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comparison 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
comparison
equal deleted inserted replaced
5:49b72f1013b3 6:b77328c96ac9
8 <requirement type="R-module">ape</requirement> 8 <requirement type="R-module">ape</requirement>
9 </requirements> 9 </requirements>
10 <!--<version_command> -version</version_command>--> 10 <!--<version_command> -version</version_command>-->
11 <command> 11 <command>
12 #set $blockclust_data_path = \$BLOCKCLUST_DATA_PATH 12 #set $blockclust_data_path = \$BLOCKCLUST_DATA_PATH
13
13 #if str($mode.operation) == "pre": 14 #if str($mode.operation) == "pre":
14 #set $outputdir = $tags_bed.extra_files_path 15 #set $outputdir = $tags_bed.extra_files_path
15 BlockClustPipeLine.pl -m PRE -bam $mode.reads_bam -tbed $tags_bed; 16 BlockClustPipeLine.pl -m PRE -bam $mode.reads_bam -tbed $tags_bed;
16 #end if 17 #end if
17 18
40 cp #echo os.path.join($outputdir, 'discretized.gspan.tab')# $sim_tab_out; 41 cp #echo os.path.join($outputdir, 'discretized.gspan.tab')# $sim_tab_out;
41 #end if 42 #end if
42 43
43 #if str($mode.operation) == "post": 44 #if str($mode.operation) == "post":
44 #set $outputdir = $clusters_bed.extra_files_path 45 #set $outputdir = $clusters_bed.extra_files_path
45 BlockClustPipeLine.pl -m POST -cbed $mode.clusters_bed -cm $mode.cmsearch_out -tab $mode.sim_tab_in -o $outputdir; 46 BlockClustPipeLine.pl -m POST -cbed $mode.clusters_bed -cm $mode.cmsearch_out -tab $mode.sim_tab_in -o $outputdir -rfam $blockclust_data_path/rfam_map.txt;
46 cp #echo os.path.join($outputdir, 'cluster_distribution.pdf')# $cluster_dist; 47 cp #echo os.path.join($outputdir, 'cluster_distribution.pdf')# $cluster_dist;
47 #end if 48 #end if
48 </command> 49 </command>
49 <inputs> 50 <inputs>
50 <conditional name="mode"> 51 <conditional name="mode">