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
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