# HG changeset patch
# User big-tiandm
# Date 1414573418 14400
# Node ID b75750b21aa445f35d350524fa8ea814e20b9265
# Parent  7d12d9b130bcd9bbfa3bbc8f32fab42ee0c45b36
Deleted selected files

diff -r 7d12d9b130bc -r b75750b21aa4 siRNA.xml
--- a/siRNA.xml	Wed Oct 29 05:03:28 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,106 +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>
-	<requirement type="package" version="1.5.0">libx11</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
-
-   ## Do or not annotate siRNAs by function
-    #if $params.function_anno == "yes":
-     -nat $params.nat -repeat $params.repeat
-	#end if
-   
-   ## Do or not DEG
-    #if $degseq.degseq_analysis == "yes" :
-    -deg $degseq.deg
-    #end if
-
-  -format $format -g $genome -f $gff -mis $mis -rfam $rfam -v $v -a $a -n $mapnt -d $d -p $p -l $l  -cen $cen -span $span > run.log
-
-  </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" />
-	
-    <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 ${on_string}: analysis result"/>
-
-  </outputs>
-
- <help>
-
- </help>
- </tool>
diff -r 7d12d9b130bc -r b75750b21aa4 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Oct 29 05:03:28 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,83 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="fastx_toolkit" version="0.0.13">
-        <repository changeset_revision="ec66ae4c269b" name="package_fastx_toolkit_0_0_13" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="bowtie" version="0.12.7">
-        <repository changeset_revision="9f9f38617a98" name="package_bowtie_0_12_7" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-    <set_environment version="1.0">
-        <environment_variable action="set_to" name="SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
-    </set_environment>
-    <package name="R" version="2.11.0">
-        <repository changeset_revision="8d0a55bf7aaf" name="package_r_2_11_0" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
-		<install version="1.0">
-		   <actions>
-		      <action type="shell_command">R CMD BATCH $REPOSITORY_INSTALL_DIR/install_DEG.R </action>
-		   </actions>
-		</install>
-    </package>
-
-	<package name="libx11" version="1.5.0">
-		<repositoty name="package_libx11_1_5_0" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
-	</package>
-
-
-	<package name="threads" version="1.96">
-	   <install version="1.0">
-		   <actions>
-		     <action type="download_by_url">http://www.cpan.org/authors/id/J/JD/JDHEDDEN/threads-1.96.tar.gz</action>
-			 <action type="shell_command">perl Makefile.PL PREFIX=$INSTALL_DIR </action>
-			 <action type="shell_command">make</action>
-			 <action type="shell_command">make install</action>
-			 <action type="set_environment">
-			   <environment_variable action="prepend_to" name="PERL5LIB">$INSTALL_DIR/lib</environment_variable>
-			 </action>
-		   </actions>
-	   </install>
-	</package>
-
-
-	<package name="Parallel-ForkManager" version="1.06">
-	   <install version="1.0">
-		   <actions>
-		     <action type="download_by_url">http://www.cpan.org/authors/id/S/SZ/SZABGAB/Parallel-ForkManager-1.06.tar.gz</action>
-			 <action type="shell_command">perl Makefile.PL PREFIX=$INSTALL_DIR </action>
-			 <action type="shell_command">make</action>
-			 <action type="shell_command">make install</action>
-			 <action type="set_environment">
-			   <environment_variable action="prepend_to" name="PERL5LIB">$INSTALL_DIR/lib</environment_variable>
-			 </action>
-		   </actions>
-	   </install>
-	</package>
-
-	<package name="SVG" version="2.59">
-	   <install version="1.0">
-		   <actions>
-		     <action type="download_by_url">http://www.cpan.org/authors/id/S/SZ/SZABGAB/SVG-2.59.tar.gz</action>
-			 <action type="shell_command">perl Makefile.PL PREFIX=$INSTALL_DIR </action>
-			 <action type="shell_command">make</action>
-			 <action type="shell_command">make install</action>
-			 <action type="set_environment">
-			   <environment_variable action="prepend_to" name="PERL5LIB">$INSTALL_DIR/lib</environment_variable>
-			 </action>
-		   </actions>
-	   </install>
-	</package>
-
-	<package name="Boost-Graph" version="1.4">
-	   <install version="1.0">
-		   <actions>
-		     <action type="download_by_url">http://www.cpan.org/authors/id/D/DB/DBURDICK/BoostGraph/Boost-Graph-1.4.tar.gz</action>
-			 <action type="shell_command">perl Makefile.PL PREFIX=$INSTALL_DIR </action>
-			 <action type="shell_command">make</action>
-			 <action type="shell_command">make install</action>
-			 <action type="set_environment">
-			   <environment_variable action="prepend_to" name="PERL5LIB">$INSTALL_DIR/lib</environment_variable>
-			 </action>
-		   </actions>
-	   </install>
-	</package>
-
-</tool_dependency>