Good afternoon,
It appears my Galaxy updated overnight and has caused issues that I am fairly certain I didn't introduce. Did something change or what did I do?
1 the Parameter $GALAXY_ROOT_DIR/tools/Heatmaps/' is not showing up see bottom where I dump parameters.
2. The repeat seems to always run once even when I do not click and fill it.
This was working a couple days ago. I was playing with it - but very minimally-- yeah i understand but have worked with Galaxy for awhile.
Thanks Bob
3. <?xml version="1.0" encoding="UTF-8" ?><tool id="heatmap" name="Heatmap" version="3.1.1"> <description>Create HeatMap </description><command>$GALAXY_ROOT_DIR/tools/MDA_Heatmaps/heatmap.sh '$hmname' '$hmdesc' '$inputmatrix' $rowOrderMethod $rowDistanceMeasure $rowAgglomerationMethod $columnOrderMethod $columnDistanceMeasure $columnAgglomerationMethod '$summarymethod' '$GALAXY_ROOT_DIR/tools/Heatmaps/' #for $op in $operations ${op.class_name} ${op.repeatinput.file_name} ${op.cat} #end for '$output' </command> <stdio> <exit_code range="1:" level="fatal" /> </stdio> <inputs> <param name="hmname" size="20" type="text" value="HM_name" label="User Defined HeatMap Name"/> <param name="hmdesc" size="100" optional="true" type="text" value="_" label="Optional HeatMap Description"/>
<param name="inputmatrix" type="data" label="Input Matrix" /> <param name="summarymethod" type="select" label="Data Summarization Method"> <option value="average">average</option> <option value="sample">sample</option> <option value="mode">mode</option> </param> <param name="rowOrderMethod" type="select" label="Row ordering method" help="Choices -- Hierarchical Clustering, Original Order, Random"> <option value="HierarchicalClustering">Hierarchical Clustering</option> <option value="OriginalOrder">Original Order</option> <option value="Random">Random</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> <option value="manhattan">Manhattan</option> </param> <param name="rowAgglomerationMethod" type="select" label="Row Clustering Method" help="Choices: 'average' for Average Linkage, 'complete' for Complete Linkage, 'single' for Single Linkage, 'ward', 'mcquitty', 'median', or 'centroid'."> <option value="average">Average Linkage</option> <option value="complete">Complete Linkage</option> <option value="single">Single Linkage</option> </param> <param name="columnOrderMethod" type="select" label="Column ordering method" help="Choices -- Hierarchical Clustering, Original Order, Random"> <option value="HierarchicalClustering">Hierarchical Clustering</option> <option value="OriginalOrder">Original Order</option> <option value="Random">Random</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> <option value="manhattan">Manhattan</option> <option value="correlation">Correlation</option> </param> <param name="columnAgglomerationMethod" type="select" label="Column Clustering Method" help="Choices: 'average' for Average Linkage, 'complete' for Complete Linkage, 'single' for Single Linkage, 'ward', 'mcquitty', 'median', or 'centroid'."> <option value="average">Average Linkage</option> <option value="complete">Complete Linkage</option> <option value="single">Single Linkage</option> <option value="ward">Ward</option> <option value="mcquitty">Mcquitty</option> <option value="median">Median</option> <option value="centroid">Centroid</option> </param>
<repeat name="operations" title="Covariate Bars"> <param name="class_name" size="20" type="text" value="" label="Axis Covariate Name"/> <param name="repeatinput" type="data" format="text" label="Axis Covariate File"/> <param name="cat" type="select" label="Axis Covariate Type"> <option value="row_categorical" >row categorical</option> <option value="row_continuous" >row continuous</option> <option value="column_categorical" >column categorical</option> <option value="column_continuous" >column continuous</option> </param> </repeat> </inputs> <outputs> <data name="output" label="${inputmatrix.name}_Heatmap" format="zip"/> </outputs></tool>
4. dump of part of heatmap.sh commands
echo $1 $2 $3 $4 $5 $6 $7 $8 $9 $10echo 11-14 belowecho $11 $12 $13 $14 5. shows in Stdout the 10th parameter '$GALAXY_ROOT_DIR/tools/Heatmaps/' is missing The first 10 params are:
namexyz test /home/rbrown/HM_galaxy/database/files/000/dataset_500.dat HierarchicalClustering euclidean average HierarchicalClustering euclidean average namexyz0 11-14 below namexyz1 namexyz2 namexyz3 namexyz47. and where do the namexyzN come from? I didn't click the repeat -- yes one of them should by file Output