diff jbrowse2/macros.xml @ 0:cd5d63cd0eb5 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/jbrowse2/macros.xml	Wed Jan 03 01:36:39 2024 +0000
@@ -0,0 +1,76 @@
+<?xml version="1.0"?>
+<macros>
+    <token name="@TOOL_VERSION@">2.10.0</token>
+    <xml name = "edamInc">
+        <edam_topics>
+            <edam_topic>topic_3307</edam_topic>
+            <edam_topic>topic_0092</edam_topic>
+        </edam_topics>
+        <edam_operations>
+            <edam_operation>operation_0573</edam_operation>
+            <edam_operation>operation_0564</edam_operation>
+        </edam_operations>
+    </xml>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">jbrowse2</requirement>
+            <requirement type="package" version="1.82">biopython</requirement>
+            <requirement type="package" version="0.7.0">bcbio-gff</requirement>
+            <requirement type="package" version="1.19">samtools</requirement>
+            <requirement type="package" version="6.0.1">pyyaml</requirement>
+            <requirement type="package" version="1.11">tabix</requirement>
+            <requirement type="package" version="4.6.0">findutils</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+    <token name="@DATA_DIR@">\$GALAXY_JBROWSE_SHARED_DIR</token>
+    <token name="@WRAPPER_VERSION@">galaxy0</token>
+    <token name="@ATTRIBUTION@"><![CDATA[
+**Attribution**
+This Galaxy tool relies on the JBrowse, maintained by the GMOD Community. The Galaxy wrapper is developed by the IUC
+This xml currently fails silently when profile=22.05 is set.
+]]>
+    </token>
+    <xml name="track_styling"
+       token_classname="feature"
+       token_label="product,name,id"
+       token_description="note,description"
+       token_height="10px"
+       token_maxheight="600">
+        <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"/>
+            <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'" />
+            <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."/>
+            <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."/>
+            <param label="JBrowse maxHeight"
+                type="text"
+                name="max_height"
+                value="@MAXHEIGHT@"
+                help="Maximum height that the track is permitted to reach in pixels."/>
+        </section>
+    </xml>
+
+    <xml name="input_conditional" token_label="Track Data" token_format="data">
+        <param label="@LABEL@" format="@FORMAT@" name="annotation" type="data" multiple="True"/>
+    </xml>
+    <xml name="citations">
+        <citations>
+        <citation type="doi">10.1101/gr.094607.109</citation>
+        </citations>
+    </xml>
+</macros>