# HG changeset patch
# User big-tiandm
# Date 1417760926 18000
# Node ID 8b8c356e6db507f5a34aa4f04f31b80f67e9d135
# Parent  3202911efdaef87f7fa8259e760e7743a2167994
Uploaded

diff -r 3202911efdae -r 8b8c356e6db5 miRPlant.xml
--- a/miRPlant.xml	Fri Dec 05 01:14:28 2014 -0500
+++ b/miRPlant.xml	Fri Dec 05 01:28:46 2014 -0500
@@ -91,7 +91,7 @@
 		<param name="annotate_rfam" type="select" label="annotate rfam nocoding RNAs(excluding miRNA)">
 		  <option value="yes" selected="true">yes</option>
 		  <option value="no">no</option>
-		 </param>
+		</param>
 		 <when value="yes">
 			<!--param name="rfam" type="data" label="rfam sequence file" /-->
 			<conditional name="reference_rfam">
@@ -114,19 +114,14 @@
 
 			<param name="v" type="integer" value="0" label="report end-to-end hits less than v mismatches for rfam mapping"/>
 
-			<conditional name="rfamresult">
-				<param name="delet_rfam" type="select" label="delet rfam mapped reads">
-				  <option value="yes" selected="true">yes</option>
-				  <option value="no">no</option>
-				 </param>
-			</conditional> <!-- params -->
-		 
-		 
+			<param name="delet_rfam" type="select" label="delet rfam mapped reads">
+			  <option value="yes" selected="true">yes</option>
+			  <option value="no">no</option>
+			</param>
 		 </when>
-    </conditional> <!-- params -->
+    </conditional> 
 
 
-	<!--param name="input" format="tabular"  type="data" label="input config file" /-->
 	
 	<param name="format" type="select" lable="raw data format" multiple="false">
 	  <option value="fastq">Raw data is fastq. format</option>
@@ -138,68 +133,6 @@
 	  <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="params">
-		<param name="known_microRNA" type="select" label="Analysis known microRNAs(eg. from mirbase)">
-		  <option value="yes" selected="true">yes</option>
-		  <option value="no">no</option>
-		 </param>
-		 <when value="yes">
-			<param name="mat" type="data" label="mature microRNA sequence file" />
-			<param name="pre" type="data" label="precursor microRNA sequence fie" />
-		 </when>
-    </conditional> <!-- params -->
-
-	<conditional name="params">
-		<param name="annotate_rfam" type="select" label="annotate rfam nocoding RNAs(excluding miRNA)">
-		  <option value="yes" selected="true">yes</option>
-		  <option value="no">no</option>
-		 </param>
-		 <when value="yes">
-			<!--param name="rfam" type="data" label="rfam sequence file" /-->
-		 <when value="yes">
-			<!--param name="rfam" type="data" label="rfam sequence file" /-->
-			<conditional name="reference_rfam">
-			  <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" help="If your reference 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="v" type="integer" value="0" label="report end-to-end hits less than v mismatches for rfam mapping"/>
-		 </when>
-    </conditional> <!-- params -->
-
-	<!--param type="data" name="idx2" label="rfam sequence bowtie index " -->
 	<param name="a" type="text" value="ATCTCGTATG" label="3' adapter sequence" />
 	<param name="mapnt" type="integer" value="8" label="minimum adapter map nts" />
 	<param name="min" type="integer" value="19" label="minimum microRNA length" />
diff -r 3202911efdae -r 8b8c356e6db5 microRNA.xml
--- a/microRNA.xml	Fri Dec 05 01:14:28 2014 -0500
+++ b/microRNA.xml	Fri Dec 05 01:28:46 2014 -0500
@@ -1,4 +1,4 @@
-<tool id="micrornas" name="microRNA" veision="1.0.0">
+<tool id="micrornas_v1" name="microRNA" veision="1.0.0">
   <description>Plant microRNA analysis </description>
 
   <requirements>
diff -r 3202911efdae -r 8b8c356e6db5 preProcess.xml
--- a/preProcess.xml	Fri Dec 05 01:14:28 2014 -0500
+++ b/preProcess.xml	Fri Dec 05 01:28:46 2014 -0500
@@ -101,8 +101,6 @@
 		 </param>
 		 <when value="yes">
 			<!--param name="rfam" type="data" label="rfam sequence file" /-->
-		 <when value="yes">
-			<!--param name="rfam" type="data" label="rfam sequence file" /-->
 			<conditional name="reference_rfam">
 			  <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>
@@ -123,7 +121,9 @@
 
 			<param name="v" type="integer" value="0" label="report end-to-end hits less than v mismatches for rfam mapping"/>
 		 </when>
-    </conditional> <!-- params -->
+    </conditional> 
+
+
 
   </inputs>