| Next changeset 1:a92d8689aa30 (2014-07-08) |
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Commit message:
Uploaded |
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added:
blockclust.xml tool_dependencies.xml |
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| diff -r 000000000000 -r 768a67f6ae18 blockclust.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/blockclust.xml Tue May 06 07:49:25 2014 -0400 |
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| b'@@ -0,0 +1,186 @@\n+<tool id="blockclust" name="BlockClust" version="1.0.0">\n+ <description>Non-coding RNA clustering from deep sequencing read profiles</description>\n+ <requirements>\n+ <requirement type="package" version="1.0">blockclust</requirement>\n+ <requirement type="package" version="1.1">eden</requirement>\n+ <requirement type="package" version="3.0.1">R_3_0_1</requirement>\n+ <requirement type="package" version="0.1.19">samtools</requirement>\n+ <requirement type="package" version="12.135">mcl</requirement>\n+ <requirement type="package" version="1.0">blockclust_rlibs</requirement>\n+ </requirements>\n+ <version_command>echo \'1.0\'</version_command>\n+ <command>\n+\n+ #if str($tool_mode.operation) == "pre":\n+ #set $outputdir = $tags_bed.extra_files_path\n+ BlockClustPipeLine.pl -m PRE -bam $tool_mode.reads_bam -tbed $tags_bed\n+ #elif str($tool_mode.operation) == "clust":\n+ #set $outputdir = $clusters.extra_files_path\n+ #set $accept_bed=list()\n+ #set $reject_bed=list()\n+ ## prepare annotations\n+ #if str($tool_mode.reference) == "hg19":\n+ $accept_bed.append("\\$BLOCKCLUST_DATA_PATH/annotations/hg19/hg19.accept.bed")\n+ $reject_bed.append("\\$BLOCKCLUST_DATA_PATH/annotations/hg19/hg19.reject.bed")\n+ #elif str($tool_mode.reference) == "mm10":\n+ $accept_bed.append("\\$BLOCKCLUST_DATA_PATH/annotations/mm10/mm10.accept.bed")\n+ $reject_bed.append("\\$BLOCKCLUST_DATA_PATH/annotations/mm10/mm10.reject.bed")\n+ #elif str($tool_mode.reference) == "dm3":\n+ $accept_bed.append("\\$BLOCKCLUST_DATA_PATH/annotations/dm3/dm3.accept.bed")\n+ $reject_bed.append("\\$BLOCKCLUST_DATA_PATH/annotations/dm3/dm3.reject.bed")\n+ #elif str($tool_mode.reference) == "rheMac3":\n+ $accept_bed.append("\\$BLOCKCLUST_DATA_PATH/annotations/rheMac3/rheMac3.accept.bed")\n+ $reject_bed.append("\\$BLOCKCLUST_DATA_PATH/annotations/rheMac3/rheMac3.reject.bed")\n+ #elif str($tool_mode.reference) == "panTro4":\n+ $accept_bed.append("\\$BLOCKCLUST_DATA_PATH/annotations/panTro3/panTro4.accept.bed")\n+ $reject_bed.append("\\$BLOCKCLUST_DATA_PATH/annotations/panTro3/panTro4.reject.bed")\n+ #elif str($tool_mode.reference) == "xenTro3":\n+ $accept_bed.append("\\$BLOCKCLUST_DATA_PATH/annotations/xenTro3/xenTro3.accept.bed")\n+ $reject_bed.append("\\$BLOCKCLUST_DATA_PATH/annotations/xenTro3/xenTro3.reject.bed")\n+ #elif str($tool_mode.reference) == "celWS235":\n+ $accept_bed.append("\\$BLOCKCLUST_DATA_PATH/annotations/celWS235/celWS235.accept.bed")\n+ $reject_bed.append("\\$BLOCKCLUST_DATA_PATH/annotations/celWS235/celWS235.reject.bed")\n+ #elif str($tool_mode.reference) == "tair10":\n+ $accept_bed.append("\\$BLOCKCLUST_DATA_PATH/annotations/tair10/tair10.accept.bed")\n+ $reject_bed.append("\\$BLOCKCLUST_DATA_PATH/annotations/tair10/tair10.reject.bed")\n+ #end if\n+ BlockClustPipeLine.pl -m TEST -f SEQUENCE -c \\$BLOCKCLUST_DATA_PATH/blockclust.config\n+ -t $tool_mode.input_bbo\n+ -a #echo \'\'.join( $accept_bed )\n+ -r #echo \'\'.join( $reject_bed )\n+ -o $outputdir\n+ #if str($tool_mode.pred.enable_pred) == "yes":\n+ -p\n+ -pm $tool_mode.pred.pred_mode\n+ -md \\$BLOCKCLUST_DATA_PATH/models\n+ -x 3;\n+ #if str($tool_mode.pred.pred_mode) == "nearest_neighbour":\n+ cp #echo os.path.join($outputdir,\'nearest_neighbour_predictions.txt\')# $nearest_neighbour_pred_bed;\n+ #elif str($tool_mode.pred.pred_mode) == "model_based":\n+ cp #echo os.path.join($outputdir,\'model_based_predic'..b' <option value="rheMac3">Monkey (rheMac3)</option>\n+ <option value="panTro4">Chimp (panTro4)</option>\n+ <option value="xenTro3">Frog (xenTro3)</option>\n+ <option value="celWS235">C. elegans (celWS235)</option>\n+ <option value="tair10">Arabidopsis thaliana (tair10)</option>\n+ </param>\n+ <conditional name="pred">\n+ <param name="enable_pred" type="select" label="Would you like to perform classification?">\n+ <option value="no">No</option>\n+ <option value="yes">Yes</option>\n+ </param>\n+ <when value="yes">\n+ <param name="pred_mode" type="select" label="Mode of classification">\n+ <option value="model_based">Model based</option>\n+ <option value="nearest_neighbour">Nearest neighbour</option>\n+ </param>\n+ </when>\n+ </conditional>\n+ </when>\n+ <when value="post">\n+ <param name="cmsearch_out" type="data" format="tabular" label="Output of cmsearch tool" />\n+ <param name="clusters_bed" type="data" format="bed" label="BED file containing clusters (output of BlockClust)" />\n+ <param name="sim_tab_in" type="data" format="tabular" label="Pairwise similarities file" />\n+ </when>\n+ </conditional>\n+ </inputs>\n+\n+ <outputs>\n+ <data format="bed" name="tags_bed" label="BlockClust: BAM to BED on ${on_string}">\n+ <filter> tool_mode["operation"]=="pre"</filter>\n+ </data>\n+ <data format="pdf" name="hclust_plot" label="BlockClust: Hierarchical clustering plot on ${on_string}" >\n+ <filter> tool_mode["operation"]=="clust"</filter>\n+ </data>\n+ <data format="bed" name="clusters" label="BlockClust: Clustering BED on ${on_string}">\n+ <filter> tool_mode["operation"]=="clust"</filter>\n+ </data>\n+ <data format="bed" name="model_based_pred_bed" label="BlockClust: Model based prediction BED on ${on_string}">\n+ <filter>\n+ ((\n+ tool_mode["operation"] == \'clust\' and \n+ tool_mode["pred"]["enable_pred"] == "yes" and\n+ tool_mode["pred"]["pred_mode"] == "model_based"\n+ ))\n+ </filter>\n+ </data>\n+ <data format="bed" name="nearest_neighbour_pred_bed" label="BlockClust: Nearest neighbour prediction BED on ${on_string}">\n+ <filter>\n+ ((\n+ tool_mode["operation"] == \'clust\' and \n+ tool_mode["pred"]["enable_pred"] == "yes" and\n+ tool_mode["pred"]["pred_mode"] == "nearest_neighbour"\n+ ))\n+ </filter>\n+ </data>\n+ <data format="tabular" name="sim_tab_out" label="BlockClust: Pairwise similarities on ${on_string}">\n+ <filter> tool_mode["operation"]=="clust"</filter>\n+ </data>\n+ <data format="pdf" name="cluster_dist" label="BlockClust: Cluster distribution on ${on_string}" >\n+ <filter> tool_mode["operation"]=="post"</filter>\n+ </data>\n+ <data format="pdf" name="cluster_hclust" label="BlockClust: Hierarchical clustering plot of cluster centroids on ${on_string}" >\n+ <filter> tool_mode["operation"]=="post"</filter>\n+ </data>\n+ </outputs>\n+ <help>\n+\n+.. class:: infomark\n+\n+**What it does** \n+\n+Clusters the read profiles (i.e., blockgroups) from the blockbuster tool.\n+\n+**Inputs**\n+\n+BlockClust needs output of tool blockbuster as input \n+\n+**Output**\n+\n+BlockClust produces a fasta file containing clusters.\n+\n+------\n+\n+**Licenses**\n+\n+If **BlockClust** is used to obtain results for scientific publications it\n+should be cited as [1]_.\n+\n+**References** \n+\n+.. [1] \n+\n+\n+ </help>\n+</tool>\n' |
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| diff -r 000000000000 -r 768a67f6ae18 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue May 06 07:49:25 2014 -0400 |
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| @@ -0,0 +1,98 @@ +<?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" /> + </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" /> + </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" /> + </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" /> + </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"> + <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> + <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/plyr_1.8.tar.gz</package> + <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/digest_0.6.4.tar.gz</package> + <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/gtable_0.1.2.tar.gz</package> + <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/dichromat_2.0-0.tar.gz</package> + <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/colorspace_1.2-4.tar.gz</package> + <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/munsell_0.4.2.tar.gz</package> + <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/labeling_0.2.tar.gz</package> + <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/scales_0.2.3.tar.gz</package> + <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/proto_0.3-10.tar.gz</package> + <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/reshape2_1.2.2.tar.gz</package> + <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/ggplot2_0.9.3.1.tar.gz</package> + <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/squash_1.0.1.tar.gz</package> + </action> + </actions> + </install> + <readme> + + </readme> + </package> + <package name="blockclust" version="1.0"> + <install version="1.0"> + <actions> + <action type="download_by_url">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-1.0.tar.gz</action> + <action type="shell_command">make</action> + <action type="move_file"> + <source>BlockClust</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>BlockClustPipeLine.pl</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>perf</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>plotClusters.R</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>blockclust.config</source> + <destination>$INSTALL_DIR/data/</destination> + </action> + <action type="move_file"> + <source>rfam_map.txt</source> + <destination>$INSTALL_DIR/data/</destination> + </action> + <action type="make_directory">$INSTALL_DIR/data/annotations</action> + <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/dm3.tar.gz</action> + <action type="shell_command">tar xfvz dm3.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/hg19.tar.gz</action> + <action type="shell_command">tar xfvz hg19.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/mm10.tar.gz</action> + <action type="shell_command">tar xfvz mm10.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/panTro4.tar.gz</action> + <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/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 $INSTALL_DIR/data/</action> + <action type="set_environment"> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> + <environment_variable action="set_to" name="BLOCKCLUST_DATA_PATH">$INSTALL_DIR/data</environment_variable> + </action> + </actions> + </install> + <readme> + + </readme> + </package> +</tool_dependency> |