--- a/discosnp_pp.xml	Fri Oct 20 03:15:43 2017 -0400
+++ b/discosnp_pp.xml	Fri Nov 24 12:49:33 2017 -0500
@@ -1,12 +1,10 @@
 <?xml version='1.0' encoding='utf-8'?>
-<tool profile="16.04" id="discosnp_pp" name="DiscoSnp++" version="2.2.10">
+<tool profile="16.04" id="discosnp_pp" name="DiscoSnp++" version="@DISCOSNP_VERSION@">
     <description>is an efficient tool for detecting SNPs without a reference genome.</description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <requirements>
-        <requirement type="package" version="2.2.10">discosnp</requirement>
-    </requirements>
+    <expand macro="discosnp_requirements" />
     <command><![CDATA[
         ## simple option
         #if str( $input_type_options.input_type) == "single"
@@ -21,28 +19,14 @@
         #end if
 
         #if str($VCF_option.mapping) == 'reference'
-            #set $reference_file = str($VCF_option.G) + "." + $VCF_option.G.ext
+            #set $reference_file = os.path.basename(str($VCF_option.G)) + "." + $VCF_option.G.ext
             ln -sf '${VCF_option.G}' '${reference_file}' &&
         #end if
 
         run_discoSnp++.sh
-        -r input.lst
-        -b ${b}
-        -D ${D}
-        -P ${P}
-        ${low_complexity}
-        -k ${k}
+        @discosnp_inputs@
         ${t}
         ${T}
-
-        #if str($coverage_options_type.coverage_options) == 'auto'
-            -c auto
-        #else
-            -c '${coverage_options_type.c}'
-        #end if
-        -C ${C}
-        -d ${d}
-
         #if str($VCF_option.mapping) == 'reference'
             -G '${reference_file}'
             -M ${VCF_option.M}
@@ -53,23 +37,8 @@
 
   <inputs>
 
-      <conditional name="input_type_options">
-          <param name="input_type" type="select" label="Input options">
-              <option value="single">Single end reads</option>
-              <option value="paired">Paired end reads</option>
-              <option value="mix">Both single and paired reads</option>
-          </param>
-          <when value="single">
-              <param name='list_reads' argument="-r" format="fasta,fastq" type="data" multiple="true" label="Single read files" />
-          </when>
-          <when value="paired">
-              <param name='list_paired_reads' argument="-r" format="fasta,fastq" type="data_collection" collection_type="list:paired" multiple='true' label="List of paired read files" />
-          </when>
-          <when value="mix">
-              <param name='list_reads' argument="-r" format="fasta,fastq" type="data" multiple="true" label="Single read files" />
-              <param name='list_paired_reads' argument="-r" format="fasta,fastq" type="data_collection" collection_type="list:paired" multiple='true' label="List of paired read files"/>
-          </when>
-      </conditional>
+
+      <expand macro="discosnp_inputs" />
 
       <param argument="-b" type="select" label="Branching strategy">
           <option value="0">variants for which any of the two paths is branching are discarded</option>
@@ -77,29 +46,11 @@
           <option value="2">No limitation on branching</option>
       </param>
 
-      <param argument="-D" type="integer" label="Deletion size" value="0" help="If different of 0, discoSnp++ will search for deletions of size from 1 to D included"/>
-      <param argument="-P" type="integer" label="Maximum SNPs per bubble" value="1" help="discoSnp++ will search up to P SNPs in a unique bubble"/>
-      <param name="low_complexity" type="boolean" checked="false" truevalue="-l" falsevalue="" label="Remove low complexity bubbles" />
-      <param argument="-k" type="integer" label="Size of kmers" value="31" />
+      <expand macro="discosnp_options" />
 
       <param argument="-t" type="boolean" checked="false" truevalue="-t" falsevalue="" label="Extends each polymorphism with left and right unitigs" />
       <param argument="-T" type="boolean" checked="false" truevalue="-T" falsevalue="" label="Extends each polymorphism with left and right contigs" />
 
-
-      <conditional name="coverage_options_type" >
-          <param name="coverage_options" type="select" label="Coverage option">
-              <option value="auto"></option>
-              <option value="custom"></option>
-          </param>
-          <when value="auto" />
-          <when value="custom">
-              <param argument="-c" type="text" label="Minimal coverage per read set" value="4" help="e.g. 4 / 4,5,17 / 4,auto,auto"/>
-          </when>
-      </conditional>
-
-      <param argument="-C" type="integer" label="Maximal coverage per read set" value="2147483647" help="default value = 2^31-1" />
-      <param argument="-d" type="integer" label="Max number of errors per read" value="1" help="Max number of errors per read" />
-
       <conditional name="VCF_option" >
           <param name="mapping" type="select" label="VCF option">
               <option value="default">Do not use reference genome</option>
@@ -158,42 +109,17 @@
 **Description**
 
 Software discoSnp is designed for discovering Single Nucleotide Polymorphism (SNP) from raw set(s) of reads obtained with Next Generation Sequencers (NGS).
+
 Note that number of input read sets is not constrained, it can be one, two, or more. Note also that no other data as reference genome or annotations are needed.
+
 The software is composed by two modules. First module, kissnp2, detects SNPs from read sets. A second module, kissreads, enhance the kissnp2 results by computing per read set  and for each found SNP i/ its mean read coverage and ii/ the (phred) quality of reads generating the polymorphism.
 
 Note that from release of DiscoSnp++-2.0.6, the tool also detects close SNPs and indels.
 
--------
-
-.. class:: warningmark
-
-**Input parameters**
-
--Sequences files in fasta or fastq each allele will be counted in each file individually
-
--Use collections: data list and/or data list paired
-
--Fasta sequence of a genome if case of you are willing to map the sequence extension on a reference in order to get a compliant VCF
-
--------
-
-.. class:: warningmark
-
-**Ouput parameters**
-
--VCF file with coordinates on the higher branch sequences or on a reference genome if provided
-
--Fasta file with sequence extensions around the SNP.
-
-
--------
-
-**Web site**
-
-https://colibread.inria.fr/software/discosnp/
+@discosnp_help@
 
   ]]></help>
     <expand macro="citations">
-        <citation type="doi">10.1093/nar/gku1187</citation>
+        <expand macro="discosnp_citation" />
     </expand>
 </tool>