| Previous changeset 6:1f13d304ddbd (2019-06-20) Next changeset 8:c1be063b2454 (2020-07-06) |
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GalaxyMapGen.jar heatmap_advanced.sh mda_advanced_heatmap_gen.xml mda_heatmap_viz.zip |
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| diff -r 1f13d304ddbd -r c5489978071a GalaxyMapGen.jar |
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| Binary file GalaxyMapGen.jar has changed |
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| diff -r 1f13d304ddbd -r c5489978071a heatmap_advanced.sh --- a/heatmap_advanced.sh Thu Jun 20 11:36:53 2019 -0400 +++ b/heatmap_advanced.sh Tue Jan 28 15:33:09 2020 -0500 |
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| @@ -59,11 +59,17 @@ if [ $ctr -gt 1 ] then currParm=$(cut -d'|' -f1 <<< $i) - if [ $currParm != "matrix_files" ] && [ $currParm != "row_configuration" ] && [ $currParm != "col_configuration" ] && [ $currParm != "classification" ] && [ $currParm != "attribute" ] + if [ $currParm != "matrix_files" ] && [ $currParm != "row_configuration" ] && [ $currParm != "col_configuration" ] && [ $currParm != "classification" ] && [ $currParm != "attribute" ] && [ $currParm != "chm_name" ] then #Parse pipe-delimited parameter parameter parmJson=$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 <<< $i) @@ -318,7 +324,10 @@ classIter=$((classIter+1)) className=$(cut -d'|' -f3 <<< $i) #Parse pipe-delimited 3-part classification bar parameter - classJson=$classJson' {"'$(cut -d'|' -f2 <<< $i)'":"'$(cut -d'|' -f3 <<< $i)'","'$(cut -d'|' -f4 <<< $i)'":"'$(cut -d'|' -f5 <<< $i)'","'$(cut -d'|' -f8 <<< $i)'":"'$(cut -d'|' -f9 <<< $i)'","'$(cut -d'|' -f12 <<< $i)'":"'$(cut -d'|' -f13 <<< $i)'","'$(cut -d'|' -f14 <<< $i)'":"'$(cut -d'|' -f15 <<< $i)'"' + if [[ -z "$className" ]]; then + className="covar"$classIter + fi + classJson=$classJson' {"'$(cut -d'|' -f2 <<< $i)'":"'$className'","'$(cut -d'|' -f4 <<< $i)'":"'$(cut -d'|' -f5 <<< $i)'","'$(cut -d'|' -f8 <<< $i)'":"'$(cut -d'|' -f9 <<< $i)'","'$(cut -d'|' -f12 <<< $i)'":"'$(cut -d'|' -f13 <<< $i)'","'$(cut -d'|' -f14 <<< $i)'":"'$(cut -d'|' -f15 <<< $i)'"' classCat=$(cut -d'|' -f7 <<< $i) classColorType=$(cut -d'_' -f2 <<< $classCat) classJson=$classJson',' @@ -357,8 +366,12 @@ if [ `echo "$output" | grep -c "Inf in foreign function call"` -gt 0 ] then echo ""; - echo "NOTE 1: This error can occur when a covariate file has inadvertently been selected as an Input Matrix. Check your Input Matrix entry."; - echo "NOTE 2: This error can occur when there is no variation in a data rows or columns in the input matrix. Try a different distance measure or remove rows/columns without variation."; + echo ""; + 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 1f13d304ddbd -r c5489978071a mda_advanced_heatmap_gen.xml --- a/mda_advanced_heatmap_gen.xml Thu Jun 20 11:36:53 2019 -0400 +++ b/mda_advanced_heatmap_gen.xml Tue Jan 28 15:33:09 2020 -0500 |
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| b'@@ -26,14 +26,12 @@\n <repeat name="matrices" title="Heat Map Matrices">\r\n \t<param name="dataLayer" type="data" format="Tabular" label="Input Data Matrix" help="Tab delimited text file with row labels, column labels, and data."/>\r\n \t<param name="dataLayerName" size="40" type="text" value="Data_Layer_name" label="Data Layer Name" help="Name for data layer (no spaces).">\r\n- <sanitizer>\r\n- <valid>\r\n- <add preset="string.printable"/>\r\n+\t <sanitizer>\r\n+ \t<valid initial="string.printable">\r\n \t<remove value="""/>\r\n \t<remove value="'"/>\r\n- <remove value=" "/> \r\n </valid>\r\n- </sanitizer>\r\n+\t </sanitizer>\r\n </param> \r\n \t <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.">\r\n \t\t\t<option value="average">Average</option>\r\n@@ -73,23 +71,19 @@\n \t </param>\r\n </repeat>\r\n <param name="hmname" size="40" type="text" value="Heat_Map_name" label="Heat Map Name" help="Short Name for heat map (no spaces)."/>\r\n- <sanitizer>\r\n- <valid>\r\n- <add preset="string.printable"/>\r\n+\t <sanitizer>\r\n+ \t<valid initial="string.printable">\r\n \t<remove value="""/>\r\n \t<remove value="'"/>\r\n- <remove value=" "/> \r\n </valid>\r\n- </sanitizer>\r\n+\t </sanitizer>\r\n <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."/>\r\n- <sanitizer>\r\n- <valid>\r\n- <add preset="string.printable"/>\r\n+\t <sanitizer>\r\n+ \t<valid initial="string.printable">\r\n \t<remove value="""/>\r\n \t<remove value="'"/>\r\n- <remove value=" "/> \r\n </valid>\r\n- </sanitizer>\r\n+\t </sanitizer>\r\n <param name="summaryDisplayWidth" \ttype="select" label="Summary Display Width %" help="Sets the percentage of the viewer display of the summary panel.">\r\n \t\t<option value="50">50%</option>\r\n \t\t<option value="10">10%</option>\r\n@@ -183,6 +177,8 @@\n \t\t\t <param name="rowDistanceMeasure" type="text" size="0" hidden="true" value="n/a"/>\r\n \t\t\t <param name="rowAgglomerationMethod" type="text" size="0" hidden="true" value="n/a"/>\r\n \t \t\t <param name="rowDendroCut" type="text" size="0" hidden="true" value="0"/>\r\n+\t \t\t <param name="rowDendroShow" type="text" size="0" hidden="true" value="ALL"/>\r\n+\t \t\t <param name="rowDendroHeight" type="text" size="0" hidden="true" value="0"/>\r\n \t\t\t<conditional name="rcutrows">\r\n \t\t\t\t\t<param name="raddcuts" type="select" label="Add row gap(s)" help="To separate portions of the heat map with gaps, select a gap method.">\r\n \t\t\t\t\t\t<option value="none">None</option>\r\n@@ -200,6 +196,8 @@\n \t\t\t <param name="rowDistanceMeasure" type="text" size="0" hidden="true" value="n/a"/>\r\n \t\t\t <param name="rowAgglomerationMethod" type="text" size="0" hidden="true" value="n/a"/>\r\n \t \t\t <param name="rowDendroCut" type="text" size="0" hidden="true" value="0"/>\r\n+\t \t\t <param name="rowDendroShow" type="text" size="0" hidden="true" value="ALL"/>\r\n+\t \t\t <param name="rowDendroHeight" type="text" size="0" hidden="true" value="0"/>\r\n \t\t\t<conditional name="rcutrows">\r\n \t\t\t\t\t<param name="raddcuts" type="select" label="Add row gap(s)" help="To separate portions of the heat map with gaps, select a gap method.">\r\n \t\t\t\t\t\t<option value="none">None</option>\r\n@@ -318,6 +316,8 @@\n \t\t <param name="columnDistanceMeasure" type="text" size="0" hidden="true" value="n/a"/>\r\n \t\t <param name="columnAgglomerationMethod" type="text" size="0" hidden="true" value="n/a"/>\r\n \t\t <param name="colDendroCut" type="text" size="0" hidde'..b'gaps, select a gap method.">\r\n \t\t\t\t\t<option value="none">None</option>\r\n@@ -335,6 +335,8 @@\n \t\t <param name="columnDistanceMeasure" type="text" size="0" hidden="true" value="n/a"/>\r\n \t\t <param name="columnAgglomerationMethod" type="text" size="0" hidden="true" value="n/a"/>\r\n \t\t <param name="colDendroCut" type="text" size="0" hidden="true" value="0"/>\r\n+ \t\t <param name="columnDendroShow" type="text" size="0" hidden="true" value="ALL"/>\r\n+ \t\t <param name="columnDendroHeight" type="text" size="0" hidden="true" value="0"/>\r\n \t\t\t<conditional name="ccutrows">\r\n \t\t\t\t<param name="caddcuts" type="select" label="Add column gap(s)" help="To separate portions of the heat map with gaps, select a gap method.">\r\n \t\t\t\t\t<option value="none">None</option>\r\n@@ -373,17 +375,22 @@\n </param> \r\n <repeat name="operations" title="Covariate Bars">\r\n <param name="class_name" size="25" type="text" value="" label="Covariate Name" help="Covariate heat map display label.">\r\n- <sanitizer>\r\n- <valid>\r\n- <add preset="string.printable"/>\r\n+\t <sanitizer>\r\n+ \t<valid initial="string.printable">\r\n \t<remove value="""/>\r\n \t<remove value="'"/>\r\n- <remove value=" "/> \r\n </valid>\r\n- </sanitizer>\r\n+\t </sanitizer>\r\n+ </param>\r\n+ <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."/>\r\n+\t\t<param name="classHeight" size="10" type="text" value="15" label="Covariate Display Height" help="Set the display height for column covariates and width for row covariates.">\r\n+\t\t <sanitizer>\r\n+\t \t<valid initial="string.digits">\r\n+\t \t<remove value="""/>\r\n+\t \t<remove value="'"/>\r\n+\t </valid>\r\n+\t\t </sanitizer>\r\n </param>\r\n- <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."/>\r\n-\t\t<param name="classHeight" size="10" type="text" value="15" label="Covariate Display Height" help="Set the display height for column covariates and width for row covariates."/>\r\n <conditional name="cattype">\r\n \t\t\t<param name="cat" type="select" label="Covariate Type" help="Identify the covariate as belonging to rows or columns and containing categorical or continuous values.">\r\n \t\t\t <option value="row_discrete" >Row Categorical</option>\r\n@@ -459,24 +466,20 @@\n </repeat> \r\n <repeat name="hm_attribute" title="Heat Map Attributes">\r\n <param name="attrbute_key" size="50" type="text" value="" label="Heat Map Attribute Key" help="For map level attributes. Enter the key (no spaces).">\r\n- <sanitizer invalid_char="_">\r\n- <valid initial="">\r\n- <add preset="string.letters"/>\r\n- <add preset="string.digits"/>\r\n+\t <sanitizer>\r\n+ \t<valid initial="string.printable">\r\n+ \t<remove value="""/>\r\n+ \t<remove value="'"/>\r\n </valid>\r\n- <mapping initial="">\r\n- </mapping>\r\n- </sanitizer>\r\n+\t </sanitizer>\r\n </param>\r\n <param name="attrbute_value" size="50" type="text" label="Heat Map Attributes Value" help="For map level attributes. Enter the value (no spaces).">\r\n- <sanitizer invalid_char="_">\r\n- <valid initial="">\r\n- <add preset="string.letters"/>\r\n- <add preset="string.digits"/>\r\n+\t <sanitizer>\r\n+ \t<valid initial="string.printable">\r\n+ \t<remove value="""/>\r\n+ \t<remove value="'"/>\r\n </valid>\r\n- <mapping initial="">\r\n- </mapping>\r\n- </sanitizer>\r\n+\t </sanitizer>\r\n </param>\r\n </repeat> \r\n </inputs>\r\n' |
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| diff -r 1f13d304ddbd -r c5489978071a mda_heatmap_viz.zip |
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| Binary file mda_heatmap_viz.zip has changed |