diff macros.xml @ 0:18b91d72794b draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Tue Oct 05 20:05:50 2021 +0000
@@ -0,0 +1,63 @@
+<macros>
+    <token name="@WRAPPER_VERSION@">1.0.0</token>
+    <token name="@VERSION_SUFFIX@">1.0.0</token>
+    <token name="@PROFILE@">20.09</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="38.92">bbmap</requirement>
+        </requirements>
+    </xml>
+    <macro name="dbKeyActionsBBMap">
+        <expand macro="dbKeyActions">
+            <option type="from_data_table" name="fasta_indexes" column="1" offset="0">
+                <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
+                <filter type="param_value" ref="ref_source_cond.reference" column="1"/>
+            </option>
+        </expand>
+    </macro>
+    <macro name="dbKeyActions">
+        <actions>
+            <conditional name="ref_source_cond.ref_source">
+                <when value="cached">
+                    <action type="metadata" name="dbkey">
+                        <yield/>
+                    </action>
+                </when>
+                <when value="history">
+                    <action type="metadata" name="dbkey">
+                        <option type="from_param" name="ref_source_cond.reference" param_attribute="dbkey"/>
+                    </action>
+                </when>
+            </conditional>
+        </actions>
+    </macro>
+    <macro name="reference_source_cond">
+        <conditional name="ref_source_cond">
+            <param name="ref_source" type="select" label="Select reference genome source; a cached reference or one from the history">
+                <option value="cached" selected="True">Use a cached reference</option>
+                <option value="history">Use a reference from the history</option>
+            </param>
+            <when value="cached">
+                <param name="reference" type="select" label="Using reference genome">
+                    <options from_data_table="fasta_indexes">
+                        <filter type="sort_by" column="2"/>
+                        <validator type="no_options" message="A built-in reference genome is not available"/>
+                    </options>
+                </param>
+            </when>
+            <when value="history">
+                <param name="reference" type="data" format="fasta" label="Using reference genome">
+                    <validator type="no_options" message="The current history does not include a fasta dataset"/>
+                </param>
+            </when>
+        </conditional>
+    </macro>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">
+                https://doi.org/10.1371/journal.pone.0185056
+            </citation>
+        </citations>
+    </xml>
+</macros>
+