Mercurial > repos > rnateam > blockclust

diff blockclust.xml @ 6:b77328c96ac9 draft

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Uploaded
author rnateam
date Tue, 22 Oct 2013 11:27:29 -0400
parents 49b72f1013b3
children 171f6015180f
line wrap: on
line diff
--- a/blockclust.xml	Tue Oct 22 10:15:09 2013 -0400
+++ b/blockclust.xml	Tue Oct 22 11:27:29 2013 -0400
@@ -10,6 +10,7 @@
     <!--<version_command> -version</version_command>-->
     <command>
         #set $blockclust_data_path = \$BLOCKCLUST_DATA_PATH
+
         #if str($mode.operation) == "pre":
             #set $outputdir = $tags_bed.extra_files_path
             BlockClustPipeLine.pl -m PRE -bam $mode.reads_bam -tbed $tags_bed;
@@ -42,7 +43,7 @@
     
         #if str($mode.operation) == "post":
             #set $outputdir = $clusters_bed.extra_files_path
-            BlockClustPipeLine.pl -m POST -cbed $mode.clusters_bed -cm $mode.cmsearch_out -tab $mode.sim_tab_in -o $outputdir;
+            BlockClustPipeLine.pl -m POST -cbed $mode.clusters_bed -cm $mode.cmsearch_out -tab $mode.sim_tab_in -o $outputdir -rfam $blockclust_data_path/rfam_map.txt;
             cp #echo os.path.join($outputdir, 'cluster_distribution.pdf')# $cluster_dist;
         #end if
     </command>