| Previous changeset 86:1e1d2724581f (2017-01-18) Next changeset 88:f5a4d8e45351 (2017-01-18) |
|
Commit message:
Uploaded |
|
modified:
mda_heatmap_gen_toolshed.xml |
| b |
| diff -r 1e1d2724581f -r 59668298e53b mda_heatmap_gen_toolshed.xml --- a/mda_heatmap_gen_toolshed.xml Wed Jan 18 10:16:50 2017 -0500 +++ b/mda_heatmap_gen_toolshed.xml Wed Jan 18 10:17:38 2017 -0500 |
| b |
| @@ -1,7 +1,7 @@ <?xml version="1.0" encoding="UTF-8" ?> <tool id="mda_heatmap_gen_toolshed" name="NG-CHM Generator" version="5.6.7"> <description>Create Clustered Heat Maps</description> -<command interpreter="bash" detect_errors="aggressive">$GALAXY_ROOT_DIR/../shed_tools/toolshed.g2.bx.psu.edu/repos/insilico-bob/ngchm/*/ngchm/MDAheatmap/ngchm-software/heatmap.sh '$hmname' '$hmdesc' '$inputmatrix' $rowOrderMethod $rowDistanceMeasure $rowAgglomerationMethod $columnOrderMethod $columnDistanceMeasure $columnAgglomerationMethod '$summarymethod' '$__tool_directory__' +<command interpreter="bash" detect_errors="aggressive">$GALAXY_ROOT_DIR/../shed_tools/toolshed.g2.bx.psu.edu/repos/insilico-bob/ngchm/*/ngchm/MDAheatmap/ngchm-software/heatmap.sh '$hmname' '$hmdesc' '$inputmatrix' $rowOrderMethod $rowDistanceMeasure $rowAgglomerationMethod $columnOrderMethod $columnDistanceMeasure $columnAgglomerationMethod '$summarymethod' $rowDendroCut $colDendroCut '$__tool_directory__' #for $op in $operations ${op.class_name} ${op.repeatinput.file_name} @@ -26,6 +26,19 @@ <option value="Original">Original Order</option> <option value="Random">Random</option> </param> + <when value="Hierarchical"> + <param name="rowDendroCut" type="select" label="Create Categorical Covariate bar based on top (value selected) Dendro sections" > + <option value="0" selected="true" >0</option> + <option value="2" >2</option> + <option value="3" >3</option> + <option value="4" >4</option> + <option value="5" >5</option> + <option value="6" >6</option> + <option value="7" >7</option> + <option value="8" >8</option> + <option value="9" >9</option> + <option value="10" >10</option> + </param> <param name="rowDistanceMeasure" type="select" label="Row Distance Metric" help="euclidean, binary, manhattan, maximum, canberra, minkowski, or correlation"> <option value="euclidean">Euclidean</option> <option value="binary">Binary</option> @@ -44,11 +57,25 @@ <option value="median">Median</option> <option value="centroid">Centroid</option> </param> + </when> <param name="columnOrderMethod" type="select" label="Column ordering method" help="Choices -- Hierarchical Clustering, Original Order, Random"> <option value="Hierarchical">Hierarchical Clustering</option> <option value="Original">Original Order</option> <option value="Random">Random</option> </param> + <when value="Hierarchical"> + <param name="colDendroCut" type="select" label="Create Categorical Covariate bar based on top (value selected) Dendro sections" > + <option value="0" selected="true" >0</option> + <option value="2" >2</option> + <option value="3" >3</option> + <option value="4" >4</option> + <option value="5" >5</option> + <option value="6" >6</option> + <option value="7" >7</option> + <option value="8" >8</option> + <option value="9" >9</option> + <option value="10" >10</option> + </param> <param name="columnDistanceMeasure" type="select" label="Column Distance Metric" help="euclidean, binary, manhattan, maximum, canberra, minkowski, or correlation"> <option value="euclidean">Euclidean</option> <option value="binary">Binary</option> @@ -67,6 +94,7 @@ <option value="median">Median</option> <option value="centroid">Centroid</option> </param> + </when> <repeat name="operations" title="Covariate Bars"> <param name="class_name" size="20" type="text" value="" label="Axis Covariate Name"> <sanitizer invalid_char="_"> |