--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/art_solid.xml	Thu Jun 11 11:51:06 2015 -0400
@@ -0,0 +1,161 @@
+<tool id="art_solid" name="ART SOLiD" version="2014.11.03.0">
+  <description>simulates SOLiD data</description>
+  <macros>
+      <import>macros.xml</import>
+  </macros>
+  <expand macro="stdio" />
+  <command><![CDATA[
+art_SOLiD
+
+$sam
+
+#if $rndSeed and $rndSeed > -1:
+    -r $rndSeed
+#end if
+
+#if $generate.amplicon.use_amplicon == "amplicon_true":
+    -A
+
+    #if $generate.choice == "single_end":
+    s
+    #else if $generate.choice == "paired_end":
+    p
+    #else:
+    m
+    #end if
+
+#end if
+
+$input_seq_file
+output
+
+#if $generate.choice == "single_end":
+    $generate.LEN_READ
+    $fold_coverage
+#else if $generate.choice == "paired_end":
+    $generate.LEN_READ_F3
+    $generate.LEN_READ_F5
+    $fold_coverage
+    $generate.fragment_size
+    $generate.fragment_sd
+#else:
+    $generate.LEN_READ
+    $fold_coverage
+    $generate.fragment_size
+    $generate.fragment_sd
+#end if
+
+#if $generate.amplicon.use_amplicon == "amplicon_true":
+    #if $generate.choice == "single_end":
+        $generate.amplicon.reads_per_amplicon
+    #else:
+        $generate.amplicon.read_pairs_per_amplicon
+    #end if
+#end if
+]]></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"/>
+
+    <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="paired_end">Mate Pair</option>
+        </param>
+        <when value="single_end">
+            <param name="LEN_READ" type="integer" label="Length of F3/R3 reads" value="100" />
+            <expand macro="amplicon" />
+        </when>
+        <when value="paired_end">
+            <param name="LEN_READ_F3" type="integer" label="Length of F3 reads" value="100" />
+            <param name="LEN_READ_F5" type="integer" label="Length of F5 reads" value="100" />
+            <expand macro="frag_len_sd" />
+            <expand macro="amplicon_pair" />
+        </when>
+        <when value="mate_pair">
+            <param name="LEN_READ" type="integer" label="Length of F3/R3 reads" value="100" />
+            <expand macro="frag_len_sd" />
+            <expand macro="amplicon_pair" />
+        </when>
+    </conditional>
+
+    <expand macro="sam" />
+    <expand macro="rndSeed" />
+
+  </inputs>
+  <outputs>
+
+        <!-- Single End -->
+        <data format="fastq" name="output_fq1_single" from_work_dir="output.fq" label="Simulated of SOLiD 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="output_F3.fq" label="Simulated of SOLiD sequencing of $input_seq_file.name (F3)">
+            <filter>generate['choice'] == "paired_end"</filter>
+        </data>
+        <data format="fastq" name="output_fq2_paired" from_work_dir="output_F5.fq" label="Simulated of SOLiD sequencing of $input_seq_file.name (F5)">
+            <filter>generate['choice'] == "paired_end"</filter>
+        </data>
+
+        <!-- Mate Pair -->
+        <data format="fastq" name="output_fq1_mate" from_work_dir="output_F3.fq" label="Simulated of SOLiD sequencing of $input_seq_file.name (Forward)">
+            <filter>generate['choice'] == "mate_pair"</filter>
+        </data>
+        <data format="fastq" name="output_fq2_mate" from_work_dir="output_R3.fq" label="Simulated of SOLiD sequencing of $input_seq_file.name (Reverse)">
+            <filter>generate['choice'] == "mate_pair"</filter>
+        </data>
+
+        <data format="sam" name="output_sam" from_work_dir="output.sam" label="Mapping of Simulated SOLiD data to $input_seq_file.name">
+            <filter>sam</filter>
+        </data>
+        <!-- todo? map file -->
+  </outputs>
+  <tests>
+      <!--  Single End tests -->
+      <test>
+          <param name="rndSeed" value="42" />
+          <param name="input_seq_file" value="input.fa" />
+          <param name="LEN_READ" value="25" />
+          <param name="fold_coverage" value="10" />
+          <param name="choice" value="single_end" />
+          <param name="sam" value="False" />
+
+          <output name="output_fq1_single" file="art.solid.01.fq" />
+      </test>
+      <test>
+          <param name="rndSeed" value="42" />
+          <param name="input_seq_file" value="input.fa" />
+          <param name="fold_coverage" value="20" />
+          <param name="choice" value="paired_end" />
+          <param name="LEN_READ_F3" value="50" />
+          <param name="LEN_READ_F5" value="50" />
+          <param name="fragment_size" value="75" />
+          <param name="fragment_sd" value="10" />
+          <param name="sam" value="True" />
+
+          <output name="output_fq1_paired" file="art.solid.02_F3.fq" />
+          <output name="output_fq2_paired" file="art.solid.02_F5.fq" />
+          <output name="output_sam" file="art.solid.02.sam" lines_diff="2"/>
+      </test>
+  </tests>
+  <help><![CDATA[
+Art SOLiD Simulator
+===================
+
+ART_SOLiD  is a simulation program to generate sequence read data of SOLiD
+sequencing reads. ART generates reads according to a SOLiD read error profile.
+The built-in error profile is an empiricial error profile summarized from large
+SOLiD sequencing data. ART has been using for testing or benchmarking a variety
+of method or tools for next-generation sequencing data analysis, including read
+alignment, de novo assembly, detection of SNP, CNV, or other structure
+variation.
+
+art_SOLiD can generate both single-end, matepair, and paired-end of SOLiD
+sequencing platform. art_SOLiD also support amplicon sequencing simulation with
+RNA references.
+      ]]></help>
+  <expand macro="citation" />
+</tool>
+