| Previous changeset 93:13a7954ccbe7 (2017-01-18) Next changeset 95:ff23e572316e (2017-01-19) |
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modified:
mda_heatmap_gen_toolshed.xml |
| b |
| diff -r 13a7954ccbe7 -r 301c8672bb83 mda_heatmap_gen_toolshed.xml --- a/mda_heatmap_gen_toolshed.xml Wed Jan 18 12:00:45 2017 -0500 +++ b/mda_heatmap_gen_toolshed.xml Thu Jan 19 11:56:26 2017 -0500 |
| b |
| @@ -1,7 +1,8 @@ <?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' ${d_rows.rowOrderMethod} ${d_rows.rowDistanceMeasure} ${d_rows.rowAgglomerationMethod} ${d_cols.columnOrderMethod} ${d_cols.columnDistanceMeasure} ${d_cols.columnAgglomerationMethod} $summarymethod '$__tool_directory__' ${d_rows.rowDendroCut} ${d_cols.colDendroCut} +<!-- <command interpreter="bash" detect_errors="aggressive">$GALAXY_ROOT_DIR/../shed_tools/toolshed.g2.bx.psu.edu/repos/insilico-bob/ngchm/*/ngchm/MDAheatmap/ngchm-software/heatmap.sh '$hmname' '$hmdesc' '$inputmatrix' ${d_rows.rowOrderMethod} ${d_rows.rowDistanceMeasure} ${d_rows.rowAgglomerationMethod} ${d_cols.columnOrderMethod} ${d_cols.columnDistanceMeasure} ${d_cols.columnAgglomerationMethod} $summarymethod '$__tool_directory__' ${d_rows.rowDendroCut} ${d_cols.colDendroCut} --> +<command interpreter="bash" detect_errors="aggressive">$__tool_directory__/heatmap.sh '$hmname' '$hmdesc' '$inputmatrix' ${d_rows.rowOrderMethod} ${d_rows.rowDistanceMeasure} ${d_rows.rowAgglomerationMethod} ${d_cols.columnOrderMethod} ${d_cols.columnDistanceMeasure} ${d_cols.columnAgglomerationMethod} $summarymethod '$__tool_directory__' ${d_rows.rowDendroCut} ${d_cols.colDendroCut} #for $op in $operations ${op.class_name} ${op.repeatinput.file_name} @@ -28,18 +29,6 @@ <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> @@ -58,17 +47,8 @@ <option value="median">Median</option> <option value="centroid">Centroid</option> </param> - </when> - </conditional> - <conditional name="d_cols"> - <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> + <param name="rowDendroCut" type="select" label="Create Categorical Covariate bar based on top (value selected) Dendro sections" > + <option value="0" selected="true" >None</option> <option value="2" >2</option> <option value="3" >3</option> <option value="4" >4</option> @@ -79,6 +59,15 @@ <option value="9" >9</option> <option value="10" >10</option> </param> + </when> + </conditional> + <conditional name="d_cols"> + <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="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> @@ -97,6 +86,18 @@ <option value="median">Median</option> <option value="centroid">Centroid</option> </param> + <param name="colDendroCut" type="select" label="Create Categorical Covariate bar based on top (value selected) Dendro sections" > + <option value="0" selected="true" >None</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> </when> </conditional> <repeat name="operations" title="Covariate Bars"> |