diff macros.xml @ 29:5614cf75bb24 draft

Uploaded
author iuc
date Thu, 31 Dec 2015 11:51:40 -0500
parents 7978dcbd752c
children 12d5699f92e9
line wrap: on
line diff
--- a/macros.xml	Wed Dec 30 18:09:50 2015 -0500
+++ b/macros.xml	Thu Dec 31 11:51:40 2015 -0500
@@ -25,7 +25,7 @@
   <token name="@ATTRIBUTION@"><![CDATA[
 **Attribution**
 
-This Galaxy tool relies on the JBrowse, maintained by the GMOD Community
+This Galaxy tool relies on the JBrowse, maintained by the GMOD Community. The Galaxy wrapper is developed by Eric Rasche
 ]]>
   </token>
   <xml name="auto_manual_tk"
@@ -64,19 +64,19 @@
   </xml>
 
   <xml name="auto_color"
-      token_cond_label="Color"
-      token_cond_name="color"
-      token_select_label="Color Selection"
-      token_select_name="color_select"
-      token_automatic_label="Automatically selected"
-      token_manual_label="Manual Color Selection">
+       token_cond_label="Color"
+       token_cond_name="color"
+       token_select_label="Color Selection"
+       token_select_name="color_select"
+       token_automatic_label="Automatically selected"
+       token_manual_label="Manual Color Selection">
     <expand macro="auto_manual_tk"
-        cond_label="@COND_LABEL@"
-        cond_name="@COND_NAME@"
-        select_label="@SELECT_LABEL@"
-        select_name="@SELECT_NAME@"
-        automatic_label="@AUTOMATIC_LABEL@"
-        manual_label="@MANUAL_LABEL@">
+            cond_label="@COND_LABEL@"
+            cond_name="@COND_NAME@"
+            select_label="@SELECT_LABEL@"
+            select_name="@SELECT_NAME@"
+            automatic_label="@AUTOMATIC_LABEL@"
+            manual_label="@MANUAL_LABEL@">
       <expand macro="jb_color" />
         <yield />
     </expand>
@@ -110,15 +110,15 @@
               token_automatic_label="Automatically selected"
               token_manual_label="Manual Color Selection">
         <expand macro="jb_color"
-            label="JBrowse style.pos_color"
-            name="style_pos_color"
-            value="blue"
-            help="CSS color, default 'blue'. When drawing bicolor plots, the fill color to use for values that are above the pivot point." />
+                label="JBrowse style.pos_color"
+                name="style_pos_color"
+                value="blue"
+                help="CSS color, default 'blue'. When drawing bicolor plots, the fill color to use for values that are above the pivot point." />
         <expand macro="jb_color"
-            label="JBrowse style.neg_color"
-            name="style_neg_color"
-            value="red"
-            help=" CSS color, default 'red'. When drawing bicolor plots, the fill color to use for values that are below the pivot point." />
+                label="JBrowse style.neg_color"
+                name="style_neg_color"
+                value="red"
+                help=" CSS color, default 'red'. When drawing bicolor plots, the fill color to use for values that are below the pivot point." />
       </expand>
 
       <conditional name="bicolor_pivot" label="Bicolor Pivot">
@@ -137,8 +137,8 @@
   </xml>
 
   <xml name="color_selection"
-      token_scaling_lin_select="true"
-      token_scaling_log_select="false"
+       token_scaling_lin_select="true"
+       token_scaling_log_select="false"
       >
     <section name="jbcolor_scale" title="JBrowse Feature Score Scaling &amp; Coloring Options [Advanced]" expanded="false">
       <conditional name="color_score" label="JBrowse style.color &amp; Score relationship">
@@ -154,7 +154,7 @@
         <when value="score">
             <!-- Scaling -->
             <param type="select" label="JBrowse style.color function's score scaling" name="score_scaling"
-                help="How should the colors be distributed across the values? For blast results which distributes scores on the scale of approximately [1e-500, 10], it makes sense to request a logarithmic scaling of the color values. Logarithmic is indeed the default for blast. However other analysis methods may produce scores on ranges such as [0, 100] where a linear scale would be more appropriate for color distribution.">
+                   help="How should the colors be distributed across the values? For blast results which distributes scores on the scale of approximately [1e-500, 10], it makes sense to request a logarithmic scaling of the color values. Logarithmic is indeed the default for blast. However other analysis methods may produce scores on ranges such as [0, 100] where a linear scale would be more appropriate for color distribution.">
               <option value="linear"      selected="@SCALING_LIN_SELECT@" >Linear scaling</option>
               <option value="logarithmic" selected=""                     >Logarithmic scaling</option>
               <option value="blast"       selected="@SCALING_LOG_SELECT@" >Blast scaling</option>
@@ -194,30 +194,30 @@
     </section>
   </xml>
   <xml name="track_styling"
-      token_classname="feature"
-      token_label="name,id"
-      token_description="note,description"
-      token_height="100px">
+       token_classname="feature"
+       token_label="name,id"
+       token_description="note,description"
+       token_height="100px">
     <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false">
         <param label="JBrowse style.className" type="text"
-            name="style_classname"
-            value="@CLASSNAME@"
-            help="Set CSS style.className property"/>
+               name="style_classname"
+               value="@CLASSNAME@"
+               help="Set CSS style.className property"/>
         <param label="JBrowse style.label"
-            type="text"
-            name="style_label"
-            value="@LABEL@"
-            help="Comma-separated list of case-insensitive feature tags to use for showing the feature's label. The first one found will be used. Default 'name,id'" />
+               type="text"
+               name="style_label"
+               value="@LABEL@"
+               help="Comma-separated list of case-insensitive feature tags to use for showing the feature's label. The first one found will be used. Default 'name,id'" />
         <param label="JBrowse style.description"
-            type="text"
-            name="style_description"
-            value="@DESCRIPTION@"
-            help="Comma-separated list of case-insensitive feature tags to check for the feature's long description. The first one found will be used."/>
+               type="text"
+               name="style_description"
+               value="@DESCRIPTION@"
+               help="Comma-separated list of case-insensitive feature tags to check for the feature's long description. The first one found will be used."/>
         <param label="JBrowse style.height"
-            type="text"
-            name="style_height"
-            value="@HEIGHT@"
-            help="Height in pixels of glyphs. Default value varies from glyph to glyph. Note that the 'compact' displayMode uses style->height * 0.35 so changing style height can adjust the compact visualization."/>
+               type="text"
+               name="style_height"
+               value="@HEIGHT@"
+               help="Height in pixels of glyphs. Default value varies from glyph to glyph. Note that the 'compact' displayMode uses style->height * 0.35 so changing style height can adjust the compact visualization."/>
     </section>
   </xml>