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comparison blockclust.xml @ 1:a92d8689aa30 draft

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Uploaded
author rnateam
date Tue, 08 Jul 2014 11:59:49 -0400
parents 768a67f6ae18
children f973ec6e5192
comparison
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0:768a67f6ae18 1:a92d8689aa30
10 </requirements> 10 </requirements>
11 <version_command>echo '1.0'</version_command> 11 <version_command>echo '1.0'</version_command>
12 <command> 12 <command>
13 13
14 #if str($tool_mode.operation) == "pre": 14 #if str($tool_mode.operation) == "pre":
15 #set $outputdir = $tags_bed.extra_files_path
16 BlockClustPipeLine.pl -m PRE -bam $tool_mode.reads_bam -tbed $tags_bed 15 BlockClustPipeLine.pl -m PRE -bam $tool_mode.reads_bam -tbed $tags_bed
17 #elif str($tool_mode.operation) == "clust": 16 #elif str($tool_mode.operation) == "clust":
18 #set $outputdir = $clusters.extra_files_path 17 #set $outputdir = $clusters.files_path
19 #set $accept_bed=list() 18 #set $accept_bed=list()
20 #set $reject_bed=list() 19 #set $reject_bed=list()
21 ## prepare annotations 20 ## prepare annotations
22 #if str($tool_mode.reference) == "hg19": 21 #if str($tool_mode.reference) == "hg19":
23 $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/hg19/hg19.accept.bed") 22 $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/hg19/hg19.accept.bed")
65 64
66 cp #echo os.path.join($outputdir, 'mcl_clusters','all_clusters.bed')# $clusters; 65 cp #echo os.path.join($outputdir, 'mcl_clusters','all_clusters.bed')# $clusters;
67 cp #echo os.path.join($outputdir, 'hclust_tree.pdf')# $hclust_plot; 66 cp #echo os.path.join($outputdir, 'hclust_tree.pdf')# $hclust_plot;
68 cp #echo os.path.join($outputdir, 'discretized.gspan.tab')# $sim_tab_out 67 cp #echo os.path.join($outputdir, 'discretized.gspan.tab')# $sim_tab_out
69 #elif str($tool_mode.operation) == "post": 68 #elif str($tool_mode.operation) == "post":
70 #set $outputdir = $clusters_bed.extra_files_path 69 BlockClustPipeLine.pl -m POST -cbed $tool_mode.clusters_bed -cm $tool_mode.cmsearch_out -tab $tool_mode.sim_tab_in -o ./;
71 BlockClustPipeLine.pl -m POST -cbed $tool_mode.clusters_bed -cm $tool_mode.cmsearch_out -tab $tool_mode.sim_tab_in -o $outputdir;
72 cp #echo os.path.join($outputdir, 'cluster_distribution.pdf')# $cluster_dist;
73 cp #echo os.path.join($outputdir, 'hclust_tree_clusters.pdf')# $cluster_hclust
74 #end if 70 #end if
75 </command> 71 </command>
76 <inputs> 72 <inputs>
77 <conditional name="tool_mode"> 73 <conditional name="tool_mode">
78 <param name="operation" type="select" label="Select mode of operation"> 74 <param name="operation" type="select" label="Select mode of operation">
145 </filter> 141 </filter>
146 </data> 142 </data>
147 <data format="tabular" name="sim_tab_out" label="BlockClust: Pairwise similarities on ${on_string}"> 143 <data format="tabular" name="sim_tab_out" label="BlockClust: Pairwise similarities on ${on_string}">
148 <filter> tool_mode["operation"]=="clust"</filter> 144 <filter> tool_mode["operation"]=="clust"</filter>
149 </data> 145 </data>
150 <data format="pdf" name="cluster_dist" label="BlockClust: Cluster distribution on ${on_string}" > 146 <data format="pdf" name="cluster_dist" from_work_dir="cluster_distribution.pdf" label="BlockClust: Cluster distribution on ${on_string}" >
151 <filter> tool_mode["operation"]=="post"</filter> 147 <filter> tool_mode["operation"]=="post"</filter>
152 </data> 148 </data>
153 <data format="pdf" name="cluster_hclust" label="BlockClust: Hierarchical clustering plot of cluster centroids on ${on_string}" > 149 <data format="pdf" name="cluster_hclust" from_work_dir="hclust_tree_clusters.pdf" label="BlockClust: Hierarchical clustering plot of cluster centroids on ${on_string}" >
154 <filter> tool_mode["operation"]=="post"</filter> 150 <filter> tool_mode["operation"]=="post"</filter>
155 </data> 151 </data>
156 </outputs> 152 </outputs>
157 <help> 153 <help>
158 154