Mercurial > repos > rnateam > blockclust
comparison 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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| 11:c1e76070760c | 12:69a7a16f26e4 |
|---|---|
| 8 <requirement type="R-module">ape</requirement> | 8 <requirement type="R-module">ape</requirement> |
| 9 <requirement type="set_environment">BLOCKCLUST_DATA_PATH</requirement> | 9 <requirement type="set_environment">BLOCKCLUST_DATA_PATH</requirement> |
| 10 </requirements> | 10 </requirements> |
| 11 <!--<version_command> -version</version_command>--> | 11 <!--<version_command> -version</version_command>--> |
| 12 <command> | 12 <command> |
| 13 #if str($mode.operation) == "pre": | 13 #if str($tool_mode.operation) == "pre": |
| 14 #set $outputdir = $tags_bed.extra_files_path | 14 #set $outputdir = $tags_bed.extra_files_path |
| 15 BlockClustPipeLine.pl -m PRE -bam $mode.reads_bam -tbed $tags_bed; | 15 BlockClustPipeLine.pl -m PRE -bam $tool_mode.reads_bam -tbed $tags_bed; |
| 16 #end if | 16 #end if |
| 17 | 17 |
| 18 #if str($mode.operation) == "clust": | 18 #if str($tool_mode.operation) == "clust": |
| 19 #set $outputdir = $clusters.extra_files_path | 19 #set $outputdir = $clusters.extra_files_path |
| 20 #set $accept_bed=list() | 20 #set $accept_bed=list() |
| 21 #set $reject_bed=list() | 21 #set $reject_bed=list() |
| 22 ## prepare annotations | 22 ## prepare annotations |
| 23 #if str($mode.reference) == "hg19": | 23 #if str($tool_mode.reference) == "hg19": |
| 24 $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/hg19/hg19.accept.bed") | 24 $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/hg19/hg19.accept.bed") |
| 25 $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/hg19/hg19.reject.bed") | 25 $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/hg19/hg19.reject.bed") |
| 26 #elif str($mode.reference) == "mm10": | 26 #elif str($tool_mode.reference) == "mm10": |
| 27 $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/mm10/mm10.accept.bed") | 27 $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/mm10/mm10.accept.bed") |
| 28 $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/mm10/mm10.reject.bed") | 28 $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/mm10/mm10.reject.bed") |
| 29 #elif str($mode.reference) == "dm3": | 29 #elif str($tool_mode.reference) == "dm3": |
| 30 $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/dm3/dm3.accept.bed") | 30 $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/dm3/dm3.accept.bed") |
| 31 $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/dm3/dm3.reject.bed") | 31 $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/dm3/dm3.reject.bed") |
| 32 #end if | 32 #end if |
| 33 BlockClustPipeLine.pl -m TEST -f SEQUENCE -c \$BLOCKCLUST_DATA_PATH/blockclust.config | 33 BlockClustPipeLine.pl -m TEST -f SEQUENCE -c \$BLOCKCLUST_DATA_PATH/blockclust.config |
| 34 -t $mode.input_bbo | 34 -t $tool_mode.input_bbo |
| 35 -a #echo ''.join( $accept_bed ) | 35 -a #echo ''.join( $accept_bed ) |
| 36 -r #echo ''.join( $reject_bed ) | 36 -r #echo ''.join( $reject_bed ) |
| 37 -o $outputdir; | 37 -o $outputdir |
| 38 #if str($tool_mode.pred.enable_pred) == "yes": | |
| 39 -p | |
| 40 -pm $tool_mode.pred.pred_mode | |
| 41 -md \$BLOCKCLUST_DATA_PATH/models | |
| 42 -x 3; | |
| 43 #if str($tool_mode.pred.pred_mode) == "nearest_neighbour": | |
| 44 cp #echo os.path.join($outputdir,'nearest_neighbour_predictions.txt')# $nearest_neighbour_pred_bed; | |
| 45 #elif str($tool_mode.pred.pred_mode) == "model_based": | |
| 46 cp #echo os.path.join($outputdir,'model_based_predictions.txt')# $model_based_pred_bed; | |
| 47 #end if | |
| 48 #else: | |
| 49 ; | |
| 50 #end if | |
| 51 | |
| 38 cp #echo os.path.join($outputdir, 'mcl_clusters','all_clusters.bed')# $clusters; | 52 cp #echo os.path.join($outputdir, 'mcl_clusters','all_clusters.bed')# $clusters; |
| 39 cp #echo os.path.join($outputdir, 'hclust_tree.pdf')# $hclust_plot; | 53 cp #echo os.path.join($outputdir, 'hclust_tree.pdf')# $hclust_plot; |
| 40 cp #echo os.path.join($outputdir, 'discretized.gspan.tab')# $sim_tab_out; | 54 cp #echo os.path.join($outputdir, 'discretized.gspan.tab')# $sim_tab_out; |
| 41 #end if | 55 #end if |
| 42 | 56 |
| 43 #if str($mode.operation) == "post": | 57 #if str($tool_mode.operation) == "post": |
| 44 #set $outputdir = $clusters_bed.extra_files_path | 58 #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 -rfam \$BLOCKCLUST_DATA_PATH/rfam_map.txt; | 59 BlockClustPipeLine.pl -m POST -cbed $tool_mode.clusters_bed -cm $tool_mode.cmsearch_out -tab $tool_mode.sim_tab_in -o $outputdir; |
| 46 cp #echo os.path.join($outputdir, 'cluster_distribution.pdf')# $cluster_dist; | 60 cp #echo os.path.join($outputdir, 'cluster_distribution.pdf')# $cluster_dist; |
| 47 #end if | 61 #end if |
| 48 </command> | 62 </command> |
| 49 <inputs> | 63 <inputs> |
| 50 <conditional name="mode"> | 64 <conditional name="tool_mode"> |
| 51 <param name="operation" type="select" label="Select mode of operation"> | 65 <param name="operation" type="select" label="Select mode of operation"> |
| 52 <option value="pre">Pre-processing </option> | 66 <option value="pre">Pre-processing </option> |
| 53 <option value="clust">Clustering</option> | 67 <option value="clust">Clustering</option> |
| 54 <option value="post">Post-processing</option> | 68 <option value="post">Post-processing</option> |
| 55 </param> | 69 </param> |
| 61 <param name="reference" type="select" label="Select reference genome"> | 75 <param name="reference" type="select" label="Select reference genome"> |
| 62 <option value="hg19">Human (hg19)</option> | 76 <option value="hg19">Human (hg19)</option> |
| 63 <option value="mm10">Mouse (mm10)</option> | 77 <option value="mm10">Mouse (mm10)</option> |
| 64 <option value="dm3">Fly (dm3)</option> | 78 <option value="dm3">Fly (dm3)</option> |
| 65 </param> | 79 </param> |
| 80 <conditional name="pred"> | |
| 81 <param name="enable_pred" type="select" label="Would you like to perform classification?"> | |
| 82 <option value="no">No</option> | |
| 83 <option value="yes">Yes</option> | |
| 84 </param> | |
| 85 <when value="yes"> | |
| 86 <param name="pred_mode" type="select" label="Mode of classification"> | |
| 87 <option value="model_based">Model based</option> | |
| 88 <option value="nearest_neighbour">Nearest neighbour</option> | |
| 89 </param> | |
| 90 </when> | |
| 91 </conditional> | |
| 66 </when> | 92 </when> |
| 67 <when value="post"> | 93 <when value="post"> |
| 68 <param name="cmsearch_out" type="data" format="tabular" label="Output of cmsearch tool" /> | 94 <param name="cmsearch_out" type="data" format="tabular" label="Output of cmsearch tool" /> |
| 69 <param name="clusters_bed" type="data" format="bed" label="BED file containing clusters (output of BlockClust)" /> | 95 <param name="clusters_bed" type="data" format="bed" label="BED file containing clusters (output of BlockClust)" /> |
| 70 <param name="sim_tab_in" type="data" format="tabular" label="Pairwise similarities file" /> | 96 <param name="sim_tab_in" type="data" format="tabular" label="Pairwise similarities file" /> |
| 72 </conditional> | 98 </conditional> |
| 73 </inputs> | 99 </inputs> |
| 74 | 100 |
| 75 <outputs> | 101 <outputs> |
| 76 <data format="bed" name="tags_bed" label="BlockClust: BAM to BED on ${on_string}"> | 102 <data format="bed" name="tags_bed" label="BlockClust: BAM to BED on ${on_string}"> |
| 77 <filter> mode["operation"]=="pre"</filter> | 103 <filter> tool_mode["operation"]=="pre"</filter> |
| 78 </data> | 104 </data> |
| 79 <data format="pdf" name="hclust_plot" label="BlockClust: Hierarchical clustering plot on ${on_string}" > | 105 <data format="pdf" name="hclust_plot" label="BlockClust: Hierarchical clustering plot on ${on_string}" > |
| 80 <filter> mode["operation"]=="clust"</filter> | 106 <filter> tool_mode["operation"]=="clust"</filter> |
| 81 </data> | 107 </data> |
| 82 <data format="bed" name="clusters" label="BlockClust: Clustering BED on ${on_string}"> | 108 <data format="bed" name="clusters" label="BlockClust: Clustering BED on ${on_string}"> |
| 83 <filter> mode["operation"]=="clust"</filter> | 109 <filter> tool_mode["operation"]=="clust"</filter> |
| 110 </data> | |
| 111 <data format="bed" name="model_based_pred_bed" label="BlockClust: Model based prediction BED on ${on_string}"> | |
| 112 <filter> | |
| 113 (( | |
| 114 tool_mode["operation"] == 'clust' and | |
| 115 tool_mode["pred"]["enable_pred"] == "yes" and | |
| 116 tool_mode["pred"]["pred_mode"] == "model_based" | |
| 117 )) | |
| 118 </filter> | |
| 119 </data> | |
| 120 <data format="bed" name="nearest_neighbour_pred_bed" label="BlockClust: Nearest neighbour prediction BED on ${on_string}"> | |
| 121 <filter> | |
| 122 (( | |
| 123 tool_mode["operation"] == 'clust' and | |
| 124 tool_mode["pred"]["enable_pred"] == "yes" and | |
| 125 tool_mode["pred"]["pred_mode"] == "nearest_neighbour" | |
| 126 )) | |
| 127 </filter> | |
| 84 </data> | 128 </data> |
| 85 <data format="tabular" name="sim_tab_out" label="BlockClust: Pairwise similarities on ${on_string}"> | 129 <data format="tabular" name="sim_tab_out" label="BlockClust: Pairwise similarities on ${on_string}"> |
| 86 <filter> mode["operation"]=="clust"</filter> | 130 <filter> tool_mode["operation"]=="clust"</filter> |
| 87 </data> | 131 </data> |
| 88 <data format="tabular" name="analysis" label="BlockClust: Cluster analysis on ${on_string}" > | 132 <data format="tabular" name="analysis" label="BlockClust: Cluster analysis on ${on_string}" > |
| 89 <filter> mode["operation"]=="post"</filter> | 133 <filter> tool_mode["operation"]=="post"</filter> |
| 90 </data> | 134 </data> |
| 91 <data format="pdf" name="cluster_dist" label="BlockClust: Cluster distribution on ${on_string}" > | 135 <data format="pdf" name="cluster_dist" label="BlockClust: Cluster distribution on ${on_string}" > |
| 92 <filter> mode["operation"]=="post"</filter> | 136 <filter> tool_mode["operation"]=="post"</filter> |
| 93 </data> | 137 </data> |
| 94 </outputs> | 138 </outputs> |
| 95 <help> | 139 <help> |
| 96 | 140 |
| 97 .. class:: infomark | 141 .. class:: infomark |