diff busco_plugin.xml @ 24:f7e2f1eb3a16 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/busco_plugin.xml	Mon Sep 02 14:22:54 2024 +0000
@@ -0,0 +1,48 @@
+<macros>
+    <token name="@BUSCO_COMMAND@"><![CDATA[
+        ## Searches for files "short_summary_[samplename].txt"
+        #for $file in $repeat.software_cond.input
+            @ESCAPE_IDENTIFIER@
+            #set file_path = os.path.join($software_dir, 'short_summary_' + str($identifier))
+            ln -s '$file' '$file_path' &&
+        #end for
+    ]]></token>
+    <xml name="busco_form">
+        <param name="input" type="data" format="txt" multiple="true" label="Output of BUSCO"/>
+    </xml>
+    <!-- add here your test files and tests, the more stringent the better -->
+    <xml name="busco_test">
+        <test expect_num_outputs="3">
+            <repeat name="results">
+                <conditional name="software_cond">
+                    <param name="software" value="busco"/>
+                    <param name="input" value="busco.txt"/>
+                </conditional>
+            </repeat>
+            <param name="title" value="Title of the report"/>
+            <param name="comment" value="Commment for the report"/>
+            <param name="flat" value="true"/>
+            <param name="export" value="true"/>
+            <output name="html_report">
+                <assert_contents>
+                    <has_text text="Title of the report"/>
+                    <has_text text="Commment for the report"/>
+                    <has_text text="busco-lineage-fungi_odb9"/>
+                </assert_contents>
+            </output>
+            <!-- Not sure why this is empty 
+            <output name="stats">
+                <assert_contents>
+                    <has_text text="R1_fq"/>
+                    <has_text text="result_right"/>
+                    <has_text text="25839_merged"/>
+                    <has_text text="C2"/>
+                    <has_n_lines n="11"/>
+                    <has_n_columns n="22"/>
+                </assert_contents>
+            </output>
+            -->
+            <output_collection name="plots" type="list" count="1"/>
+        </test>
+    </xml>
+</macros>