--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/art_illumina.xml	Thu Jun 11 11:51:06 2015 -0400
@@ -0,0 +1,158 @@
+<tool id="art_illumina" name="ART Illumina" version="2014.11.03.0">
+  <description>simulates sequencing data</description>
+  <macros>
+      <import>macros.xml</import>
+  </macros>
+  <expand macro="stdio" />
+  <command><![CDATA[
+art_illumina
+
+#if str($sam) == "-s":
+    --samout
+#end if
+
+#if not str($aln) == "-a":
+    --noALN
+#end if
+
+#if str($generate.choice) == "paired_end":
+    --paired
+    --mflen $generate.fragment_size
+    --sdev $generate.fragment_sd
+#else if str($generate.choice) == "mate_pair":
+    --matepair
+    --mflen $generate.fragment_size
+    --sdev $generate.fragment_sd
+#end if
+
+--in $input_seq_file
+--len $read_length
+--fcov $fold_coverage
+
+$amplicon
+
+--insRate $insRate
+--insRate2 $insRate2
+--delRate $delRate
+--delRate2 $delRate2
+
+#if $rndSeed and $rndSeed > -1:
+    --rndSeed $rndSeed
+#end if
+
+--out output;
+]]></command>
+  <inputs>
+    <param label="DNA/RNA reference sequence" format="fasta" name="input_seq_file" type="data"/>
+    <param label="the fold of read coverage over the reference sequences" name="fold_coverage" type="integer" value="20"/>
+    <param label="length of reads to be simulated" name="read_length" type="integer" value="100"/>
+    <param label="amplicon sequencing simulation" name="amplicon" type="boolean" truevalue="--amplicon" falsevalue="" />
+
+    <conditional name="generate">
+        <param name="choice" type="select" label="Type of data to generate">
+            <option value="single_end">Single-End</option>
+            <option value="paired_end">Paired-End</option>
+            <option value="mate_pair">Mate-Pair</option>
+        </param>
+        <when value="single_end">
+        </when>
+        <when value="paired_end">
+            <expand macro="frag_len_sd" />
+        </when>
+        <when value="mate_pair">
+            <expand macro="frag_len_sd" />
+        </when>
+    </conditional>
+
+    <expand macro="aln" />
+    <expand macro="sam" />
+
+    <param label="the first-read insertion rate" help="(--insRate)" name="insRate" type="float" value="0.00009" />
+    <param label="the second-read insertion rate" help="(--insRate2)" name="insRate2" type="float" value="0.00015" />
+    <param label="the first-read deletion rate" help="(--delRate)" name="delRate" type="float" value="0.00011" />
+    <param label="the second-read deletion rate" help="(--delRate2)" name="delRate2" type="float" value="0.00023" />
+
+    <expand macro="rndSeed" />
+    <!-- todo: id, errfree, masN, qShift(2), sepProf -->
+  </inputs>
+  <outputs>
+        <!-- Single End -->
+        <data format="fastq" name="output_fq1_single" from_work_dir="output.fq" label="Simulated of Illumina sequencing of $input_seq_file.name">
+            <filter>generate['choice'] == "single_end"</filter>
+        </data>
+
+        <!-- Paired End -->
+        <data format="fastq" name="output_fq1_paired" from_work_dir="output1.fq" label="Simulated of Illumina sequencing of $input_seq_file.name (Forward)">
+            <filter>generate['choice'] != "single_end"</filter>
+        </data>
+        <data format="fastq" name="output_fq2_paired" from_work_dir="output2.fq" label="Simulated of Illumina sequencing of $input_seq_file.name (Reverse)">
+            <filter>generate['choice'] != "single_end"</filter>
+        </data>
+        <data format="sam" name="output_sam" from_work_dir="output.sam" label="Mapping of Simulated Illumina data to $input_seq_file.name">
+            <filter>sam</filter>
+        </data>
+
+        <!-- Single End -->
+        <data format="aln" name="output_aln1_single" from_work_dir="output.aln" label="Alignment of Simulated Illumina data to $input_seq_file.name">
+            <filter>aln and generate['choice'] == "single_end"</filter>
+        </data>
+
+        <!-- paired end -->
+        <data format="aln" name="output_aln1_paired" from_work_dir="output1.aln" label="Alignment of Simulated Illumina data to $input_seq_file.name">
+            <filter>aln and generate['choice'] != "single_end"</filter>
+        </data>
+        <data format="aln" name="output_aln2_paired" from_work_dir="output2.aln" label="Alignment of Simulated Illumina data to $input_seq_file.name">
+            <filter>aln and generate['choice'] != "single_end"</filter>
+        </data>
+  </outputs>
+  <tests>
+      <test>
+          <param name="rndSeed" value="42" />
+          <param name="input_seq_file" value="input.fa" />
+          <param name="fold_coverage" value="20" />
+          <param name="read_length" value="200" />
+          <param name="choice" value="single_end" />
+          <param name="aln" value="True" />
+          <param name="sam" value="True" />
+
+          <output name="output_fq1_single" file="art.illumina.01.fq" />
+          <output name="output_aln1_single" file="art.illumina.01.aln" lines_diff="2"/>
+          <output name="output_sam" file="art.illumina.01.sam" lines_diff="2"/>
+      </test>
+      <test>
+          <param name="rndSeed" value="42" />
+          <param name="input_seq_file" value="input.fa" />
+          <param name="fold_coverage" value="20" />
+          <param name="read_length" value="200" />
+          <param name="choice" value="paired_end" />
+          <param name="fragment_size" value="300" />
+          <param name="fragment_sd" value="10" />
+          <param name="aln" value="True" />
+          <param name="sam" value="True" />
+
+          <output name="output_fq1_paired" file="art.illumina.021.fq" />
+          <output name="output_fq2_paired" file="art.illumina.022.fq" />
+          <output name="output_aln1_paired" file="art.illumina.021.aln" lines_diff="2"/>
+          <output name="output_aln2_paired" file="art.illumina.022.aln" lines_diff="2"/>
+          <output name="output_sam" file="art.illumina.02.sam" lines_diff="2"/>
+      </test>
+  </tests>
+  <help><![CDATA[
+Art Illumina Simulator
+======================
+
+ART (art_Illumina Q version) is a simulation program to generate sequence read
+data of Illumina sequencers. ART generates reads according to the empirical
+read quality profile summarized from large real read data. ART has been using
+for testing or benchmarking a variety of methods or tools for next-generation
+sequencing data analysis, including read alignment, de novo assembly, detection
+of SNP, CNV, or other structure variation.
+
+art_Illumina can generate single-end, paired-end,  mate-pair reads, and
+amplicon sequencing simulation of Illumina sequencing platform. Its outputs
+include FASTQ read, ALN and/or SAM alignment files.
+
+      ]]></help>
+  <expand macro="citation" />
+</tool>
+