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comparison blockclust.xml @ 8:c1cc480c53da draft

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Uploaded
author rnateam
date Sun, 21 Sep 2014 20:41:10 -0400
parents 6721468f2f9f
children 24d09ba85e45
comparison
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7:e6f49ee3509c 8:c1cc480c53da
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>