made collection ops help sections slightly more readable

galaxyproject · Mar 21, 2017 · e3255fd · e3255fd
1 parent e3e24fa
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diff --git a/lib/galaxy/tools/filter_failed_collection.xml b/lib/galaxy/tools/filter_failed_collection.xml
@@ -34,12 +34,13 @@
             </output_collection>
         </test>
     </tests>
-    <help>
-        This tool takes a list dataset collection and filters out the failed
-        datasets from it. This is useful for continuing a multi-sample analysis
-        when one of more of the samples fails at some point.
+    <help><![CDATA[
 
-        This tool will create new history datasets from your collection
-        but your quota usage will not increase.
-    </help>
+This tool takes a list dataset collection and filters out datasets in the failed state. This is useful for continuing a multi-sample analysis when one of more of the samples fails at some point.
+
+.. class:: infomark
+
+This tool will create new history datasets from your collection but your quota usage will not increase.
+
+      ]]></help>
 </tool>
diff --git a/lib/galaxy/tools/flatten_collection.xml b/lib/galaxy/tools/flatten_collection.xml
@@ -44,13 +44,13 @@
             </output_collection>
         </test>
     </tests>
-    <help>
-        This tool takes nested collections such as a list of lists or a list of
-        dataset pairs - and produces a flat list from the inputs. The collection
-        identifiers are merged together to create new collection identifiers in
-        the flattened result.
+    <help><![CDATA[
 
-        This tool will create new history datasets from your collection
-        but your quota usage will not increase.
-    </help>
+This tool takes nested collections such as a list of lists or a list of dataset pairs - and produces a flat list from the inputs. The collection identifiers are merged together to create new collection identifiers in the flattened result.
+
+.. class:: infomark
+
+This tool will create new history datasets from your collection but your quota usage will not increase.
+
+     ]]></help>
 </tool>
diff --git a/lib/galaxy/tools/merge_collection.xml b/lib/galaxy/tools/merge_collection.xml
@@ -270,10 +270,13 @@
       </output_collection>
     </test>
   </tests>
-  <help>
-    This tool takes two list and creates a single unified list.
+  <help><![CDATA[
+
+This tool takes two lists and creates a single unified list.
     
-    This tool will create new history datasets for your collection
-    but your quota usage will not increase.
-  </help>
+.. class:: infomark
+
+This tool will create new history datasets for your collection but your quota usage will not increase.
+
+  ]]></help>
 </tool>
diff --git a/lib/galaxy/tools/unzip_collection.xml b/lib/galaxy/tools/unzip_collection.xml
@@ -12,12 +12,19 @@
     <data name="forward" label="${on_string} (forward)" />
     <data name="reverse" label="${on_string} (reverse)" />
   </outputs>
-  <help>
-    This tool takes a paired dataset collection and builds two datasets
-    from it. If mapped over a list of paired datasets, this tool will
-    produce two lists of datasets.
+  <help><![CDATA[
 
-    This tool will create new history datasets from your collection
-    but your quota usage will not increase.
-  </help>
+This tool takes a paired dataset collection and builds two datasets from it. If mapped over a list of paired datasets, this tool will produce two lists of datasets. 
+
+----
+
+**Example**
+
+If a collection consists of two forward and two reverse datasets (e.g., forward and reverse reads from a sequencing experiment) this tool will output two collection: one consisting of forward reads and one of reverse.
+
+.. class:: infomark
+
+This tool will create new history datasets from your collection but your quota usage will not increase.
+
+  ]]></help>
 </tool>
diff --git a/lib/galaxy/tools/zip_collection.xml b/lib/galaxy/tools/zip_collection.xml
@@ -15,12 +15,19 @@
       <data name="reverse" />
     </collection>
   </outputs>
-  <help>
-    This tool takes two datasets and creates a dataset pair from
-    them. Mapping over two lists, this tool can be used to build
-    a list of dataset pairs from two individual lists of datasets.
+  <help><![CDATA[
+
+This tool takes two datasets and creates a dataset pair from them. Mapping over two lists, this tool can be used to build a list of dataset pairs from two individual lists of datasets.
+
+----
+
+**Example**
+
+If you have one collection containing only forward reads and one containing only reverse, this tools will "zip" them together into a simple paired collection.
     
-    This tool will create new history datasets for your collection
-    but your quota usage will not increase.
-  </help>
+.. class:: infomark
+
+This tool will create new history datasets for your collection but your quota usage will not increase.
+
+  ]]></help>
 </tool>