branching</option>
+      </param>
+
+      <param argument="-a" type="integer" label="Maximal size of ambiguity of INDELs" value="20" help="INDELS whose ambiguity is higher than this value are not output"/>
+
+      <expand macro="discosnp_options" />
+
+  </inputs>
+
+  <outputs>
+      <data name="vcf" from_work_dir="*_coherent_sorted_with_clusters.vcf" format="vcf" label="VCF with ${tool.name} on $on_string"/>
+      <data name="fasta" from_work_dir="discoRad_*_coherent.fa" format="fasta" label="Fasta with ${tool.name} on $on_string"/>
+  </outputs>
+
+  <tests>
+      <test>
+          <conditional name="input_type_options">
+              <param name="input_type" value="single"/>
+              <param name="list_reads" value="discosnpRAD/loci_reads" ftype="fasta" />
+          </conditional>
+          <param name="D" value="0"/>
+          <param name="P" value="4"/>
+          <param name="k" value="31"/>
+          <param name="b" value="2"/>
+          <output name="fasta" file="discosnpRAD/fasta.fa"/>
+          <output name="vcf" file="discosnpRAD/vcf_file.vcf" compare="diff" lines_diff="2"/>
+      </test>
+  </tests>
+
+  <help><![CDATA[
+
+**Description**
+
+Software discoSnp is designed for discovering Single Nucleotide Polymorphism (SNP) from raw set(s) of reads obtained with Next Generation Sequencers (NGS).
+
+DiscoSnpRad uses options specific to RAD-Seq: branching strategy, kind of extensions, abundance threshold, and kind of bubbles to be found.
+
+Moreover, it clusters variants per locus by calling the `discoRAD_finalization.sh` pipeline. Cluster information is  reported in the final provided VCF file.
+
+Note that from release of DiscoSnp++-2.0.6, the tool also detects close SNPs and indels.
+
+@discosnp_help@
+
+
+  ]]></help>
+    <expand macro="citations">
+        <expand macro="discosnp_citation" />
+    </expand>
+</tool>