Mercurial > repos > rnateam > blockclust
changeset 14:0fbc8cdc1cd0 draft
Uploaded
| author | rnateam |
|---|---|
| date | Wed, 22 Jan 2014 11:20:03 -0500 |
| parents | bcb191e42032 |
| children | 6ee2478c4fdc |
| files | blockclust.xml tool_dependencies.xml |
| diffstat | 2 files changed, 45 insertions(+), 14 deletions(-) [+] |
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--- a/blockclust.xml Mon Oct 28 11:26:22 2013 -0400 +++ b/blockclust.xml Wed Jan 22 11:20:03 2014 -0500 @@ -1,20 +1,20 @@ -<tool id="blockclust" name="BlockClust" version="0.1"> +<tool id="blockclust" name="BlockClust" version="1.0.0"> <description>Non-coding RNA clustering from deep sequencing read profiles</description> <requirements> <requirement type="package" version="1.0">blockclust</requirement> + <requirement type="package" version="1.1">eden</requirement> <requirement type="package" version="3.0.1">R_3_0_1</requirement> <requirement type="package" version="0.1.19 ">samtools</requirement> + <requirement type="package" version="12.135">mcl</requirement> <requirement type="package" version="1.0">blockclust_rlibs</requirement> - <requirement type="set_environment">BLOCKCLUST_DATA_PATH</requirement> </requirements> - <!--<version_command> -version</version_command>--> + <version_command>echo '1.0'</version_command> <command> + #if str($tool_mode.operation) == "pre": #set $outputdir = $tags_bed.extra_files_path - BlockClustPipeLine.pl -m PRE -bam $tool_mode.reads_bam -tbed $tags_bed; - #end if - - #if str($tool_mode.operation) == "clust": + 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 $accept_bed=list() #set $reject_bed=list() @@ -28,6 +28,21 @@ #elif str($tool_mode.reference) == "dm3": $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/dm3/dm3.accept.bed") $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/dm3/dm3.reject.bed") + #elif str($tool_mode.reference) == "rheMac3": + $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/rheMac3/rheMac3.accept.bed") + $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/rheMac3/rheMac3.reject.bed") + #elif str($tool_mode.reference) == "panTro4": + $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/panTro3/panTro4.accept.bed") + $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/panTro3/panTro4.reject.bed") + #elif str($tool_mode.reference) == "xenTro3": + $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/xenTro3/xenTro3.accept.bed") + $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/xenTro3/xenTro3.reject.bed") + #elif str($tool_mode.reference) == "celWS235": + $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/celWS235/celWS235.accept.bed") + $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/celWS235/celWS235.reject.bed") + #elif str($tool_mode.reference) == "tair10": + $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/tair10/tair10.accept.bed") + $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/tair10/tair10.reject.bed") #end if BlockClustPipeLine.pl -m TEST -f SEQUENCE -c \$BLOCKCLUST_DATA_PATH/blockclust.config -t $tool_mode.input_bbo @@ -50,13 +65,12 @@ cp #echo os.path.join($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')# $sim_tab_out; - #end if - - #if str($tool_mode.operation) == "post": + 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 #end if </command> <inputs> @@ -75,6 +89,11 @@ <option value="hg19">Human (hg19)</option> <option value="mm10">Mouse (mm10)</option> <option value="dm3">Fly (dm3)</option> + <option value="rheMac3">Monkey (rheMac3)</option> + <option value="panTro4">Chimp (panTro4)</option> + <option value="xenTro3">Frog (xenTro3)</option> + <option value="celWS235">C. elegans (celWS235)</option> + <option value="tair10">Arabidopsis thaliana (tair10)</option> </param> <conditional name="pred"> <param name="enable_pred" type="select" label="Would you like to perform classification?"> @@ -128,10 +147,10 @@ <data format="tabular" name="sim_tab_out" label="BlockClust: Pairwise similarities on ${on_string}"> <filter> tool_mode["operation"]=="clust"</filter> </data> - <data format="tabular" name="analysis" label="BlockClust: Cluster analysis on ${on_string}" > + <data format="pdf" name="cluster_dist" label="BlockClust: Cluster distribution on ${on_string}" > <filter> tool_mode["operation"]=="post"</filter> </data> - <data format="pdf" name="cluster_dist" label="BlockClust: Cluster distribution on ${on_string}" > + <data format="pdf" name="cluster_hclust" label="BlockClust: Hierarchical clustering plot of cluster centroids on ${on_string}" > <filter> tool_mode["operation"]=="post"</filter> </data> </outputs>
--- a/tool_dependencies.xml Mon Oct 28 11:26:22 2013 -0400 +++ b/tool_dependencies.xml Wed Jan 22 11:20:03 2014 -0500 @@ -4,7 +4,13 @@ <repository changeset_revision="54195f1d4b0f" name="package_samtools_0_1_19" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" /> </package> <package name="R_3_0_1" version="3.0.1"> - <repository changeset_revision="e16e08f41ed7" name="package_r_3_0_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="1d5b86c2e93d" name="package_r_3_0_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + </package> + <package name="eden" version="1.1"> + <repository changeset_revision="25d3b2b5b677" name="package_eden_1_1" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + </package> + <package name="mcl" version="12.135 "> + <repository changeset_revision="7003196be1b1" name="package_mcl_12_135" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" /> </package> <package name="blockclust_rlibs" version="1.0"> <install version="1.0"> @@ -72,6 +78,12 @@ <action type="shell_command">tar xfvz panTro4.tar.gz -C $INSTALL_DIR/data/annotations/</action> <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/rheMac3.tar.gz</action> <action type="shell_command">tar xfvz rheMac3.tar.gz -C $INSTALL_DIR/data/annotations/</action> + <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/xenTro3.tar.gz</action> + <action type="shell_command">tar xfvz xenTro3.tar.gz -C $INSTALL_DIR/data/annotations/</action> + <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/celWS235.tar.gz</action> + <action type="shell_command">tar xfvz celWS235.tar.gz -C $INSTALL_DIR/data/annotations/</action> + <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/tair10.tar.gz</action> + <action type="shell_command">tar xfvz tair10.tar.gz -C $INSTALL_DIR/data/annotations/</action> <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/models.tar.gz</action> <action type="shell_command">tar xfvz models.tar.gz -C $INSTALL_DIR/data/</action> <action type="set_environment">