diff blockclust.xml @ 14:0fbc8cdc1cd0 draft

Uploaded

--- a/blockclust.xml	Mon Oct 28 11:26:22 2013 -0400
+++ b/blockclust.xml	Wed Jan 22 11:20:03 2014 -0500
@@ -1,20 +1,20 @@
-<tool id="blockclust" name="BlockClust" version="0.1">
+<tool id="blockclust" name="BlockClust" version="1.0.0">
     <description>Non-coding RNA clustering from deep sequencing read profiles</description>
     <requirements>
         <requirement type="package" version="1.0">blockclust</requirement>
+        <requirement type="package" version="1.1">eden</requirement>
         <requirement type="package" version="3.0.1">R_3_0_1</requirement>
         <requirement type="package" version="0.1.19 ">samtools</requirement>
+        <requirement type="package" version="12.135">mcl</requirement>
         <requirement type="package" version="1.0">blockclust_rlibs</requirement>
-        <requirement type="set_environment">BLOCKCLUST_DATA_PATH</requirement>
     </requirements>
-    <!--<version_command> -version</version_command>-->
+    <version_command>echo '1.0'</version_command>
     <command>
+
         #if str($tool_mode.operation) == "pre":
             #set $outputdir = $tags_bed.extra_files_path
-            BlockClustPipeLine.pl -m PRE -bam $tool_mode.reads_bam -tbed $tags_bed;
-        #end if
-
-        #if str($tool_mode.operation) == "clust":
+            BlockClustPipeLine.pl -m PRE -bam $tool_mode.reads_bam -tbed $tags_bed
+        #elif str($tool_mode.operation) == "clust":
             #set $outputdir = $clusters.extra_files_path
             #set $accept_bed=list()
             #set $reject_bed=list()
@@ -28,6 +28,21 @@
             #elif str($tool_mode.reference) == "dm3":
                 $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/dm3/dm3.accept.bed")
                 $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/dm3/dm3.reject.bed")
+                #elif str($tool_mode.reference) == "rheMac3":
+                $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/rheMac3/rheMac3.accept.bed")
+                $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/rheMac3/rheMac3.reject.bed")
+            #elif str($tool_mode.reference) == "panTro4":
+                $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/panTro3/panTro4.accept.bed")
+                $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/panTro3/panTro4.reject.bed")
+            #elif str($tool_mode.reference) == "xenTro3":
+                $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/xenTro3/xenTro3.accept.bed")
+                $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/xenTro3/xenTro3.reject.bed")
+            #elif str($tool_mode.reference) == "celWS235":
+                $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/celWS235/celWS235.accept.bed")
+                $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/celWS235/celWS235.reject.bed")
+            #elif str($tool_mode.reference) == "tair10":
+                $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/tair10/tair10.accept.bed")
+                $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/tair10/tair10.reject.bed")
             #end if
             BlockClustPipeLine.pl -m TEST -f SEQUENCE -c \$BLOCKCLUST_DATA_PATH/blockclust.config
             -t $tool_mode.input_bbo
@@ -50,13 +65,12 @@
 
             cp #echo os.path.join($outputdir, 'mcl_clusters','all_clusters.bed')# $clusters;
             cp #echo os.path.join($outputdir, 'hclust_tree.pdf')# $hclust_plot;
-            cp #echo os.path.join($outputdir, 'discretized.gspan.tab')# $sim_tab_out;
-        #end if
-    
-        #if str($tool_mode.operation) == "post":
+            cp #echo os.path.join($outputdir, 'discretized.gspan.tab')# $sim_tab_out
+        #elif str($tool_mode.operation) == "post":
             #set $outputdir = $clusters_bed.extra_files_path
             BlockClustPipeLine.pl -m POST -cbed $tool_mode.clusters_bed -cm $tool_mode.cmsearch_out -tab $tool_mode.sim_tab_in -o $outputdir;
             cp #echo os.path.join($outputdir, 'cluster_distribution.pdf')# $cluster_dist;
+            cp #echo os.path.join($outputdir, 'hclust_tree_clusters.pdf')# $cluster_hclust
         #end if
     </command>
     <inputs>
@@ -75,6 +89,11 @@
                     <option value="hg19">Human (hg19)</option>
                     <option value="mm10">Mouse (mm10)</option>
                     <option value="dm3">Fly (dm3)</option>
+                    <option value="rheMac3">Monkey (rheMac3)</option>
+                    <option value="panTro4">Chimp (panTro4)</option>
+                    <option value="xenTro3">Frog (xenTro3)</option>
+                    <option value="celWS235">C. elegans (celWS235)</option>
+                    <option value="tair10">Arabidopsis thaliana (tair10)</option>
                 </param>
                 <conditional name="pred">
                     <param name="enable_pred" type="select" label="Would you like to perform classification?">
@@ -128,10 +147,10 @@
         <data format="tabular" name="sim_tab_out" label="BlockClust: Pairwise similarities on ${on_string}">
             <filter> tool_mode["operation"]=="clust"</filter>
         </data>
-        <data format="tabular" name="analysis" label="BlockClust: Cluster analysis on ${on_string}" >
+        <data format="pdf" name="cluster_dist" label="BlockClust: Cluster distribution on ${on_string}" >
             <filter> tool_mode["operation"]=="post"</filter>
         </data>
-        <data format="pdf" name="cluster_dist" label="BlockClust: Cluster distribution on ${on_string}" >
+        <data format="pdf" name="cluster_hclust" label="BlockClust: Hierarchical clustering plot of cluster centroids on ${on_string}" >
             <filter> tool_mode["operation"]=="post"</filter>
         </data>
     </outputs>