| Previous changeset 40:8f8ab332a050 (2019-06-20) Next changeset 42:2f57ac512f46 (2020-07-06) |
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modified:
GalaxyMapGen.jar heatmap.sh mda_heatmap_gen.xml mda_heatmap_viz.zip |
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| diff -r 8f8ab332a050 -r 8acca16f3921 GalaxyMapGen.jar |
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| Binary file GalaxyMapGen.jar has changed |
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| diff -r 8f8ab332a050 -r 8acca16f3921 heatmap.sh --- a/heatmap.sh Thu Jun 20 11:39:46 2019 -0400 +++ b/heatmap.sh Tue Jan 28 15:32:19 2020 -0500 |
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| @@ -42,11 +42,17 @@ if [ $ctr -gt 1 ] then currParm=$(cut -d'|' -f1 <<< $i) - if [ $currParm != "matrix_files" ] && [ $currParm != "row_configuration" ] && [ $currParm != "col_configuration" ] && [ $currParm != "classification" ] + if [ $currParm != "matrix_files" ] && [ $currParm != "row_configuration" ] && [ $currParm != "col_configuration" ] && [ $currParm != "classification" ] && [ $currParm != "chm_name" ] then #Parse pipe-delimited parameter parameter parmJson=$parmJson' "'$(cut -d'|' -f1 <<< $i)'":"'$(cut -d'|' -f2 <<< $i)'",' fi + if [ $currParm = "chm_name" ] + then + currVal=$(cut -d'|' -f2 <<< $i) + currEdit=$(echo "$currVal" | sed 's/\//_/g') + parmJson=$parmJson' "'$(cut -d'|' -f1 <<< $i)'":"'$currEdit'",' + fi if [ $currParm = "row_configuration" ] then rowOrder=$(cut -d'|' -f3 <<< $i) @@ -108,7 +114,11 @@ then classIter=$((classIter+1)) #Parse pipe-delimited 3-part classification bar parameter - classJson=$classJson' {"'$(cut -d'|' -f2 <<< $i)'":"'$(cut -d'|' -f3 <<< $i)'","'$(cut -d'|' -f4 <<< $i)'":"'$(cut -d'|' -f5 <<< $i)'"' + className=$(cut -d'|' -f3 <<< $i) + if [[ -z "$className" ]]; then + className="covar"$classIter + fi + classJson=$classJson' {"'$(cut -d'|' -f2 <<< $i)'":"'$className'","'$(cut -d'|' -f4 <<< $i)'":"'$(cut -d'|' -f5 <<< $i)'"' classCat=$(cut -d'|' -f7 <<< $i) classColorType=$(cut -d'_' -f2 <<< $classCat) classJson=$classJson',' @@ -135,8 +145,11 @@ if [ `echo "$output" | grep -c "Inf in foreign function call"` -gt 0 ] then echo ""; - echo "Note: This error can occur when there is no variation in a row or column. Try a different distance measure or remove rows/columns without variation."; - echo "This error may also be caused when a covariate file has inadvertently been selected as an Input Matrix. Check your Input Matrix entry."; + echo "R CLUSTERING: Error in clustering the matrix provided (View Details - stdout). " + echo "Note: This error can occur when:" + echo " 1. There is invalid numeric data in the matrix provided. Try using Matrix Manipulation tools to fix invalid data."; + echo " 2. There is no variation in a row or column in the matrix. Try a different distance measure or remove rows/columns without variation using Matrix Manipulation tools."; + echo " 3. A covariate file has inadvertently been selected as an Input Matrix. Check your Input Matrix entry."; fi exit $rc; fi |
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| diff -r 8f8ab332a050 -r 8acca16f3921 mda_heatmap_gen.xml --- a/mda_heatmap_gen.xml Thu Jun 20 11:39:46 2019 -0400 +++ b/mda_heatmap_gen.xml Tue Jan 28 15:32:19 2020 -0500 |
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| @@ -19,28 +19,20 @@ </stdio> <inputs> <param name="inputmatrix" type="data" format="Tabular" label="Input Data Matrix" help="Tab delimited text file with row labels, column labels, and data." /> - <param name="hmname" size="40" type="text" value="Heat_Map_name" label="Heat Map Name" help="Short Name for heat map (no spaces)."/> - <sanitizer> - <valid> - <add preset="string.printable"/> + <param name="hmname" size="40" type="text" value="Heat_Map_name" label="Heat Map Name" help="Short Name for heat map (no spaces)." optional="false"/> + <sanitizer> + <valid initial="string.printable"> <remove value="""/> <remove value="'"/> - <remove value=" "/> </valid> - </sanitizer> - <param name="hmdesc" size="100" optional="true" type="text" value="Heat_Map_description" label="Heat Map Description" help="Longer description of the heat map contents."/> - <sanitizer> - <valid> - <add preset="string.printable"/> - <add value="string.letters"/> - <add value="string.digits"/> - <add value="-"/> - <add value="_"/> + </sanitizer> + <param name="hmdesc" size="100" optional="true" type="text" value="Heat_Map_description" label="Heat Map Description" help="Longer description of the heat map contents."/> + <sanitizer> + <valid initial="string.printable"> <remove value="""/> <remove value="'"/> - <remove value=" "/> </valid> - </sanitizer> + </sanitizer> <param name="summarymethod" type="select" label="Data Summarization Method" help="For large matrices, the selected method is used to aggregate data values in the summary view."> <option value="average">Average</option> <option value="sample">Sample</option> @@ -117,15 +109,13 @@ </when> </conditional> <repeat name="operations" title="Covariate Bars"> - <param name="class_name" size="25" type="text" value="" label="Covariate Name" help="Covariate heat map display label."> - <sanitizer> - <valid> - <add preset="string.printable"/> + <param name="class_name" size="25" type="text" value="" label="Covariate Name" optional="false" help="Covariate heat map display label."> + <sanitizer> + <valid initial="string.printable"> <remove value="""/> <remove value="'"/> - <remove value=" "/> </valid> - </sanitizer> + </sanitizer> </param> <param name="repeatinput" type="data" format="Tabular" label="Covariate File" help="Tab delimited text file with row or column label and covariate value on each line."/> <param name="cat" type="select" label="Axis Covariate Type" help="Identify the covariate as belonging to rows or columns and containing categorical or continuous values."> |
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| diff -r 8f8ab332a050 -r 8acca16f3921 mda_heatmap_viz.zip |
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| Binary file mda_heatmap_viz.zip has changed |