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comparison blockclust.xml @ 10:24d09ba85e45 draft

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author rnateam
date Tue, 03 Feb 2015 05:49:47 -0500
parents c1cc480c53da
children 6ecd674b5b62
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9:57f66041cc0f 10:24d09ba85e45
1 <tool id="blockclust" name="BlockClust" version="1.0.0"> 1 <tool id="blockclust" name="BlockClust" version="1.0.0">
2 <description>efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles</description> 2 <description>efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.0">blockclust</requirement> 4 <requirement type="package" version="1.0">blockclust</requirement>
5 <requirement type="package" version="1.1">eden</requirement> 5 <requirement type="package" version="1.1">eden</requirement>
6 <requirement type="package" version="3.0.1">R_3_0_1</requirement> 6 <requirement type="package" version="3.0.3">R</requirement>
7 <requirement type="package" version="0.1.19">samtools</requirement> 7 <requirement type="package" version="0.1.19">samtools</requirement>
8 <requirement type="package" version="12.135">mcl</requirement> 8 <requirement type="package" version="12.135">mcl</requirement>
9 <requirement type="package" version="1.0">blockclust_rlibs</requirement> 9 <requirement type="package" version="1.0">blockclust_rlibs</requirement>
10 </requirements> 10 </requirements>
11 <version_command>echo '1.0'</version_command> 11 <version_command>echo '1.0'</version_command>
12 <command> 12 <command>
13 <![CDATA[
13 #if str($tool_mode.operation) == "pre": 14 #if str($tool_mode.operation) == "pre":
14 BlockClustPipeLine.pl -m PRE -bam $tool_mode.reads_bam -tbed $tags_bed 15 BlockClustPipeLine.pl -m PRE -bam $tool_mode.reads_bam -tbed $tags_bed
15 #elif str($tool_mode.operation) == "clust": 16 #elif str($tool_mode.operation) == "clust":
16 #set $outputdir = $clusters.files_path 17 #set $outputdir = $clusters.files_path
17 #set $accept_bed=list() 18 #set $accept_bed=list()
47 -a #echo ''.join( $accept_bed ) 48 -a #echo ''.join( $accept_bed )
48 -r #echo ''.join( $reject_bed ) 49 -r #echo ''.join( $reject_bed )
49 -o $outputdir 50 -o $outputdir
50 #if $tool_mode.nochr: 51 #if $tool_mode.nochr:
51 -nochr 52 -nochr
52 #end if 53 #end if
53 #if str($tool_mode.pred.enable_pred) == "yes": 54 #if str($tool_mode.pred.enable_pred) == "yes":
54 -p 55 -p
55 -pm $tool_mode.pred.pred_mode 56 -pm $tool_mode.pred.pred_mode
56 -md \$BLOCKCLUST_DATA_PATH/models; 57 -md \$BLOCKCLUST_DATA_PATH/models;
57 #if str($tool_mode.pred.pred_mode) == "nearest_neighbour": 58 #if str($tool_mode.pred.pred_mode) == "nearest_neighbour":
67 cp #echo os.path.join($outputdir, 'hclust_tree.pdf')# $hclust_plot; 68 cp #echo os.path.join($outputdir, 'hclust_tree.pdf')# $hclust_plot;
68 cp #echo os.path.join($outputdir, 'discretized.gspan.tab')# $sim_tab_out 69 cp #echo os.path.join($outputdir, 'discretized.gspan.tab')# $sim_tab_out
69 #elif str($tool_mode.operation) == "post": 70 #elif str($tool_mode.operation) == "post":
70 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 ./; 71 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 ./;
71 #end if 72 #end if
73 ]]>
72 </command> 74 </command>
73 <inputs> 75 <inputs>
74 <conditional name="tool_mode"> 76 <conditional name="tool_mode">
75 <param name="operation" type="select" label="Select mode of operation"> 77 <param name="operation" type="select" label="Select mode of operation">
76 <option value="pre">Pre-processing </option> 78 <option value="pre">Pre-processing </option>
125 <filter> tool_mode["operation"]=="clust"</filter> 127 <filter> tool_mode["operation"]=="clust"</filter>
126 </data> 128 </data>
127 <data format="bed" name="model_based_pred_bed" label="BlockClust: Model based predictions BED on ${on_string}"> 129 <data format="bed" name="model_based_pred_bed" label="BlockClust: Model based predictions BED on ${on_string}">
128 <filter> 130 <filter>
129 (( 131 ((
130 tool_mode["operation"] == 'clust' and 132 tool_mode["operation"] == 'clust' and
131 tool_mode["pred"]["enable_pred"] == "yes" and 133 tool_mode["pred"]["enable_pred"] == "yes" and
132 tool_mode["pred"]["pred_mode"] == "model_based" 134 tool_mode["pred"]["pred_mode"] == "model_based"
133 )) 135 ))
134 </filter> 136 </filter>
135 </data> 137 </data>
136 <data format="bed" name="nearest_neighbour_pred_bed" label="BlockClust: Nearest neighbor predictions BED on ${on_string}"> 138 <data format="bed" name="nearest_neighbour_pred_bed" label="BlockClust: Nearest neighbor predictions BED on ${on_string}">
137 <filter> 139 <filter>
138 (( 140 ((
139 tool_mode["operation"] == 'clust' and 141 tool_mode["operation"] == 'clust' and
140 tool_mode["pred"]["enable_pred"] == "yes" and 142 tool_mode["pred"]["enable_pred"] == "yes" and
141 tool_mode["pred"]["pred_mode"] == "nearest_neighbour" 143 tool_mode["pred"]["pred_mode"] == "nearest_neighbour"
142 )) 144 ))
143 </filter> 145 </filter>
144 </data> 146 </data>
151 <data format="pdf" name="cluster_hclust" from_work_dir="hclust_tree_clusters.pdf" label="BlockClust: Hierarchical clustering plot of cluster centroids on ${on_string}" > 153 <data format="pdf" name="cluster_hclust" from_work_dir="hclust_tree_clusters.pdf" label="BlockClust: Hierarchical clustering plot of cluster centroids on ${on_string}" >
152 <filter> tool_mode["operation"]=="post"</filter> 154 <filter> tool_mode["operation"]=="post"</filter>
153 </data> 155 </data>
154 </outputs> 156 </outputs>
155 <help> 157 <help>
158 <![CDATA[
156 159
157 .. class:: infomark 160 .. class:: infomark
158 161
159 **What it does** 162 **What it does**
160 163
161 BlockClust is an efficient approach to detect transcripts with similar 164 BlockClust is an efficient approach to detect transcripts with similar
162 processing patterns. We propose a novel way to encode expression profiles 165 processing patterns. We propose a novel way to encode expression profiles
163 in compact discrete structures, which can then be processed using 166 in compact discrete structures, which can then be processed using
164 fast graph-kernel techniques. BlockClust allows both clustering and 167 fast graph-kernel techniques. BlockClust allows both clustering and
165 classification of small non-coding RNAs. 168 classification of small non-coding RNAs.
166 169
167 BlockClust runs in three operating modes: 170 BlockClust runs in three operating modes:
168 171
169 1) Pre-processing - converts given mapped reads (BAM) into BED file of tags 172 1) Pre-processing - converts given mapped reads (BAM) into BED file of tags
170 173
171 2) Clustering and classification - of given input blockgroups (output of blockbuster tool) as explained in the original paper. 174 2) Clustering and classification - of given input blockgroups (output of blockbuster tool) as explained in the original paper.
172 175
205 * Plot of distribution of ncRNA families per predicted cluster (overview of cluster precissions). The annotation of ncRNA families are retrieved by searching cluster instances against Rfam database. 208 * Plot of distribution of ncRNA families per predicted cluster (overview of cluster precissions). The annotation of ncRNA families are retrieved by searching cluster instances against Rfam database.
206 * Hierarchical clustering made out of centroids of each BlockClust predicted cluster 209 * Hierarchical clustering made out of centroids of each BlockClust predicted cluster
207 210
208 ------ 211 ------
209 212
210 **References** 213 **References**
211 214
212 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. 215 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.
213 216
214 217
218 ]]>
215 </help> 219 </help>
216 </tool> 220 </tool>