diff macros.xml @ 1:85195e0d4b71 draft

planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Fri Sep 29 13:32:23 2017 -0400
@@ -0,0 +1,105 @@
+<macros>
+    <xml name="verify_hub_structure" token_genome="Dbia3" token_test="common">
+        <!--genomes.txt -->
+        <extra_files type="file" name="myHub/genomes.txt" value="@TEST@/myHub/genomes.txt" />
+
+        <extra_files type="file" name="myHub/@GENOME@.html" value="@TEST@/myHub/@GENOME@.html"/>
+        <!-- hub.txt -->
+        <extra_files type="file" name="myHub/hub.txt" value="@TEST@/myHub/hub.txt" lines_diff="2">
+            <assert_contents>
+                <has_text text="email"/>
+            </assert_contents>
+        </extra_files>
+        <!-- 2bit file -->
+        <extra_files type="file" name="myHub/@GENOME@/@GENOME@.2bit" value="common/@GENOME@.2bit" />
+        <!-- groups.txt -->
+        <extra_files type="file" name="myHub/@GENOME@/groups.txt" value="@TEST@/myHub/@GENOME@/groups.txt" />
+        <!-- description.html -->
+        <extra_files type="file" name="myHub/@GENOME@/description.html" value="@TEST@/myHub/@GENOME@/description.html"/>
+        <!-- trackDb.txt -->
+        <extra_files type="file" name="myHub/@GENOME@/trackDb.txt">
+            <assert_contents>
+                <has_text text="track"/>
+                <has_text text="longLabel"/>
+                <has_text text="shortLabel"/>
+                <has_text text="bigDataUrl"/>
+                <has_text text="type"/>
+                <has_text text="visibility"/>
+                <has_text text="thickDrawItem"/>
+                <has_text text="priority"/>
+                <has_text text="color"/>
+                <has_text text="group"/>
+            </assert_contents>
+        </extra_files>
+    </xml>
+
+    <xml name="verify_hub_structure_no_track" token_genome="Dbia3" token_test="common">
+        <!--genomes.txt -->
+        <extra_files type="file" name="myHub/genomes.txt" value="@TEST@/myHub/genomes.txt" />
+
+        <extra_files type="file" name="myHub/@GENOME@.html" value="@TEST@/myHub/@GENOME@.html"/>
+        <!-- hub.txt -->
+        <extra_files type="file" name="myHub/hub.txt" value="@TEST@/myHub/hub.txt" lines_diff="2">
+            <assert_contents>
+                <has_text text="email"/>
+            </assert_contents>
+        </extra_files>
+        <!-- 2bit file -->
+        <extra_files type="file" name="myHub/@GENOME@/@GENOME@.2bit" value="common/@GENOME@.2bit" />
+        <!-- description.html -->
+        <extra_files type="file" name="myHub/@GENOME@/description.html" value="@TEST@/myHub/@GENOME@/description.html"/>
+    </xml>
+
+    <xml name="add_trix_file">
+        <conditional name="add_trix_index">
+            <param name="add_trix_index_selector" type="select" label="Add TRIX files that maps free text to a set of indices" >
+                <option value="no" selected="true">No</option>
+                <option value="yes">Yes</option>
+            </param>
+
+            <when value="yes">
+                <param 
+                    name="trix_id" 
+                    value="name" 
+                    type="text"
+                    size="30"
+                    label="Specify Trix identifier"
+                    help="More about Trix index: https://genome.ucsc.edu/goldenpath/help/trix.html"
+                />
+                <conditional name="index_files">
+                    <param name="index_files_type" type="select" label="Single files or an index collection" help="Select between provide individual trix files (ix and ixx) or an trix index collection">
+                        <option value="collection">Index collection</option>
+                        <option value="single">Single files</option>
+                    </param>
+                    <when value="collection">
+                        <param 
+                            name="index_collection" 
+                            format="txt" 
+                            type="data_collection" 
+                            collection_type="list" 
+                            label="Select dataset collection" 
+                            help="Specify dataset collection containing ix and ixx files"
+                        />
+                    </when>
+                    <when value="single">
+                        <param
+                            format="txt"
+                            name="index_ix"
+                            type="data"
+                            label="Trix index file (ix)"
+                        />
+                        <param
+                            format="txt"
+                            name="index_ixx"
+                            type="data"
+                            label="Trix index file (ixx)"
+                        />
+                    </when>
+                </conditional>
+            </when>
+            <when value="no">
+            </when>
+        </conditional>
+    </xml>
+
+</macros>
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