--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/art_454.xml	Thu Jun 11 11:51:06 2015 -0400
@@ -0,0 +1,155 @@
+<tool id="art_454" name="ART 454" version="2014.11.03.0">
+  <description>simulates pyrosequencing data</description>
+  <macros>
+      <import>macros.xml</import>
+  </macros>
+  <expand macro="stdio" />
+  <command><![CDATA[
+art_454 $t
+
+$aln
+$sam
+
+#if $rndSeed and $rndSeed > -1:
+-r $rndSeed
+#end if
+
+#if $c
+-c $c
+#end if
+
+#if $generate.amplicon.use_amplicon == "amplicon_true":
+    #if $generate.choice == "single_end":
+        -A
+    #else:
+        -B
+    #end if
+#end if
+
+$input_seq_file
+output
+
+#if $generate.choice == "single_end":
+    $fold_coverage
+#else:
+    $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>
+        </param>
+        <when value="single_end">
+            <expand macro="amplicon" />
+        </when>
+        <when value="paired_end">
+            <expand macro="frag_len_sd" />
+            <expand macro="amplicon_pair" />
+        </when>
+    </conditional>
+
+
+    <expand macro="sam" />
+    <expand macro="aln" />
+
+    <param type="boolean" label="indicate to simulate reads from the built-in GS FLX Titanium profile (-t)" name="t" truevalue="-t" falsevalue="" optional="true"  />
+    <param label="specify the number of flow cycles by the sequencer [100 for GS-FLX, 200 for GS-FLX Titanium] (-c)" name="c" type="integer" value="100" optional="true" />
+
+    <expand macro="rndSeed" />
+  </inputs>
+  <outputs>
+        <!-- Single End -->
+        <data format="fastq" name="output_fq1_single" from_work_dir="output.fq" label="Simulated of 454 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 454 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 454 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 454 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 454 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 454 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 454 data to $input_seq_file.name">
+            <filter>generate['choice'] != "single_end" and generate['amplicon']['use_amplicon'] == "amplicon_true"</filter>
+        </data>
+  </outputs>
+  <tests>
+      <!--  Single End tests -->
+      <test>
+          <param name="rndSeed" value="42" />
+          <param name="input_seq_file" value="input.fa" />
+          <param name="fold_coverage" value="20" />
+          <param name="choice" value="single_end" />
+          <output name="output_fq1_single" file="art.454.01.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="single_end" />
+          <param name="sam" value="True" />
+          <output name="output_fq1_single" file="art.454.01.fq" />
+          <output name="output_sam" file="art.454.01.sam" lines_diff="2"/>
+      </test>
+      <!-- Paired End tests -->
+      <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="fragment_size" value="105" />
+          <param name="fragment_sd" value="5" />
+          <param name="sam" value="True" />
+          <output name="output_fq1_paired" file="art.454.021.fq" />
+          <output name="output_fq2_paired" file="art.454.022.fq" />
+          <output name="output_sam" file="art.454.02.sam" lines_diff="2"/>
+      </test>
+  </tests>
+  <help><![CDATA[
+Art 454 Pyrosequencing Simulator
+================================
+
+ART_454 is a simulation program to generate sequence read data of Roche 454
+Pyrosequencing sequencers. ART generates reads according to the empirical read
+quality profile and the calibrated error profile of uncall/overcall
+homopolymers from real 454 read 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_454 can generate both single-end and paired-end of 454 sequencing platform.
+Besides for regular genome DNA and cDNA sequencing simulation, art_454 also
+supports amplicon sequencing. The reference sequences can be either DNA or RNA.
+      ]]></help>
+  <expand macro="citation" />
+</tool>
+