Mercurial > repos > rnateam > blockclust
changeset 8:c1cc480c53da draft
Uploaded
| author | rnateam |
|---|---|
| date | Sun, 21 Sep 2014 20:41:10 -0400 |
| parents | e6f49ee3509c |
| children | 57f66041cc0f |
| files | blockclust.xml tool_dependencies.xml |
| diffstat | 2 files changed, 7 insertions(+), 4 deletions(-) [+] |
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--- a/blockclust.xml Mon Jul 21 09:19:13 2014 -0400 +++ b/blockclust.xml Sun Sep 21 20:41:10 2014 -0400 @@ -42,16 +42,18 @@ $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 -f SEQUENCE -c \$BLOCKCLUST_DATA_PATH/blockclust.config + BlockClustPipeLine.pl -m TEST -c \$BLOCKCLUST_DATA_PATH/blockclust.config -t $tool_mode.input_bbo -a #echo ''.join( $accept_bed ) -r #echo ''.join( $reject_bed ) -o $outputdir + #if $tool_mode.nochr: + -nochr + #end if #if str($tool_mode.pred.enable_pred) == "yes": -p -pm $tool_mode.pred.pred_mode - -md \$BLOCKCLUST_DATA_PATH/models - -x 3; + -md \$BLOCKCLUST_DATA_PATH/models; #if str($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": @@ -90,6 +92,7 @@ <option value="celWS235">C. elegans (celWS235)</option> <option value="tair10">Arabidopsis thaliana (tair10)</option> </param> + <param name="nochr" type="boolean" label="My input files have no 'chr' for chromosome names" checked="False"/> <conditional name="pred"> <param name="enable_pred" type="select" label="Would you like to perform classification?"> <option value="no">No</option>
--- a/tool_dependencies.xml Mon Jul 21 09:19:13 2014 -0400 +++ b/tool_dependencies.xml Sun Sep 21 20:41:10 2014 -0400 @@ -1,7 +1,7 @@ <?xml version="1.0"?> <tool_dependency> <package name="samtools" version="0.1.19"> - <repository changeset_revision="279806044d60" name="package_samtools_0_1_19" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="923adc89c666" name="package_samtools_0_1_19" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="R_3_0_1" version="3.0.1"> <repository changeset_revision="c5ff6dd33c79" name="package_r_3_0_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />