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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