Mercurial > repos > iuc > jbrowse
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 & Coloring Options [Advanced]" expanded="false"> <conditional name="color_score" label="JBrowse style.color & 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>
