changeset 11:6dc768c94b79 draft

Uploaded

--- a/ctd2galaxy.py	Mon Aug 12 10:31:58 2013 -0400
+++ b/ctd2galaxy.py	Mon Aug 12 10:42:35 2013 -0400
@@ -475,7 +475,7 @@
         if param_node.name.endswith('-file-ext'):
             return  # Skip if extension to override.
         args = {}
-        if param_node.tags and 'required' not in param_node.tags.split(','):
+        if not param_node.required:
             args['optional'] = 'true'  # false would be default
         if param_node.type_ == 'input-file':
             args['type'] = 'data'
@@ -542,7 +542,7 @@
             # The name of the variable that is used.
             var_name = '$' + ce.mapping_path.replace('-', '_').replace('.', '_')
             # Check whether it is optional.
-            optional = bool(ce.param_node.tags and 'required' not in ce.param_node.tags.split(','))
+            optional = not ce.param_node.required
             # Check whether it is a boolean.
             bool_param = False
             if ce.param_node.type_ == 'string' and ce.param_node.restrictions and \

--- a/roi_feature_projection.xml	Mon Aug 12 10:31:58 2013 -0400
+++ b/roi_feature_projection.xml	Mon Aug 12 10:42:35 2013 -0400
@@ -27,14 +27,14 @@
     <description>Region Of Interest Projection.</description>
     <inputs>
         <param label="BED, GFF, or GTF file to read." type="data" name="roi_feature_projection_in_features" format="bed,gff,gtf" />
-        <param type="text" name="roi_feature_projection_gff_type" value="" label="The GFF/GTF record type (value of third column) to keep.  Keep all if not set or input file type is not GFF/GTF." />
+        <param type="text" name="roi_feature_projection_gff_type" value="" label="The GFF/GTF record type (value of third column) to keep.  Keep all if not set or input file type is not GFF/GTF." optional="true" />
         <param falsevalue="" truevalue="--verbose" type="boolean" name="roi_feature_projection_verbose" label="Enable verbose output." />
         <param label="ROI file to read." type="data" name="roi_feature_projection_in_roi" format="roi" />
         <param falsevalue="" truevalue="--strand-specific" type="boolean" name="roi_feature_projection_strand_specific" label="Enable strand-specific mode if set." />
         <param falsevalue="" truevalue="--very-verbose" type="boolean" name="roi_feature_projection_very_verbose" label="Enable very verbose output." />
         <param falsevalue="" truevalue="--quiet" type="boolean" name="roi_feature_projection_quiet" label="Set verbosity to a minimum." />
-        <param label="Path to FASTA file with genome; optional.  When given, this is used for computing the overall region's C+G content." type="data" name="roi_feature_projection_genome" format="fasta,fa" />
-        <param type="text" name="roi_feature_projection_gff_group_by" value="" label='The GFF/GTF tag to use for grouping, e.g. "Parent", "transcript_id". No grouping if empty.  When using the grouping feature, the --mode is automatically set to projection.' />
+        <param label="Path to FASTA file with genome; optional.  When given, this is used for computing the overall region's C+G content." type="data" name="roi_feature_projection_genome" format="fasta,fa" optional="true" />
+        <param type="text" name="roi_feature_projection_gff_group_by" value="" label='The GFF/GTF tag to use for grouping, e.g. "Parent", "transcript_id". No grouping if empty.  When using the grouping feature, the --mode is automatically set to projection.' optional="true" />
         <param type="select" name="roi_feature_projection_mode" value="projection" label="The mode in which to combine the ROI and BED/GFF file.  See section Combination Modes below for details.">
             <option value="intersection">intersection</option>
             <option value="projection">projection</option>

--- a/roi_plot_thumbnails.xml	Mon Aug 12 10:31:58 2013 -0400
+++ b/roi_plot_thumbnails.xml	Mon Aug 12 10:42:35 2013 -0400
@@ -38,7 +38,7 @@
       <option value="">this frame</option>
     </param>
 
-    <param name="igv_host" type="text" label="Host for the IGV link." value="localhost" />
+    <param name="igv_host" type="text" label="Host for the IGV link." value="localhost"  />
     <param name="igv_port" type="integer" label="Port for the IGV link." value="60151" />
 
     <param name="ucsc_org" type="text" label="UCSC Genome Browser org value." value="human" />