--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/siRNA_pipeline.xml	Sun Jan 04 02:47:25 2015 -0500
@@ -0,0 +1,221 @@
+<tool id="plant_sirna_pipeline_v1" name="siRNA_pipeline" veision="1.0.0">
+  <description>Program for plant siRNA analysis (rawdata preprocess -> genome alignment -> non-coding annotate ->  siRNA analysis)</description>
+
+  <requirements>
+    <requirement type="set_environment">SCRIPT_PATH</requirement>
+    <requirement type="package" version="0.12.7">bowtie</requirement>
+    <requirement type="package" version="3.0.1">R</requirement>
+	<requirement type="package" version="0.0.13">fastx_toolkit </requirement>
+	<requirement type="package" version="1.96">threads</requirement>
+	<requirement type="package" version="1.06">Parallel-ForkManager</requirement>
+	<requirement type="package" version="2.59">SVG</requirement>
+	<requirement type="package" version="1.4_001">Boost-Graph</requirement>
+  </requirements>
+
+  <command interpreter="perl">siRNA_pipeline.pl 
+   ## Change this to accommodate the number of threads you have available.
+        -t \${GALAXY_SLOTS:-4}
+
+	-path \$SCRIPT_PATH
+
+    #for $j, $s in enumerate( $series )
+    ##rank_of_series=$j
+    -i ${s.input}
+    -tag ${s.tag}
+    #end for
+
+      ## prepare bowtie index
+      #set index_path = ''
+      #if str($reference_genome.source) == "history":
+          #set index_path = $reference_genome.own_file
+		-g  $index_path 
+	  #else:
+          #set index_path = $reference_genome.index.fields.path
+		-g ${index_path}.fa -idx $index_path 
+	  #end if
+
+
+	  ## prepare Rfam bowtie index
+	  #set rfam_index_path = ''
+	  #if str($reference_rfam.source) == "history":
+		  #set rfam_index_path = $reference_rfam.own_file
+		-rfam $rfam_index_path -v $v 
+	  #else:
+		  #set rfam_index_path = $reference_rfam.index.fields.path
+		-rfam ${rfam_index_path}.fa -idx2 $rfam_index_path -v $v 
+	  #end if
+
+
+
+   ## Do or not annotate siRNAs by function
+    #if $params.function_anno == "yes":
+
+      ## prepare bowtie index
+      #set nat_path = ''
+      #if str($params.nat_file.source) == "history":
+          #set nat_path = $params.nat_file.nat
+
+	  #else:
+          #set nat_path = $params.nat_file.index.fields.path
+	  #end if
+
+      ## prepare bowtie index
+      #set repeat_path = ''
+      #if str($params.repeat_file.source) == "history":
+          #set repeat_path = $params.repeat_file.repeat
+
+	  #else:
+          #set repeat_path = $params.repeat_file.index.fields.path
+	  #end if
+
+
+	 -nat $nat_path -repeat $repeat_path
+	#end if
+   
+   ## Do or not DEG
+    #if $degseq.degseq_analysis == "yes" :
+    -deg $degseq.deg
+    #end if
+
+  -format $format -phred $phred -f $gff -mis $mis -a $a -n $mapnt -d $d -p $p -l $l  -cen $cen -span $span > run.log
+
+  </command>
+
+  <inputs>
+
+   <repeat name="series" title="Raw sequence data file">
+     <param name="input" type="data" label="Raw data file"/>
+     <param name="tag" type="text" data_ref="input" label="Sample name of raw data"/>
+   </repeat>
+
+	<param name="format" type="select" label="raw data format" multiple="false">
+	  <option value="fastq">Raw data is fastq. format</option>
+	  <option value="fasta">Raw data is fasta. format</option>
+	</param>
+	
+	<param name="phred" type="select" label="input quals are Phred+64 or Phred+33" multiple="false">
+	  <option value="64">Phred+64</option>
+	  <option value="33" selected="true">Phred+33</option>
+	</param>
+
+        <conditional name="reference_genome">
+          <param name="source" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
+            <option value="indexed">Use a built-in index</option>
+            <option value="history">Use one from the history</option>
+          </param>
+          <when value="indexed">
+            <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
+              <options from_data_table="bowtie_indexes">
+                <filter type="sort_by" column="2"/>
+                <validator type="no_options" message="No indexes are available for the selected input dataset"/>
+              </options>
+            </param>
+          </when>
+          <when value="history">
+            <param name="own_file" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
+          </when>
+        </conditional>	<!--param type="data" name="index" label="genome sequence bowtie index"/-->
+
+	        <conditional name="reference_rfam">
+          <param name="source" type="select" label="Will you select a rfam reference  from your history or use a built-in index?" help="Built-ins were indexed using default options">
+            <option value="indexed">Use a built-in index</option>
+            <option value="history">Use one from the history</option>
+          </param>
+          <when value="indexed">
+            <param name="index" type="select" label="Select a non-coding reference " help="If your rfam of interest is not listed, contact the Galaxy team">
+              <options from_data_table="rfam_bowtie_indexes">
+                <filter type="sort_by" column="2"/>
+                <validator type="no_options" message="No indexes are available for the selected input dataset"/>
+              </options>
+            </param>
+          </when>
+          <when value="history">
+            <param name="own_file" type="data" format="fasta" metadata_name="dbkey" label="Select the reference" />
+          </when>
+        </conditional>
+
+	<param name="gff" type="data" label="gff file" />
+	<param name="mis" type="integer" value="0" label="number of allowed mismatches when mapping reads to genome" />
+	<param name="v" type="integer" value="0" label="report end-to-end hits less than v mismatches for non-coding alignment"/>
+	<param name="a" type="text" value="TGGAATTCTCGGGTGCCAAGG" label="3' adapter sequence" />
+	<param name="mapnt" type="integer" value="25" label="a read is allowed to map up to this number of positions in the genome" />
+	<param name="d" type="integer" value="100" label="distance of tag to merged a cluster" />
+
+	<param name="p" type="select" label="siRNA cluster identify method" multiple="false">
+	  <option value="F">conventional</option>
+	  <option value="T">NIBLES</option>
+	</param>
+	<param name="l" type="integer" value="1000" label="the length of the upstream and downstream,used in position annotate" />
+
+
+	<conditional name="params">
+		<param name="function_anno" type="select" label="Do or not annotate siRNAs by function">
+		  <option value="no" selected="true">no</option>
+		  <option value="yes">yes</option>
+		 </param>
+		 <when value="yes">
+
+
+        <conditional name="nat_file">
+          <param name="source" type="select" label="Will you select a atural antisense transcripts file from your history ?" help="down load from ***">
+            <option value="indexed">Use a built-in file</option>
+            <option value="history">Use one from the history</option>
+          </param>
+          <when value="indexed">
+            <param name="index" type="select" label="Select a atural antisense transcripts file" help="If your species of interest is not listed, contact the Galaxy team">
+              <options from_data_table="nat_annotate">
+                <filter type="sort_by" column="2"/>
+                <validator type="no_options" message="No files are available for the selected input dataset"/>
+              </options>
+            </param>
+          </when>
+          <when value="history">
+            <param name="nat" type="data" format="txt" metadata_name="dbkey" label="atural antisense transcripts file" />
+		  </when>
+        </conditional>	<!--param type="data" name="index" label="genome sequence bowtie index"/-->
+
+        <conditional name="repeat_file">
+          <param name="source" type="select" label="Will you select a repeat information file from your history ?" help="down load from ***">
+            <option value="indexed">Use a built-in file</option>
+            <option value="history">Use one from the history</option>
+          </param>
+          <when value="indexed">
+            <param name="index" type="select" label="Select a repeat information file" help="If your species of interest is not listed, contact the Galaxy team">
+              <options from_data_table="repeat_annotate">
+                <filter type="sort_by" column="2"/>
+                <validator type="no_options" message="No files are available for the selected input dataset"/>
+              </options>
+            </param>
+          </when>
+          <when value="history">
+			<param name="repeat" type="data" metadata_name="dbkey" label="repeat information file out of Repeatmasker" />
+		  </when>
+        </conditional>	<!--param type="data" name="index" label="genome sequence bowtie index"/-->
+		 </when>
+    </conditional> <!-- params -->
+	
+	<param name="cen" type="data" label="centromere file input" />
+	<param name="span" type="integer" value="50000" label="plot span" />
+	
+    <conditional name="degseq">
+       <param name="degseq_analysis" type="select" label="Do or not identify Difference Expression Clusters">
+		  <option value="no" selected="true">no</option>
+		  <option value="yes">yes</option>
+       </param>
+       <when value="yes">
+			<param name="deg" type="data" label="file config of de sample" />
+        </when>
+    </conditional>
+    
+  </inputs>
+
+  <outputs>
+   <data format="txt" name="siRNA cluster" from_work_dir="cluster_runs/total.result" label="${tool.name} on ${on_string}: siRNA cluster"/>
+   <data format="html" name="analysis result" from_work_dir="cluster_runs/result.html" label="${tool.name} on ${on_string}: analysis result"/>
+
+  </outputs>
+
+ <help>
+
+ </help>
+ </tool>