# HG changeset patch # User rnateam # Date 1542633014 18000 # Node ID aab6cf87b40a0b824cbc650d63504b85b931abf8 # Parent 6ecd674b5b62fe9167229c9812f80124bf20263a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust commit 8a847f019b21abaf4de2612dead57163b2c92d81 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 @@ -1,74 +1,43 @@ - + efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles - blockclust - eden - R - samtools - mcl - blockclust_rlibs + blockclust - echo '1.0' - -blockclust.py -v + @@ -76,13 +45,13 @@ - + - + @@ -102,8 +71,8 @@ - - + + @@ -118,42 +87,101 @@ - tool_mode["operation"]=="pre" + tool_mode["operation"]=="pre" - - tool_mode["operation"]=="clust" + + tool_mode["operation"]=="analysis" - - tool_mode["operation"]=="clust" + + tool_mode["operation"]=="analysis" - + (( - tool_mode["operation"] == 'clust' and + tool_mode["operation"] == 'analysis' and tool_mode["pred"]["enable_pred"] == "yes" and - tool_mode["pred"]["pred_mode"] == "model_based" + tool_mode["pred"]["pred_mode"] == "MODEL" + )) + + + + + (( + tool_mode["operation"] == 'analysis' and + tool_mode["pred"]["enable_pred"] == "yes" and + tool_mode["pred"]["pred_mode"] == "NEAREST" )) - - - (( - tool_mode["operation"] == 'clust' and - tool_mode["pred"]["enable_pred"] == "yes" and - tool_mode["pred"]["pred_mode"] == "nearest_neighbour" - )) - - - - tool_mode["operation"]=="clust" + + tool_mode["operation"]=="analysis" - tool_mode["operation"]=="post" + tool_mode["operation"]=="post" - tool_mode["operation"]=="post" + tool_mode["operation"]=="post" + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cluster_939 chr1 173833959 173834043 - 451.50 51 3 +chr1 173833973 173834009 tag_494715|1 1.000000 - 1 +chr1 173833970 173833996 tag_615439|1 1.000000 - 1 +chr1 173833970 173833996 tag_615372|1 1.000000 - 1 +chr1 173833970 173834004 tag_604763|1 1.000000 - 1 +chr1 173833970 173833992 tag_1773442|1 1.000000 - 1 +chr1 173833970 173833996 tag_1086667|1 1.000000 - 1 +chr1 173833970 173833991 tag_445309|1 1.000000 - 1 +chr1 173833970 173833999 tag_986404|1 1.000000 - 1 +chr1 173833970 173834000 tag_959571|1 1.000000 - 1 +chr1 173833970 173833993 tag_907644|1 1.000000 - 1 +chr1 173833970 173833998 tag_885788|1 1.000000 - 1 +chr1 173833970 173834000 tag_877925|1 1.000000 - 1 +chr1 173833970 173833991 tag_870314|1 1.000000 - 1 +chr1 173833970 173833996 tag_817326|1 1.000000 - 1 +chr1 173833970 173833992 tag_1436162|1 0.500000 - 1 +chr1 173833970 173834002 tag_180348|2 2.000000 - 1 +chr1 173833970 173834000 tag_54619|6 6.000000 - 1 +chr1 173833970 173833990 tag_31437|11 11.000000 - 1 +chr1 173833970 173833997 tag_21828|17 17.000000 - 1 +chr1 173833970 173833998 tag_18525|20 20.000000 - 1 +chr1 173833970 173833993 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tag_1772046|1 1.000000 - 2 +chr1 173834015 173834042 tag_653136|1 1.000000 - 2 +chr1 173834014 173834042 tag_873957|1 1.000000 - 2 +chr1 173834013 173834042 tag_1701612|1 1.000000 - 2 +chr1 173834012 173834042 tag_1612183|1 1.000000 - 2 +chr1 173834008 173834043 tag_1774651|1 1.000000 - 2 +chr1 173834007 173834043 tag_1420129|1 1.000000 - 2 +chr1 173834007 173834043 tag_139153|2 2.000000 - 2 +chr1 173834006 173834042 tag_1054353|1 1.000000 - 2 +chr1 173834006 173834042 tag_18530|20 20.000000 - 2 +chr1 173834023 173834042 tag_885887|1 1.000000 - 3 +chr1 173834021 173834042 tag_549350|1 1.000000 - 3 +>cluster_940 chr1 173834480 173834567 - 354.50 46 4 +chr1 173834490 173834511 tag_1307815|1 1.000000 - 1 +chr1 173834490 173834509 tag_2551|227 227.000000 - 1 +chr1 173834488 173834507 tag_104865|3 3.000000 - 1 +chr1 173834488 173834509 tag_104283|3 3.000000 - 1 +chr1 173834488 173834508 tag_1332791|1 1.000000 - 1 +chr1 173834487 173834508 tag_876963|1 1.000000 - 1 +chr1 173834487 173834507 tag_37578|9 9.000000 - 1 +chr1 173834487 173834509 tag_23539|15 15.000000 - 1 +chr1 173834481 173834507 tag_714997|1 1.000000 - 1 +chr1 173834548 173834567 tag_313337|1 1.000000 - 2 +chr1 173834547 173834567 tag_1079769|1 0.500000 - 2 +chr1 173834547 173834566 tag_401803|1 1.000000 - 2 +chr1 173834547 173834567 tag_42263|8 8.000000 - 2 +chr1 173834546 173834567 tag_1849484|1 0.500000 - 2 +chr1 173834546 173834566 tag_381674|1 1.000000 - 2 +chr1 173834543 173834567 tag_983219|1 1.000000 - 2 +chr1 173834542 173834567 tag_94884|3 3.000000 - 2 +chr1 173834540 173834567 tag_621110|1 1.000000 - 2 +chr1 173834539 173834567 tag_421538|1 1.000000 - 2 +chr1 173834539 173834566 tag_234286|1 1.000000 - 2 +chr1 173834538 173834566 tag_560176|1 1.000000 - 2 +chr1 173834538 173834566 tag_1789529|1 1.000000 - 2 +chr1 173834538 173834567 tag_1073342|1 1.000000 - 2 +chr1 173834537 173834567 tag_1442897|1 1.000000 - 2 +chr1 173834537 173834567 tag_157484|2 2.000000 - 2 +chr1 173834537 173834566 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203211034 203211054 tag_1764676|1 0.333333 - 2 +chr2 203211033 203211054 tag_604872|1 1.000000 - 2 +chr2 203211029 203211054 tag_458346|1 0.500000 - 2 +chr2 203211025 203211054 tag_994128|1 1.000000 - 2 +chr2 203211060 203211079 tag_557151|1 0.500000 - 3 +chr2 203211060 203211087 tag_152519|2 1.000000 - 3 +chr2 203211057 203211079 tag_540710|1 0.500000 - 3 +chr2 203211057 203211080 tag_189493|2 1.000000 - 3 +chr2 203211056 203211080 tag_300181|1 0.500000 - 3 +chr2 203211054 203211076 tag_579039|1 0.500000 - 3 +chr2 203211054 203211080 tag_190232|2 1.000000 - 3 +chr2 203211054 203211075 tag_152988|2 1.000000 - 3 +chr2 203211054 203211077 tag_140899|2 1.000000 - 3 +chr2 203211053 203211080 tag_518279|1 0.500000 - 3 +chr2 203211053 203211079 tag_990961|1 0.500000 - 3 +chr2 203211052 203211079 tag_180193|2 1.000000 - 3 +chr2 203211050 203211077 tag_626583|1 0.500000 - 3 +chr2 203211050 203211080 tag_1063242|1 0.500000 - 3 +chr2 203211050 203211077 tag_164082|2 1.000000 - 3 +chr2 203211049 203211076 tag_591760|1 0.500000 - 3 +chr2 203211049 203211078 tag_1745134|1 0.500000 - 3 +chr2 203211049 203211077 tag_377389|1 0.500000 - 3 +chr2 203211049 203211080 tag_1451447|1 0.500000 - 3 +chr2 203211049 203211079 tag_711824|1 0.500000 - 3 +chr2 203211049 203211080 tag_1289294|1 0.500000 - 3 +chr2 203211048 203211079 tag_744436|1 0.500000 - 3 +chr2 203211047 203211075 tag_1776657|1 0.500000 - 3 +chr2 203211046 203211079 tag_1728473|1 0.500000 - 3 +chr2 203211043 203211077 tag_679069|1 0.500000 - 3 +chr2 203211000 203211023 tag_84219|3 1.500000 - 4 +chr2 203211000 203211024 tag_79090|4 2.000000 - 4 +chr2 203211000 203211019 tag_48051|6 3.000000 - 4 +chr2 203211044 203211066 tag_1663547|1 0.500000 - 5 +chr2 203211044 203211068 tag_961039|1 0.500000 - 5 +chr2 203211043 203211066 tag_872911|1 0.500000 - 5 +chr2 203211041 203211069 tag_1431114|1 0.500000 - 5 +chr2 203211013 203211034 tag_331039|1 1.000000 - 6 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 @@ -1,104 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/ape_3.0-11.tar.gz - https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/plyr_1.8.tar.gz - https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/digest_0.6.4.tar.gz - https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/gtable_0.1.2.tar.gz - https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/dichromat_2.0-0.tar.gz - https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/colorspace_1.2-4.tar.gz - https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/munsell_0.4.2.tar.gz - https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/labeling_0.2.tar.gz - https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/RColorBrewer_1.0-5.tar.gz - https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/stringr_0.6.2.tar.gz - https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/scales_0.2.3.tar.gz - https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/proto_0.3-10.tar.gz - https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/reshape2_1.2.2.tar.gz - https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/ggplot2_0.9.3.1.tar.gz - https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/squash_1.0.1.tar.gz - - - - - - - - - - - https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-1.0.tar.gz - make - - BlockClust - $INSTALL_DIR/bin - - - BlockClustPipeLine.pl - $INSTALL_DIR/bin - - - filterKnownBlockGroups.pl - $INSTALL_DIR/bin - - - perf - $INSTALL_DIR/bin - - - plotClusters.R - $INSTALL_DIR/bin - - - blockclust.config - $INSTALL_DIR/data/ - - - rfam_map.txt - $INSTALL_DIR/data/ - - $INSTALL_DIR/data/annotations - https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/dm3.tar.gz - tar xfvz dm3.tar.gz -C $INSTALL_DIR/data/annotations/ - https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/hg19.tar.gz - tar xfvz hg19.tar.gz -C $INSTALL_DIR/data/annotations/ - https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/mm10.tar.gz - tar xfvz mm10.tar.gz -C $INSTALL_DIR/data/annotations/ - https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/panTro4.tar.gz - tar xfvz panTro4.tar.gz -C $INSTALL_DIR/data/annotations/ - https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/rheMac3.tar.gz - tar xfvz rheMac3.tar.gz -C $INSTALL_DIR/data/annotations/ - https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/celWS235.tar.gz - tar xfvz celWS235.tar.gz -C $INSTALL_DIR/data/annotations/ - https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/tair10.tar.gz - tar xfvz tair10.tar.gz -C $INSTALL_DIR/data/annotations/ - https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/models.tar.gz - tar xfvz models.tar.gz -C $INSTALL_DIR/data/ - - $INSTALL_DIR/bin - $INSTALL_DIR/data - - - - - - - -