| Previous changeset 11:6ecd674b5b62 (2015-02-03) Next changeset 13:dbb6ee3179bc (2023-11-04) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust commit 8a847f019b21abaf4de2612dead57163b2c92d81 |
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modified:
blockclust.xml |
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added:
test-data/test.bam test-data/test.tabular |
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removed:
tool_dependencies.xml |
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| diff -r 6ecd674b5b62 -r aab6cf87b40a blockclust.xml --- a/blockclust.xml Tue Feb 03 08:08:49 2015 -0500 +++ b/blockclust.xml Mon Nov 19 08:10:14 2018 -0500 |
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| b'@@ -1,74 +1,43 @@\n-<tool id="blockclust" name="BlockClust" version="1.0.0">\n+<tool id="blockclust" name="BlockClust" version="1.1.0">\n <description>efficient clustering and classification of non-coding RNAs from short read RNA-seq 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="3.0.3">R</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+ <requirement type="package" version="1.1.0">blockclust</requirement>\n </requirements>\n- <version_command>echo \'1.0\'</version_command>\n- <command>\n-<![CDATA[\n+ <version_command>blockclust.py -v</version_command>\n+ <command detect_errors="aggressive"><![CDATA[\n+ export BLOCKCLUST_DATA_PATH=\\$(dirname \\$(which blockclust.py))/../share/blockclust_data &&\n+\n #if str($tool_mode.operation) == "pre":\n- BlockClustPipeLine.pl -m PRE -bam $tool_mode.reads_bam -tbed $tags_bed\n- #elif str($tool_mode.operation) == "clust":\n+ ln -s \'$tool_mode.reads_bam\' reads.bam &&\n+ ln -f -s \'${$tool_mode.reads_bam.metadata.bam_index}\' reads.bam.bai &&\n+ blockclust.py \n+ -m PRE -bam reads.bam\n+ -tbed \'$tags_bed\'\n+ #elif str($tool_mode.operation) == "analysis":\n #set $outputdir = $clusters.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 -c \\$BLOCKCLUST_DATA_PATH/blockclust.config\n+ blockclust.py \n+ -o ./\n+ -m ANALYSIS\n+ -f "\\$BLOC'..b'ed_bed" label="BlockClust: Nearest neighbor predictions 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 format="tabular" name="sim_tab_out" from_work_dir="discretized.gspan.tab" label="BlockClust: Pairwise similarities on ${on_string}">\n+ <filter>tool_mode["operation"]=="analysis"</filter>\n </data>\n <data format="pdf" name="cluster_dist" from_work_dir="cluster_distribution.pdf" label="BlockClust: Cluster distribution on ${on_string}" >\n- <filter> tool_mode["operation"]=="post"</filter>\n+ <filter>tool_mode["operation"]=="post"</filter>\n </data>\n <data format="pdf" name="cluster_hclust" from_work_dir="hclust_tree_clusters.pdf" label="BlockClust: Hierarchical clustering plot of cluster centroids on ${on_string}" >\n- <filter> tool_mode["operation"]=="post"</filter>\n+ <filter>tool_mode["operation"]=="post"</filter>\n </data>\n </outputs>\n+ <tests>\n+ <!-- Test: PRE mode -->\n+\n+ <test expect_num_outputs="1">\n+ <param name="operation" value="pre"/>\n+ <param name="reads_bam" value="test.bam"/>\n+ <output name="tags_bed">\n+ <assert_contents>\n+ <has_text_matching expression="chr6\\t26555497\\t26555527\\ttag_10|1|19\\t0.052632\\t+" />\n+ <has_text_matching expression="chr11\\t122017275\\t122017297\\ttag_30|1|3\\t0.333333\\t-" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+\n+ <!-- Test: Clustering only -->\n+ <test expect_num_outputs="3">\n+ <param name="operation" value="analysis"/>\n+ <param name="input_bbo" value="test.tabular"/>\n+ <param name="reference" value="hg19"/>\n+ <param name="enable_pred" value="no"/>\n+ <output name="clusters">\n+ <assert_contents>\n+ <has_text_matching expression="chr1\\t173833959\\t173834043\\t10:snoRNA_CD-box:blockgroup_939:cluster_1\\t451.50\\t-" />\n+ <has_text_matching expression="chr13\\t92003008\\t92003075\\t8:miRNA:blockgroup_256:cluster_3\\t2950.50\\t\\+" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+\n+ <!-- Test: Model based prediction -->\n+\n+ <test expect_num_outputs="4">\n+ <param name="operation" value="analysis"/>\n+ <param name="input_bbo" value="test.tabular"/>\n+ <param name="reference" value="hg19"/>\n+ <param name="enable_pred" value="yes"/>\n+ <param name="pred_mode" value="MODEL"/>\n+ <output name="model_based_pred_bed">\n+ <assert_contents>\n+ <has_text_matching expression="chr2\\t203211000\\t203211097\\tpredicted_tRNA\\t284.07\\t-" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ \n+ <!-- Test: Nearest neighbour based prediction -->\n+\n+ <test expect_num_outputs="4">\n+ <param name="operation" value="analysis"/>\n+ <param name="input_bbo" value="test.tabular"/>\n+ <param name="reference" value="hg19"/>\n+ <param name="enable_pred" value="yes"/>\n+ <param name="pred_mode" value="NEAREST"/>\n+ <output name="nearest_neighbour_pred_bed">\n+ <assert_contents>\n+ <has_text_matching expression="chr2\\t203211000\\t203211097\\tpredicted_tRNA\\t284.07\\t-" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+\n+ </tests>\n <help>\n <![CDATA[\n \n' |
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| diff -r 6ecd674b5b62 -r aab6cf87b40a test-data/test.bam |
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| Binary file test-data/test.bam has changed |
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| diff -r 6ecd674b5b62 -r aab6cf87b40a test-data/test.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.tabular Mon Nov 19 08:10:14 2018 -0500 |
| b |
| b'@@ -0,0 +1,2111 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|
| b |
| diff -r 6ecd674b5b62 -r aab6cf87b40a tool_dependencies.xml --- a/tool_dependencies.xml Tue Feb 03 08:08:49 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,104 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="samtools" version="0.1.19"> - <repository changeset_revision="923adc89c666" name="package_samtools_0_1_19" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="R" version="3.0.3"> - <repository changeset_revision="f386d7431fe0" name="package_r_3_0_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="eden" version="1.1"> - <repository changeset_revision="8087eef83c35" name="package_eden_1_1" owner="rnateam" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="mcl" version="12.135"> - <repository changeset_revision="9f59d1a59999" name="package_mcl_12_135" owner="iuc" toolshed="https://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="f386d7431fe0" name="package_r_3_0_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> - <package name="R" version="3.0.3" /> - </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/RColorBrewer_1.0-5.tar.gz</package> - <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/stringr_0.6.2.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>$INSTALL_DIR/bin</destination> - </action> - <action type="move_file"> - <source>filterKnownBlockGroups.pl</source> - <destination>$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> |