# HG changeset patch
# User big-tiandm
# Date 1414118792 14400
# Node ID 6aa0e8d63b17589a328d472c1b1190c8af1af686
# Parent  ccabcc236bb340139938eef37bac28d0566d4a48
Deleted selected files

diff -r ccabcc236bb3 -r 6aa0e8d63b17 siRNA.xml
--- a/siRNA.xml	Thu Oct 23 22:46:25 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,90 +0,0 @@
-<tool id="plant_sirna_v1" name="siRNA" veision="1.0.0">
-  <description>tool for plant siRNA analisis</description>
-
-  <requirements>
-    <requirement type="set_environment">SCRIPT_PATH</requirement>
-    <requirement type="package" version="0.12.7">bowtie</requirement>
-    <requirement type="package" version="2.11.0">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">Boost-Graph</requirement>
-  </requirements>
-
-  <command interpreter="perl">siRNA.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
-
-  -format $format -g $genome -f $gff -mis $mis -rfam $rfam -v $v -a $a -n $mapnt -d $d -p $p -l $l  -deg $deg -cen $cen -span $span
-
-   ## Do or not annotate siRNAs by function
-    #if $params.function_anno == "yes":
-     -nat $params.nat -repeat $params.repeat
-	#end if
-
-  </command>
-
-  <inputs>
-
-   <repeat name="series" title="Series">
-     <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" lable="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="genome"  type="data" label="genome sequence fasta file"/>
-	<!--param type="data" name="index" label="genome sequence bowtie index"/-->
-	<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="rfam" type="data" label="rfam sequence file" />
-	<param name="v" type="integer" value="0" label="report end-to-end hits less than v mismatches"/>
-	<param name="a" type="text" value="ATCTCGTATG" 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" lable="cluster 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">
-			<param name="nat" type="data" label="atural antisense transcripts file" />
-			<param name="repeat" type="data" label="repeat information file out of Repeatmasker" />
-		 </when>
-    </conditional> <!-- params -->
-	
-	<param name="cen" type="data" label="centromere file input" />
-	<param name="span" type="integer" value="50000" label="plot span" />
-	<param name="deg" type="data" label="file config of de sample" />
-  </inputs>
-
-  <outputs>
-   <data format="txt" name="siRNA cluster" from_work_dir="./total.result"/>
-   <data format="txt" name="analysis result" from_work_dir="./result.html"/>
-
-  </outputs>
-
- <help>
-
- </help>
- </tool>