Mercurial > repos > rnateam > graphclust_postprocessing

diff glob_report.xml @ 3:79b9117aef01 draft

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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c
author rnateam
date Wed, 04 Jan 2017 18:15:07 -0500
parents b8e32e577597
children 4a9754d476fe
line wrap: on
line diff
--- a/glob_report.xml	Sat Dec 24 18:08:36 2016 -0500
+++ b/glob_report.xml	Wed Jan 04 18:15:07 2017 -0500
@@ -9,7 +9,6 @@
 	</stdio>
 	<command>
 		<![CDATA[
-
         unzip $FASTA  &> /dev/null &&
 
         #set $inputFiles = ""
@@ -25,17 +24,29 @@
             #set $inputFilesTrees += str($mods)+','
         #end for
         #set $inputFilesTrees = $inputFilesTrees[:-1]
-
-		    'glob_res.pl' '$inputFiles' $merge_cluster_ol $merge_overlap $min_cluster_size $cm_min_bitscore $cm_max_eval $cm_bitscore_sig $partition_type '' $cut_type '$inputFilesTrees'
+		    glob_res.pl 
+                '$inputFiles'
+                $merge_cluster_ol
+                $merge_overlap
+                $min_cluster_size
+                $cm_min_bitscore
+                $cm_max_eval
+                $cm_bitscore_sig
+                $partition_type ''
+                $cut_type
+                '$inputFilesTrees'
         #if  $iteration_num.iteration_num_selector:
           $iteration_num.CI
-
           $final_partition_soft
           $final_partition_used_cmsearch
         #end if
 
         &&
         python '$__tool_directory__/evaluation.py'
+		#if $cdhit:
+    		&&
+	    	python '$__tool_directory__/addCdhitseqs.py' '$cdhit'
+	    #end if		
 ]]>
 	</command>
 	<inputs>
@@ -44,6 +55,7 @@
 		<param type="data" name="model_tree_files" format="txt" multiple="True"/>
 		<param name="partition_type" type="boolean" checked="True" truevalue="0" falsevalue="1" label="Hard partition"/>
 		<param name="cut_type" type="boolean" checked="True" truevalue="0" falsevalue="1" label="Use CM score for cutoff" help="otherwise use E-value"/>
+		<param type="data" name="cdhit" format="txt" optional="true"/>
 		<conditional name="iteration_num">
 			<param name="iteration_num_selector" type="boolean"  checked="no" label="Multiple iterations"  help="for single iteration- NO, for multiple-YES"/>
 			<when value="true">