| Previous changeset 0:768a67f6ae18 (2014-05-06) Next changeset 2:f973ec6e5192 (2014-07-08) |
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Commit message:
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modified:
blockclust.xml tool_dependencies.xml |
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| diff -r 768a67f6ae18 -r a92d8689aa30 blockclust.xml --- a/blockclust.xml Tue May 06 07:49:25 2014 -0400 +++ b/blockclust.xml Tue Jul 08 11:59:49 2014 -0400 |
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| @@ -12,10 +12,9 @@ <command> #if str($tool_mode.operation) == "pre": - #set $outputdir = $tags_bed.extra_files_path BlockClustPipeLine.pl -m PRE -bam $tool_mode.reads_bam -tbed $tags_bed #elif str($tool_mode.operation) == "clust": - #set $outputdir = $clusters.extra_files_path + #set $outputdir = $clusters.files_path #set $accept_bed=list() #set $reject_bed=list() ## prepare annotations @@ -67,10 +66,7 @@ cp #echo os.path.join($outputdir, 'hclust_tree.pdf')# $hclust_plot; cp #echo os.path.join($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 + BlockClustPipeLine.pl -m POST -cbed $tool_mode.clusters_bed -cm $tool_mode.cmsearch_out -tab $tool_mode.sim_tab_in -o ./; #end if </command> <inputs> @@ -147,10 +143,10 @@ <data format="tabular" name="sim_tab_out" label="BlockClust: Pairwise similarities on ${on_string}"> <filter> tool_mode["operation"]=="clust"</filter> </data> - <data format="pdf" name="cluster_dist" label="BlockClust: Cluster distribution on ${on_string}" > + <data format="pdf" name="cluster_dist" from_work_dir="cluster_distribution.pdf" label="BlockClust: Cluster distribution on ${on_string}" > <filter> tool_mode["operation"]=="post"</filter> </data> - <data format="pdf" name="cluster_hclust" label="BlockClust: Hierarchical clustering plot of cluster centroids on ${on_string}" > + <data format="pdf" name="cluster_hclust" from_work_dir="hclust_tree_clusters.pdf" label="BlockClust: Hierarchical clustering plot of cluster centroids on ${on_string}" > <filter> tool_mode["operation"]=="post"</filter> </data> </outputs> |
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| diff -r 768a67f6ae18 -r a92d8689aa30 tool_dependencies.xml --- a/tool_dependencies.xml Tue May 06 07:49:25 2014 -0400 +++ b/tool_dependencies.xml Tue Jul 08 11:59:49 2014 -0400 |
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| @@ -1,22 +1,22 @@ <?xml version="1.0"?> <tool_dependency> <package name="samtools" version="0.1.19"> - <repository changeset_revision="6b6b5498d9a2" name="package_samtools_0_1_19" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="6b6b5498d9a2" name="package_samtools_0_1_19" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="R_3_0_1" version="3.0.1"> - <repository changeset_revision="c5ff6dd33c79" name="package_r_3_0_1" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="c5ff6dd33c79" name="package_r_3_0_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="eden" version="1.1"> - <repository changeset_revision="532625813f2e" name="package_eden_1_1" owner="rnateam" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="532625813f2e" name="package_eden_1_1" owner="rnateam" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="mcl" version="12.135"> - <repository changeset_revision="9f59d1a59999" name="package_mcl_12_135" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="9f59d1a59999" name="package_mcl_12_135" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="blockclust_rlibs" version="1.0"> <install version="1.0"> <actions> <action type="setup_r_environment"> - <repository changeset_revision="c5ff6dd33c79" name="package_r_3_0_1" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu"> + <repository changeset_revision="c5ff6dd33c79" name="package_r_3_0_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> <package name="R_3_0_1" version="3.0.1" /> </repository> <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/ape_3.0-11.tar.gz</package> |