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 $10
echo 11-14 below
echo $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 namexyz4

7. and where do the namexyzN  come from?  I didn't click the repeat -- yes one of them should by file Output