Mercurial > repos > rnateam > blockclust
comparison blockclust.xml @ 8:c1cc480c53da draft
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author | rnateam |
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date | Sun, 21 Sep 2014 20:41:10 -0400 |
parents | 6721468f2f9f |
children | 24d09ba85e45 |
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7:e6f49ee3509c | 8:c1cc480c53da |
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40 $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/celWS235/celWS235.reject.bed") | 40 $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/celWS235/celWS235.reject.bed") |
41 #elif str($tool_mode.reference) == "tair10": | 41 #elif str($tool_mode.reference) == "tair10": |
42 $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/tair10/tair10.accept.bed") | 42 $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/tair10/tair10.accept.bed") |
43 $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/tair10/tair10.reject.bed") | 43 $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/tair10/tair10.reject.bed") |
44 #end if | 44 #end if |
45 BlockClustPipeLine.pl -m TEST -f SEQUENCE -c \$BLOCKCLUST_DATA_PATH/blockclust.config | 45 BlockClustPipeLine.pl -m TEST -c \$BLOCKCLUST_DATA_PATH/blockclust.config |
46 -t $tool_mode.input_bbo | 46 -t $tool_mode.input_bbo |
47 -a #echo ''.join( $accept_bed ) | 47 -a #echo ''.join( $accept_bed ) |
48 -r #echo ''.join( $reject_bed ) | 48 -r #echo ''.join( $reject_bed ) |
49 -o $outputdir | 49 -o $outputdir |
50 #if $tool_mode.nochr: | |
51 -nochr | |
52 #end if | |
50 #if str($tool_mode.pred.enable_pred) == "yes": | 53 #if str($tool_mode.pred.enable_pred) == "yes": |
51 -p | 54 -p |
52 -pm $tool_mode.pred.pred_mode | 55 -pm $tool_mode.pred.pred_mode |
53 -md \$BLOCKCLUST_DATA_PATH/models | 56 -md \$BLOCKCLUST_DATA_PATH/models; |
54 -x 3; | |
55 #if str($tool_mode.pred.pred_mode) == "nearest_neighbour": | 57 #if str($tool_mode.pred.pred_mode) == "nearest_neighbour": |
56 cp #echo os.path.join($outputdir,'nearest_neighbour_predictions.txt')# $nearest_neighbour_pred_bed; | 58 cp #echo os.path.join($outputdir,'nearest_neighbour_predictions.txt')# $nearest_neighbour_pred_bed; |
57 #elif str($tool_mode.pred.pred_mode) == "model_based": | 59 #elif str($tool_mode.pred.pred_mode) == "model_based": |
58 cp #echo os.path.join($outputdir,'model_based_predictions.txt')# $model_based_pred_bed; | 60 cp #echo os.path.join($outputdir,'model_based_predictions.txt')# $model_based_pred_bed; |
59 #end if | 61 #end if |
88 <option value="panTro4">Chimp (panTro4)</option> | 90 <option value="panTro4">Chimp (panTro4)</option> |
89 <option value="xenTro3">Frog (xenTro3)</option> | 91 <option value="xenTro3">Frog (xenTro3)</option> |
90 <option value="celWS235">C. elegans (celWS235)</option> | 92 <option value="celWS235">C. elegans (celWS235)</option> |
91 <option value="tair10">Arabidopsis thaliana (tair10)</option> | 93 <option value="tair10">Arabidopsis thaliana (tair10)</option> |
92 </param> | 94 </param> |
95 <param name="nochr" type="boolean" label="My input files have no 'chr' for chromosome names" checked="False"/> | |
93 <conditional name="pred"> | 96 <conditional name="pred"> |
94 <param name="enable_pred" type="select" label="Would you like to perform classification?"> | 97 <param name="enable_pred" type="select" label="Would you like to perform classification?"> |
95 <option value="no">No</option> | 98 <option value="no">No</option> |
96 <option value="yes">Yes</option> | 99 <option value="yes">Yes</option> |
97 </param> | 100 </param> |