Mercurial > repos > george-weingart > graphlan_import

changeset 30:b4fb4d403061 draft

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Uploaded
author george-weingart
date Fri, 05 Sep 2014 17:25:38 -0400
parents 3b2b6c5e38e2
children 1cb6fc632bce
files import2graphlan.xml
diffstat 1 files changed, 55 insertions(+), 34 deletions(-) [+]
line wrap: on
line diff
--- a/import2graphlan.xml	Fri Sep 05 14:12:53 2014 -0400
+++ b/import2graphlan.xml	Fri Sep 05 17:25:38 2014 -0400
@@ -9,26 +9,26 @@
 
 	--annotations $export_annotations 
 	--external_annotations $export_external_annotations
-	--background_levels  $background_levels 
+	--background_levels  $gchoice.background_levels 
 	#if $str($background_clades)  != " ":
-               	--background_clades  $background_clades
+               	--background_clades  $gchoice.background_clades
 	#end if
 	#if $str($background_colors)  != " ":
-               	--background_colors  $background_colors
+               	--background_colors  $gchoice.background_colors
 	#end if
 	#if $str($export_title)  != " ":
-               	--title $export_title
+               	--title $gchoice.export_title
 	#end if
-	--title_font_size  $title_font_size 
-	--def_clade_size  $def_clade_size 
-	--min_clade_size  $min_clade_size 
-	--max_clade_size  $max_clade_size 
-	--def_font_size  $def_font_size 
-	--min_font_size  $min_font_size 
-	--max_font_size  $max_font_size 
-       --annotation_legend_font_size $annotation_legend_font_size
-	--abundance_threshold $abundance_threshold
-	--least_biomarkers $least_biomarkers
+	--title_font_size  $gchoice.title_font_size 
+	--def_clade_size  gchoice.$def_clade_size 
+	--min_clade_size  $gchoice.min_clade_size 
+	--max_clade_size  $gchoice.max_clade_size 
+	--def_font_size  $gchoice.def_font_size 
+	--min_font_size  $gchoice.min_font_size 
+	--max_font_size  $gchoice.max_font_size 
+       --annotation_legend_font_size $gchoice.annotation_legend_font_size
+	--abundance_threshold $gchoice.abundance_threshold
+	--least_biomarkers $gchoice.least_biomarkers
 
 	--skip_rows 1,2 
    </command>
@@ -38,26 +38,47 @@
 		<param format="lefse_internal_res" name="out_data" type="data" label="Output of  Lefse"  help="This is the  Lefse output file"/>	
 	   	<param name="export_annotations" type="text" format="text" label="Annotations" value="2,3"/>
 	   	<param name="export_external_annotations" type="text" format="text" label="External Annotations" value="4,5,6"/>   
-		<param name="background_levels" type="text" format="text" label="Background Levels" value="1,2,3"/>   
-		<param name="background_clades" type="text" format="text" label="Background Clades" value=" " />  
-		<param name="background_colors" type="text" format="text" label="Background Colors" value=" " />  
-	    	<param name="export_title" type="text" format="text" label="Title" value=" "/>
-	    	<param name="title_font_size"  type="integer" size="4" value="15"   label="Title font size"/>
-	    	<param name="def_clade_size"  type="integer" size="4" value="0"   label="Default Clade size"/>
-	    	<param name="min_clade_size"  type="integer" size="4" value="20"   label="Minimum Clade size that are Biomarkers"/>
-	    	<param name="max_clade_size"  type="integer" size="4" value="200"   label="Maximum Clade size that are Biomarkers"/>
-	    	<param name="def_font_size"  type="integer" size="4" value="10"   label="Default font size"/>
-	    	<param name="min_font_size"  type="integer" size="4" value="8"   label="Minimum font size "/>
-	    	<param name="max_font_size"  type="integer" size="4" value="12"   label="Maximum font size "/>
-	    	<param name="annotation_legend_font_size"  type="integer" size="4" value="10"   label="Annotation legend font size "/>
-	    	<param name="abundance_threshold"  type="float"   value="20.0"   label="Abundance threshold: minimun abundace value for a clade to be annotated"/>
-	    	<param name="most_abundant"  type="integer" size="4" value="0"   label=" When only lefse_input is provided, you can specify how many clades to highlight "/>
-	    	<param name="least_biomarkers"  type="integer" size="4" value="0"   label="Minimum number of biomarkers to extract  "/>
-
-        	<param name="global_choice" type="select" label="Select Global Choices" help="Select choices">
-        		<option value="d" selected='True'>Default</option>
-          		<option value="a">Advanced</option>
-        	</param>
+		
+		<conditional name="gchoice">       
+			<param name="global_choice" type="select" label="Select Global Choices" help="Select choices">
+				<option value="d" selected='True'>Default</option>
+		  		<option value="a">Advanced</option>
+			</param>
+			<when value="d">
+				<param name="background_levels" type="hidden"   value="1,2,3"/>   
+				<param name="background_clades" type="hidden"   value=" " />  
+				<param name="background_colors" type="hidden"  value=" " />  
+			    	<param name="export_title" type="hidden"   value=" "/>
+			    	<param name="title_font_size"  type="hiddenr"  value="15"/>
+			    	<param name="def_clade_size"  type="hidden" value="0"    />
+			    	<param name="min_clade_size"  type="hidden"   value="20"    />
+			    	<param name="max_clade_size"  type="hidden"  value="200"    />
+			    	<param name="def_font_size"  type="hidden"   value="10"    />
+			    	<param name="min_font_size"  type="hidden"   value="8"    />
+			    	<param name="max_font_size"  type="hidden"  value="12"    />
+			    	<param name="annotation_legend_font_size"  type="hidden"   value="10"    />
+			    	<param name="abundance_threshold"  type="hidden"   value="20.0"    />
+			    	<param name="most_abundant"  type="hidden"   value="0"    />
+				<param name="least_biomarkers"  type="hidden"   value="0"    />
+			</when>
+			<when value="a">
+				<param name="background_levels" type="text" format="text" label="Background Levels" value="1,2,3"/>   
+				<param name="background_clades" type="text" format="text" label="Background Clades" value=" " />  
+				<param name="background_colors" type="text" format="text" label="Background Colors" value=" " />  
+			    	<param name="export_title" type="text" format="text" label="Title" value=" "/>
+			    	<param name="title_font_size"  type="integer" size="4" value="15"   label="Title font size"/>
+			    	<param name="def_clade_size"  type="integer" size="4" value="0"   label="Default Clade size"/>
+			    	<param name="min_clade_size"  type="integer" size="4" value="20"   label="Minimum Clade size that are Biomarkers"/>
+			    	<param name="max_clade_size"  type="integer" size="4" value="200"   label="Maximum Clade size that are Biomarkers"/>
+			    	<param name="def_font_size"  type="integer" size="4" value="10"   label="Default font size"/>
+			    	<param name="min_font_size"  type="integer" size="4" value="8"   label="Minimum font size "/>
+			    	<param name="max_font_size"  type="integer" size="4" value="12"   label="Maximum font size "/>
+			    	<param name="annotation_legend_font_size"  type="integer" size="4" value="10"   label="Annotation legend font size "/>
+			    	<param name="abundance_threshold"  type="float"   value="20.0"   label="Abundance threshold: minimun abundace value for a clade to be annotated"/>
+			    	<param name="most_abundant"  type="integer" size="4" value="0"   label=" When only lefse_input is provided, you can specify how many clades to highlight "/>
+				<param name="least_biomarkers"  type="integer" size="4" value="0"   label="Minimum number of biomarkers to extract  "/>
+			</when>
+		 </conditional>
     </inputs>
    <outputs>
             <data  name="output_annot_file"  format="circl"  />