Mercurial > repos > rnateam > blockclust
diff blockclust.xml @ 10:24d09ba85e45 draft
Uploaded
author | rnateam |
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date | Tue, 03 Feb 2015 05:49:47 -0500 |
parents | c1cc480c53da |
children | 6ecd674b5b62 |
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--- a/blockclust.xml Sun Sep 21 23:00:44 2014 -0400 +++ b/blockclust.xml Tue Feb 03 05:49:47 2015 -0500 @@ -3,13 +3,14 @@ <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="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> </requirements> <version_command>echo '1.0'</version_command> <command> +<![CDATA[ #if str($tool_mode.operation) == "pre": BlockClustPipeLine.pl -m PRE -bam $tool_mode.reads_bam -tbed $tags_bed #elif str($tool_mode.operation) == "clust": @@ -49,7 +50,7 @@ -o $outputdir #if $tool_mode.nochr: -nochr - #end if + #end if #if str($tool_mode.pred.enable_pred) == "yes": -p -pm $tool_mode.pred.pred_mode @@ -69,6 +70,7 @@ #elif str($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 ./; #end if +]]> </command> <inputs> <conditional name="tool_mode"> @@ -127,7 +129,7 @@ <data format="bed" name="model_based_pred_bed" label="BlockClust: Model based predictions BED on ${on_string}"> <filter> (( - tool_mode["operation"] == 'clust' and + tool_mode["operation"] == 'clust' and tool_mode["pred"]["enable_pred"] == "yes" and tool_mode["pred"]["pred_mode"] == "model_based" )) @@ -136,7 +138,7 @@ <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["operation"] == 'clust' and tool_mode["pred"]["enable_pred"] == "yes" and tool_mode["pred"]["pred_mode"] == "nearest_neighbour" )) @@ -153,18 +155,19 @@ </data> </outputs> <help> +<![CDATA[ .. class:: infomark -**What it does** +**What it does** -BlockClust is an efficient approach to detect transcripts with similar +BlockClust is an efficient approach to detect transcripts with similar processing patterns. We propose a novel way to encode expression profiles -in compact discrete structures, which can then be processed using -fast graph-kernel techniques. BlockClust allows both clustering and +in compact discrete structures, which can then be processed using +fast graph-kernel techniques. BlockClust allows both clustering and classification of small non-coding RNAs. -BlockClust runs in three operating modes: +BlockClust runs in three operating modes: 1) Pre-processing - converts given mapped reads (BAM) into BED file of tags @@ -207,10 +210,11 @@ ------ -**References** +**References** Pavankumar Videm, Dominic Rose, Fabrizio Costa, and Rolf Backofen. "BlockClust: efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles." Bioinformatics 30, no. 12 (2014): i274-i282. +]]> </help> </tool>