Mercurial > repos > rnateam > blockclust
changeset 12:aab6cf87b40a draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust commit 8a847f019b21abaf4de2612dead57163b2c92d81
author | rnateam |
---|---|
date | Mon, 19 Nov 2018 08:10:14 -0500 |
parents | 6ecd674b5b62 |
children | dbb6ee3179bc |
files | blockclust.xml test-data/test.bam test-data/test.tabular tool_dependencies.xml |
diffstat | 4 files changed, 2223 insertions(+), 188 deletions(-) [+] |
line wrap: on
line diff
--- 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 @@ -<tool id="blockclust" name="BlockClust" version="1.0.0"> +<tool id="blockclust" name="BlockClust" version="1.1.0"> <description>efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles</description> <requirements> - <requirement type="package" version="1.0">blockclust</requirement> - <requirement type="package" version="1.1">eden</requirement> - <requirement type="package" version="3.0.3">R</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="package" version="1.1.0">blockclust</requirement> </requirements> - <version_command>echo '1.0'</version_command> - <command> -<![CDATA[ + <version_command>blockclust.py -v</version_command> + <command detect_errors="aggressive"><![CDATA[ + export BLOCKCLUST_DATA_PATH=\$(dirname \$(which blockclust.py))/../share/blockclust_data && + #if str($tool_mode.operation) == "pre": - BlockClustPipeLine.pl -m PRE -bam $tool_mode.reads_bam -tbed $tags_bed - #elif str($tool_mode.operation) == "clust": + ln -s '$tool_mode.reads_bam' reads.bam && + ln -f -s '${$tool_mode.reads_bam.metadata.bam_index}' reads.bam.bai && + blockclust.py + -m PRE -bam reads.bam + -tbed '$tags_bed' + #elif str($tool_mode.operation) == "analysis": #set $outputdir = $clusters.files_path - #set $accept_bed=list() - #set $reject_bed=list() - ## prepare annotations - #if str($tool_mode.reference) == "hg19": - $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/hg19/hg19.accept.bed") - $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/hg19/hg19.reject.bed") - #elif str($tool_mode.reference) == "mm10": - $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/mm10/mm10.accept.bed") - $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/mm10/mm10.reject.bed") - #elif str($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 -c \$BLOCKCLUST_DATA_PATH/blockclust.config + blockclust.py + -o ./ + -m ANALYSIS + -f "\$BLOCKCLUST_DATA_PATH/blockclust.config" -t $tool_mode.input_bbo - -a #echo ''.join( $accept_bed ) - -r #echo ''.join( $reject_bed ) - -o $outputdir + -a "\$BLOCKCLUST_DATA_PATH/$tool_mode.reference/${tool_mode.reference}.accept.bed" + -r "\$BLOCKCLUST_DATA_PATH/$tool_mode.reference/${tool_mode.reference}.reject.bed" #if $tool_mode.nochr: -nochr #end if #if str($tool_mode.pred.enable_pred) == "yes": - -p - -pm $tool_mode.pred.pred_mode - -md \$BLOCKCLUST_DATA_PATH/models; - #if str($tool_mode.pred.pred_mode) == "nearest_neighbour": - cp #echo os.path.join($outputdir,'nearest_neighbour_predictions.txt')# $nearest_neighbour_pred_bed; - #elif str($tool_mode.pred.pred_mode) == "model_based": - cp #echo os.path.join($outputdir,'model_based_predictions.txt')# $model_based_pred_bed; - #end if - #else: - ; + -c + -cm $tool_mode.pred.pred_mode + -md "\$BLOCKCLUST_DATA_PATH/models" #end if - - cp #echo os.path.join($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')# $sim_tab_out #elif str($tool_mode.operation) == "post": - BlockClustPipeLine.pl -m POST -cbed $tool_mode.clusters_bed -cm $tool_mode.cmsearch_out -tab $tool_mode.sim_tab_in -rfam \$BLOCKCLUST_DATA_PATH/rfam_map.txt -o ./; + blockclust.py + -m POST + -cbed '$tool_mode.clusters_bed' + -cs '$tool_mode.cmsearch_out' + -tab '$tool_mode.sim_tab_in' + -rfam "\$BLOCKCLUST_DATA_PATH/rfam_map.txt" + -o ./ #end if ]]> </command> @@ -76,13 +45,13 @@ <conditional name="tool_mode"> <param name="operation" type="select" label="Select mode of operation"> <option value="pre">Pre-processing </option> - <option value="clust">Clustering and classification</option> + <option value="analysis">Clustering and classification</option> <option value="post">Post-processing</option> </param> <when value="pre"> <param name="reads_bam" type="data" format="bam" label="BAM file containing alignments" /> </when> - <when value="clust"> + <when value="analysis"> <param name="input_bbo" type="data" format="tabular" label="Input blockgroups file" /> <param name="reference" type="select" label="Select reference genome"> <option value="hg19">Human (hg19)</option> @@ -102,8 +71,8 @@ </param> <when value="yes"> <param name="pred_mode" type="select" label="Mode of classification"> - <option value="model_based">Model based</option> - <option value="nearest_neighbour">Nearest neighbour</option> + <option value="MODEL">Model based</option> + <option value="NEAREST">Nearest neighbour</option> </param> </when> </conditional> @@ -118,42 +87,101 @@ <outputs> <data format="bed" name="tags_bed" label="BlockClust: BAM to BED on ${on_string}"> - <filter> tool_mode["operation"]=="pre"</filter> + <filter>tool_mode["operation"]=="pre"</filter> </data> - <data format="pdf" name="hclust_plot" label="BlockClust: Hierarchical clustering plot on ${on_string}" > - <filter> tool_mode["operation"]=="clust"</filter> + <data format="pdf" name="hclust_plot" from_work_dir="hclust_tree.pdf" label="BlockClust: Hierarchical clustering plot on ${on_string}" > + <filter>tool_mode["operation"]=="analysis"</filter> </data> - <data format="bed" name="clusters" label="BlockClust: BED of predicted clusters on ${on_string}"> - <filter> tool_mode["operation"]=="clust"</filter> + <data format="bed" name="clusters" from_work_dir="mcl_clusters/all_clusters.bed" label="BlockClust: BED of predicted clusters on ${on_string}"> + <filter>tool_mode["operation"]=="analysis"</filter> </data> - <data format="bed" name="model_based_pred_bed" label="BlockClust: Model based predictions BED on ${on_string}"> + <data format="bed" name="model_based_pred_bed" from_work_dir="model_based_predictions.txt" label="BlockClust: Model based predictions BED on ${on_string}"> <filter> (( - 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" + )) + </filter> + </data> + <data format="bed" name="nearest_neighbour_pred_bed" from_work_dir="nearest_neighbour_predictions.txt" label="BlockClust: Nearest neighbor predictions BED on ${on_string}"> + <filter> + (( + tool_mode["operation"] == 'analysis' and + tool_mode["pred"]["enable_pred"] == "yes" and + tool_mode["pred"]["pred_mode"] == "NEAREST" )) </filter> </data> - <data format="bed" name="nearest_neighbour_pred_bed" label="BlockClust: Nearest neighbor predictions BED on ${on_string}"> - <filter> - (( - tool_mode["operation"] == 'clust' and - tool_mode["pred"]["enable_pred"] == "yes" and - tool_mode["pred"]["pred_mode"] == "nearest_neighbour" - )) - </filter> - </data> - <data format="tabular" name="sim_tab_out" label="BlockClust: Pairwise similarities on ${on_string}"> - <filter> tool_mode["operation"]=="clust"</filter> + <data format="tabular" name="sim_tab_out" from_work_dir="discretized.gspan.tab" label="BlockClust: Pairwise similarities on ${on_string}"> + <filter>tool_mode["operation"]=="analysis"</filter> </data> <data format="pdf" name="cluster_dist" from_work_dir="cluster_distribution.pdf" label="BlockClust: Cluster distribution on ${on_string}" > - <filter> tool_mode["operation"]=="post"</filter> + <filter>tool_mode["operation"]=="post"</filter> </data> <data format="pdf" name="cluster_hclust" from_work_dir="hclust_tree_clusters.pdf" label="BlockClust: Hierarchical clustering plot of cluster centroids on ${on_string}" > - <filter> tool_mode["operation"]=="post"</filter> + <filter>tool_mode["operation"]=="post"</filter> </data> </outputs> + <tests> + <!-- Test: PRE mode --> + + <test expect_num_outputs="1"> + <param name="operation" value="pre"/> + <param name="reads_bam" value="test.bam"/> + <output name="tags_bed"> + <assert_contents> + <has_text_matching expression="chr6\t26555497\t26555527\ttag_10|1|19\t0.052632\t+" /> + <has_text_matching expression="chr11\t122017275\t122017297\ttag_30|1|3\t0.333333\t-" /> + </assert_contents> + </output> + </test> + + <!-- Test: Clustering only --> + <test expect_num_outputs="3"> + <param name="operation" value="analysis"/> + <param name="input_bbo" value="test.tabular"/> + <param name="reference" value="hg19"/> + <param name="enable_pred" value="no"/> + <output name="clusters"> + <assert_contents> + <has_text_matching expression="chr1\t173833959\t173834043\t10:snoRNA_CD-box:blockgroup_939:cluster_1\t451.50\t-" /> + <has_text_matching expression="chr13\t92003008\t92003075\t8:miRNA:blockgroup_256:cluster_3\t2950.50\t\+" /> + </assert_contents> + </output> + </test> + + <!-- Test: Model based prediction --> + + <test expect_num_outputs="4"> + <param name="operation" value="analysis"/> + <param name="input_bbo" value="test.tabular"/> + <param name="reference" value="hg19"/> + <param name="enable_pred" value="yes"/> + <param name="pred_mode" value="MODEL"/> + <output name="model_based_pred_bed"> + <assert_contents> + <has_text_matching expression="chr2\t203211000\t203211097\tpredicted_tRNA\t284.07\t-" /> + </assert_contents> + </output> + </test> + + <!-- Test: Nearest neighbour based prediction --> + + <test expect_num_outputs="4"> + <param name="operation" value="analysis"/> + <param name="input_bbo" value="test.tabular"/> + <param name="reference" value="hg19"/> + <param name="enable_pred" value="yes"/> + <param name="pred_mode" value="NEAREST"/> + <output name="nearest_neighbour_pred_bed"> + <assert_contents> + <has_text_matching expression="chr2\t203211000\t203211097\tpredicted_tRNA\t284.07\t-" /> + </assert_contents> + </output> + </test> + + </tests> <help> <![CDATA[
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.tabular Mon Nov 19 08:10:14 2018 -0500 @@ -0,0 +1,2111 @@ +>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 tag_17806|21 21.000000 - 1 +chr1 173833970 173833994 tag_15560|25 25.000000 - 1 +chr1 173833970 173833995 tag_15220|26 26.000000 - 1 +chr1 173833970 173834001 tag_12856|32 32.000000 - 1 +chr1 173833970 173833999 tag_11760|35 35.000000 - 1 +chr1 173833970 173833989 tag_10226|42 42.000000 - 1 +chr1 173833970 173833991 tag_9416|47 47.000000 - 1 +chr1 173833970 173833996 tag_9315|47 47.000000 - 1 +chr1 173833970 173833992 tag_7304|64 64.000000 - 1 +chr1 173833969 173833996 tag_1397646|1 1.000000 - 1 +chr1 173833968 173834002 tag_821710|1 1.000000 - 1 +chr1 173833965 173833999 tag_252059|1 1.000000 - 1 +chr1 173833964 173833996 tag_421525|1 1.000000 - 1 +chr1 173833962 173833995 tag_336214|1 1.000000 - 1 +chr1 173833960 173833992 tag_1861751|1 1.000000 - 1 +chr1 173833960 173833992 tag_482224|1 1.000000 - 1 +chr1 173833959 173833992 tag_392974|1 1.000000 - 1 +chr1 173833959 173833992 tag_709126|1 1.000000 - 1 +chr1 173834019 173834043 tag_519261|1 1.000000 - 2 +chr1 173834018 173834042 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 tag_27201|13 13.000000 - 2 +chr1 173834536 173834566 tag_895368|1 1.000000 - 2 +chr1 173834535 173834566 tag_1196414|1 1.000000 - 2 +chr1 173834534 173834566 tag_107479|3 3.000000 - 2 +chr1 173834534 173834567 tag_676425|1 1.000000 - 2 +chr1 173834533 173834567 tag_222644|1 1.000000 - 2 +chr1 173834532 173834566 tag_56426|5 5.000000 - 2 +chr1 173834532 173834567 tag_25820|14 14.000000 - 2 +chr1 173834524 173834566 tag_804228|1 1.000000 - 2 +chr1 173834511 173834539 tag_883402|1 1.000000 - 3 +chr1 173834509 173834535 tag_1025251|1 1.000000 - 3 +chr1 173834509 173834540 tag_171208|2 2.000000 - 3 +chr1 173834509 173834539 tag_75815|4 4.000000 - 3 +chr1 173834509 173834537 tag_33421|10 10.000000 - 3 +chr1 173834508 173834537 tag_247501|1 1.000000 - 3 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+ 1 +chr20 2634903 2634930 tag_1149396|1 1.000000 + 1 +chr20 2634903 2634937 tag_551396|1 1.000000 + 1 +chr20 2634903 2634930 tag_1141171|1 1.000000 + 1 +chr20 2634903 2634930 tag_1793057|1 1.000000 + 1 +chr20 2634903 2634930 tag_483937|1 1.000000 + 1 +chr20 2634903 2634930 tag_403469|1 1.000000 + 1 +chr20 2634903 2634930 tag_400865|1 1.000000 + 1 +chr20 2634903 2634931 tag_902424|1 1.000000 + 1 +chr20 2634903 2634939 tag_854785|1 1.000000 + 1 +chr20 2634903 2634937 tag_1475911|1 1.000000 + 1 +chr20 2634903 2634932 tag_213180|1 1.000000 + 1 +chr20 2634903 2634937 tag_1416825|1 1.000000 + 1 +chr20 2634903 2634931 tag_1412864|1 1.000000 + 1 +chr20 2634903 2634929 tag_762145|1 1.000000 + 1 +chr20 2634903 2634930 tag_1318744|1 1.000000 + 1 +chr20 2634903 2634931 tag_22179|16 16.000000 + 1 +chr20 2634903 2634930 tag_4169|128 128.000000 + 1 +chr20 2634902 2634939 tag_603145|1 1.000000 + 1 +chr20 2634902 2634930 tag_354254|1 1.000000 + 1 +chr20 2634902 2634931 tag_93609|3 3.000000 + 1 +chr20 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203211096 tag_1311302|1 0.500000 - 1 +chr2 203211075 203211096 tag_1115885|1 0.500000 - 1 +chr2 203211075 203211096 tag_163233|2 1.000000 - 1 +chr2 203211075 203211095 tag_76576|4 2.000000 - 1 +chr2 203211075 203211094 tag_41856|8 4.000000 - 1 +chr2 203211074 203211095 tag_1198207|1 0.500000 - 1 +chr2 203211074 203211095 tag_548666|1 0.500000 - 1 +chr2 203211074 203211094 tag_1616044|1 0.500000 - 1 +chr2 203211074 203211096 tag_835346|1 0.500000 - 1 +chr2 203211074 203211095 tag_145685|2 1.000000 - 1 +chr2 203211074 203211095 tag_125201|2 1.000000 - 1 +chr2 203211074 203211097 tag_69755|4 2.000000 - 1 +chr2 203211074 203211096 tag_30937|11 5.500000 - 1 +chr2 203211074 203211095 tag_18003|21 10.500000 - 1 +chr2 203211074 203211094 tag_9578|46 23.000000 - 1 +chr2 203211074 203211093 tag_3652|150 75.000000 - 1 +chr2 203211073 203211096 tag_512465|1 0.500000 - 1 +chr2 203211073 203211094 tag_455624|1 0.333333 - 1 +chr2 203211073 203211094 tag_746765|1 0.500000 - 1 +chr2 203211072 203211096 tag_351358|1 0.500000 - 1 +chr2 203211071 203211097 tag_1663651|1 0.500000 - 1 +chr2 203211071 203211090 tag_927449|1 0.250000 - 1 +chr2 203211071 203211092 tag_893688|1 0.500000 - 1 +chr2 203211071 203211095 tag_175941|2 1.000000 - 1 +chr2 203211071 203211093 tag_651718|1 0.500000 - 1 +chr2 203211070 203211091 tag_729469|1 0.500000 - 1 +chr2 203211069 203211090 tag_375480|1 0.250000 - 1 +chr2 203211069 203211091 tag_1528925|1 0.500000 - 1 +chr2 203211069 203211089 tag_184814|2 0.400000 - 1 +chr2 203211068 203211096 tag_1838517|1 0.500000 - 1 +chr2 203211068 203211093 tag_156910|2 1.000000 - 1 +chr2 203211068 203211095 tag_737845|1 0.500000 - 1 +chr2 203211067 203211096 tag_261803|1 0.500000 - 1 +chr2 203211064 203211093 tag_1782359|1 0.500000 - 1 +chr2 203211060 203211090 tag_425926|1 0.500000 - 1 +chr2 203211038 203211057 tag_38614|8 2.666667 - 2 +chr2 203211036 203211057 tag_1675476|1 0.333333 - 2 +chr2 203211036 203211055 tag_253639|1 0.333333 - 2 +chr2 203211035 203211057 tag_523994|1 0.333333 - 2 +chr2 203211035 203211056 tag_160200|2 0.666667 - 2 +chr2 203211035 203211056 tag_19032|20 6.666667 - 2 +chr2 203211035 203211055 tag_14319|28 9.333333 - 2 +chr2 203211035 203211054 tag_3388|163 54.333333 - 2 +chr2 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
--- 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 @@ -<?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>