Mercurial > repos > rnateam > blockclust
diff blockclust.xml @ 12:69a7a16f26e4 draft
Uploaded
| author | rnateam |
|---|---|
| date | Fri, 25 Oct 2013 07:47:01 -0400 |
| parents | e1ee289416dd |
| children | bcb191e42032 |
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--- a/blockclust.xml Thu Oct 24 06:06:52 2013 -0400 +++ b/blockclust.xml Fri Oct 25 07:47:01 2013 -0400 @@ -10,44 +10,58 @@ </requirements> <!--<version_command> -version</version_command>--> <command> - #if str($mode.operation) == "pre": + #if str($tool_mode.operation) == "pre": #set $outputdir = $tags_bed.extra_files_path - BlockClustPipeLine.pl -m PRE -bam $mode.reads_bam -tbed $tags_bed; + BlockClustPipeLine.pl -m PRE -bam $tool_mode.reads_bam -tbed $tags_bed; #end if - #if str($mode.operation) == "clust": + #if str($tool_mode.operation) == "clust": #set $outputdir = $clusters.extra_files_path #set $accept_bed=list() #set $reject_bed=list() ## prepare annotations - #if str($mode.reference) == "hg19": + #if str($tool_mode.reference) == "hg19": $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/hg19/hg19.accept.bed") $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/hg19/hg19.reject.bed") - #elif str($mode.reference) == "mm10": + #elif str($tool_mode.reference) == "mm10": $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/mm10/mm10.accept.bed") $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/mm10/mm10.reject.bed") - #elif str($mode.reference) == "dm3": + #elif str($tool_mode.reference) == "dm3": $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/dm3/dm3.accept.bed") $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/dm3/dm3.reject.bed") #end if BlockClustPipeLine.pl -m TEST -f SEQUENCE -c \$BLOCKCLUST_DATA_PATH/blockclust.config - -t $mode.input_bbo + -t $tool_mode.input_bbo -a #echo ''.join( $accept_bed ) -r #echo ''.join( $reject_bed ) - -o $outputdir; + -o $outputdir + #if str($tool_mode.pred.enable_pred) == "yes": + -p + -pm $tool_mode.pred.pred_mode + -md \$BLOCKCLUST_DATA_PATH/models + -x 3; + #if str($tool_mode.pred.pred_mode) == "nearest_neighbour": + cp #echo os.path.join($outputdir,'nearest_neighbour_predictions.txt')# $nearest_neighbour_pred_bed; + #elif str($tool_mode.pred.pred_mode) == "model_based": + cp #echo os.path.join($outputdir,'model_based_predictions.txt')# $model_based_pred_bed; + #end if + #else: + ; + #end if + cp #echo os.path.join($outputdir, 'mcl_clusters','all_clusters.bed')# $clusters; cp #echo os.path.join($outputdir, 'hclust_tree.pdf')# $hclust_plot; cp #echo os.path.join($outputdir, 'discretized.gspan.tab')# $sim_tab_out; #end if - #if str($mode.operation) == "post": + #if str($tool_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 -rfam \$BLOCKCLUST_DATA_PATH/rfam_map.txt; + 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; #end if </command> <inputs> - <conditional name="mode"> + <conditional name="tool_mode"> <param name="operation" type="select" label="Select mode of operation"> <option value="pre">Pre-processing </option> <option value="clust">Clustering</option> @@ -63,6 +77,18 @@ <option value="mm10">Mouse (mm10)</option> <option value="dm3">Fly (dm3)</option> </param> + <conditional name="pred"> + <param name="enable_pred" type="select" label="Would you like to perform classification?"> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <when value="yes"> + <param name="pred_mode" type="select" label="Mode of classification"> + <option value="model_based">Model based</option> + <option value="nearest_neighbour">Nearest neighbour</option> + </param> + </when> + </conditional> </when> <when value="post"> <param name="cmsearch_out" type="data" format="tabular" label="Output of cmsearch tool" /> @@ -74,22 +100,40 @@ <outputs> <data format="bed" name="tags_bed" label="BlockClust: BAM to BED on ${on_string}"> - <filter> mode["operation"]=="pre"</filter> + <filter> tool_mode["operation"]=="pre"</filter> </data> <data format="pdf" name="hclust_plot" label="BlockClust: Hierarchical clustering plot on ${on_string}" > - <filter> mode["operation"]=="clust"</filter> + <filter> tool_mode["operation"]=="clust"</filter> </data> <data format="bed" name="clusters" label="BlockClust: Clustering BED on ${on_string}"> - <filter> mode["operation"]=="clust"</filter> + <filter> tool_mode["operation"]=="clust"</filter> + </data> + <data format="bed" name="model_based_pred_bed" label="BlockClust: Model based prediction BED on ${on_string}"> + <filter> + (( + tool_mode["operation"] == 'clust' and + tool_mode["pred"]["enable_pred"] == "yes" and + tool_mode["pred"]["pred_mode"] == "model_based" + )) + </filter> + </data> + <data format="bed" name="nearest_neighbour_pred_bed" label="BlockClust: Nearest neighbour prediction BED on ${on_string}"> + <filter> + (( + tool_mode["operation"] == 'clust' and + tool_mode["pred"]["enable_pred"] == "yes" and + tool_mode["pred"]["pred_mode"] == "nearest_neighbour" + )) + </filter> </data> <data format="tabular" name="sim_tab_out" label="BlockClust: Pairwise similarities on ${on_string}"> - <filter> mode["operation"]=="clust"</filter> + <filter> tool_mode["operation"]=="clust"</filter> </data> <data format="tabular" name="analysis" label="BlockClust: Cluster analysis on ${on_string}" > - <filter> mode["operation"]=="post"</filter> + <filter> tool_mode["operation"]=="post"</filter> </data> <data format="pdf" name="cluster_dist" label="BlockClust: Cluster distribution on ${on_string}" > - <filter> mode["operation"]=="post"</filter> + <filter> tool_mode["operation"]=="post"</filter> </data> </outputs> <help>