Mercurial > repos > rnateam > blockclust
comparison blockclust.xml @ 14:0fbc8cdc1cd0 draft
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| author | rnateam |
|---|---|
| date | Wed, 22 Jan 2014 11:20:03 -0500 |
| parents | bcb191e42032 |
| children | 6ee2478c4fdc |
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| 13:bcb191e42032 | 14:0fbc8cdc1cd0 |
|---|---|
| 1 <tool id="blockclust" name="BlockClust" version="0.1"> | 1 <tool id="blockclust" name="BlockClust" version="1.0.0"> |
| 2 <description>Non-coding RNA clustering from deep sequencing read profiles</description> | 2 <description>Non-coding RNA clustering from deep sequencing read profiles</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="package" version="1.0">blockclust</requirement> | 4 <requirement type="package" version="1.0">blockclust</requirement> |
| 5 <requirement type="package" version="1.1">eden</requirement> | |
| 5 <requirement type="package" version="3.0.1">R_3_0_1</requirement> | 6 <requirement type="package" version="3.0.1">R_3_0_1</requirement> |
| 6 <requirement type="package" version="0.1.19 ">samtools</requirement> | 7 <requirement type="package" version="0.1.19 ">samtools</requirement> |
| 8 <requirement type="package" version="12.135">mcl</requirement> | |
| 7 <requirement type="package" version="1.0">blockclust_rlibs</requirement> | 9 <requirement type="package" version="1.0">blockclust_rlibs</requirement> |
| 8 <requirement type="set_environment">BLOCKCLUST_DATA_PATH</requirement> | |
| 9 </requirements> | 10 </requirements> |
| 10 <!--<version_command> -version</version_command>--> | 11 <version_command>echo '1.0'</version_command> |
| 11 <command> | 12 <command> |
| 13 | |
| 12 #if str($tool_mode.operation) == "pre": | 14 #if str($tool_mode.operation) == "pre": |
| 13 #set $outputdir = $tags_bed.extra_files_path | 15 #set $outputdir = $tags_bed.extra_files_path |
| 14 BlockClustPipeLine.pl -m PRE -bam $tool_mode.reads_bam -tbed $tags_bed; | 16 BlockClustPipeLine.pl -m PRE -bam $tool_mode.reads_bam -tbed $tags_bed |
| 15 #end if | 17 #elif str($tool_mode.operation) == "clust": |
| 16 | |
| 17 #if str($tool_mode.operation) == "clust": | |
| 18 #set $outputdir = $clusters.extra_files_path | 18 #set $outputdir = $clusters.extra_files_path |
| 19 #set $accept_bed=list() | 19 #set $accept_bed=list() |
| 20 #set $reject_bed=list() | 20 #set $reject_bed=list() |
| 21 ## prepare annotations | 21 ## prepare annotations |
| 22 #if str($tool_mode.reference) == "hg19": | 22 #if str($tool_mode.reference) == "hg19": |
| 26 $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/mm10/mm10.accept.bed") | 26 $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/mm10/mm10.accept.bed") |
| 27 $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/mm10/mm10.reject.bed") | 27 $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/mm10/mm10.reject.bed") |
| 28 #elif str($tool_mode.reference) == "dm3": | 28 #elif str($tool_mode.reference) == "dm3": |
| 29 $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/dm3/dm3.accept.bed") | 29 $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/dm3/dm3.accept.bed") |
| 30 $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/dm3/dm3.reject.bed") | 30 $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/dm3/dm3.reject.bed") |
| 31 #elif str($tool_mode.reference) == "rheMac3": | |
| 32 $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/rheMac3/rheMac3.accept.bed") | |
| 33 $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/rheMac3/rheMac3.reject.bed") | |
| 34 #elif str($tool_mode.reference) == "panTro4": | |
| 35 $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/panTro3/panTro4.accept.bed") | |
| 36 $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/panTro3/panTro4.reject.bed") | |
| 37 #elif str($tool_mode.reference) == "xenTro3": | |
| 38 $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/xenTro3/xenTro3.accept.bed") | |
| 39 $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/xenTro3/xenTro3.reject.bed") | |
| 40 #elif str($tool_mode.reference) == "celWS235": | |
| 41 $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/celWS235/celWS235.accept.bed") | |
| 42 $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/celWS235/celWS235.reject.bed") | |
| 43 #elif str($tool_mode.reference) == "tair10": | |
| 44 $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/tair10/tair10.accept.bed") | |
| 45 $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/tair10/tair10.reject.bed") | |
| 31 #end if | 46 #end if |
| 32 BlockClustPipeLine.pl -m TEST -f SEQUENCE -c \$BLOCKCLUST_DATA_PATH/blockclust.config | 47 BlockClustPipeLine.pl -m TEST -f SEQUENCE -c \$BLOCKCLUST_DATA_PATH/blockclust.config |
| 33 -t $tool_mode.input_bbo | 48 -t $tool_mode.input_bbo |
| 34 -a #echo ''.join( $accept_bed ) | 49 -a #echo ''.join( $accept_bed ) |
| 35 -r #echo ''.join( $reject_bed ) | 50 -r #echo ''.join( $reject_bed ) |
| 48 ; | 63 ; |
| 49 #end if | 64 #end if |
| 50 | 65 |
| 51 cp #echo os.path.join($outputdir, 'mcl_clusters','all_clusters.bed')# $clusters; | 66 cp #echo os.path.join($outputdir, 'mcl_clusters','all_clusters.bed')# $clusters; |
| 52 cp #echo os.path.join($outputdir, 'hclust_tree.pdf')# $hclust_plot; | 67 cp #echo os.path.join($outputdir, 'hclust_tree.pdf')# $hclust_plot; |
| 53 cp #echo os.path.join($outputdir, 'discretized.gspan.tab')# $sim_tab_out; | 68 cp #echo os.path.join($outputdir, 'discretized.gspan.tab')# $sim_tab_out |
| 54 #end if | 69 #elif str($tool_mode.operation) == "post": |
| 55 | |
| 56 #if str($tool_mode.operation) == "post": | |
| 57 #set $outputdir = $clusters_bed.extra_files_path | 70 #set $outputdir = $clusters_bed.extra_files_path |
| 58 BlockClustPipeLine.pl -m POST -cbed $tool_mode.clusters_bed -cm $tool_mode.cmsearch_out -tab $tool_mode.sim_tab_in -o $outputdir; | 71 BlockClustPipeLine.pl -m POST -cbed $tool_mode.clusters_bed -cm $tool_mode.cmsearch_out -tab $tool_mode.sim_tab_in -o $outputdir; |
| 59 cp #echo os.path.join($outputdir, 'cluster_distribution.pdf')# $cluster_dist; | 72 cp #echo os.path.join($outputdir, 'cluster_distribution.pdf')# $cluster_dist; |
| 73 cp #echo os.path.join($outputdir, 'hclust_tree_clusters.pdf')# $cluster_hclust | |
| 60 #end if | 74 #end if |
| 61 </command> | 75 </command> |
| 62 <inputs> | 76 <inputs> |
| 63 <conditional name="tool_mode"> | 77 <conditional name="tool_mode"> |
| 64 <param name="operation" type="select" label="Select mode of operation"> | 78 <param name="operation" type="select" label="Select mode of operation"> |
| 73 <param name="input_bbo" type="data" format="tabular" label="Input blockgroups file" /> | 87 <param name="input_bbo" type="data" format="tabular" label="Input blockgroups file" /> |
| 74 <param name="reference" type="select" label="Select reference genome"> | 88 <param name="reference" type="select" label="Select reference genome"> |
| 75 <option value="hg19">Human (hg19)</option> | 89 <option value="hg19">Human (hg19)</option> |
| 76 <option value="mm10">Mouse (mm10)</option> | 90 <option value="mm10">Mouse (mm10)</option> |
| 77 <option value="dm3">Fly (dm3)</option> | 91 <option value="dm3">Fly (dm3)</option> |
| 92 <option value="rheMac3">Monkey (rheMac3)</option> | |
| 93 <option value="panTro4">Chimp (panTro4)</option> | |
| 94 <option value="xenTro3">Frog (xenTro3)</option> | |
| 95 <option value="celWS235">C. elegans (celWS235)</option> | |
| 96 <option value="tair10">Arabidopsis thaliana (tair10)</option> | |
| 78 </param> | 97 </param> |
| 79 <conditional name="pred"> | 98 <conditional name="pred"> |
| 80 <param name="enable_pred" type="select" label="Would you like to perform classification?"> | 99 <param name="enable_pred" type="select" label="Would you like to perform classification?"> |
| 81 <option value="no">No</option> | 100 <option value="no">No</option> |
| 82 <option value="yes">Yes</option> | 101 <option value="yes">Yes</option> |
| 126 </filter> | 145 </filter> |
| 127 </data> | 146 </data> |
| 128 <data format="tabular" name="sim_tab_out" label="BlockClust: Pairwise similarities on ${on_string}"> | 147 <data format="tabular" name="sim_tab_out" label="BlockClust: Pairwise similarities on ${on_string}"> |
| 129 <filter> tool_mode["operation"]=="clust"</filter> | 148 <filter> tool_mode["operation"]=="clust"</filter> |
| 130 </data> | 149 </data> |
| 131 <data format="tabular" name="analysis" label="BlockClust: Cluster analysis on ${on_string}" > | 150 <data format="pdf" name="cluster_dist" label="BlockClust: Cluster distribution on ${on_string}" > |
| 132 <filter> tool_mode["operation"]=="post"</filter> | 151 <filter> tool_mode["operation"]=="post"</filter> |
| 133 </data> | 152 </data> |
| 134 <data format="pdf" name="cluster_dist" label="BlockClust: Cluster distribution on ${on_string}" > | 153 <data format="pdf" name="cluster_hclust" label="BlockClust: Hierarchical clustering plot of cluster centroids on ${on_string}" > |
| 135 <filter> tool_mode["operation"]=="post"</filter> | 154 <filter> tool_mode["operation"]=="post"</filter> |
| 136 </data> | 155 </data> |
| 137 </outputs> | 156 </outputs> |
| 138 <help> | 157 <help> |
| 139 | 158 |