Mercurial > repos > iuc > multiqc

diff gatk_plugin.xml @ 24:f7e2f1eb3a16 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
author: iuc
date: Mon, 02 Sep 2024 14:22:54 +0000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gatk_plugin.xml	Mon Sep 02 14:22:54 2024 +0000
@@ -0,0 +1,59 @@
+<macros>
+    <token name="@GATK_COMMAND@"><![CDATA[
+        #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
+            #if str($repeat2.type) == "varianteval"
+                #set $pattern = "#:GATKTable:TiTvVariantEvaluator"
+                @LN_2_FILES@
+            #elif str($repeat2.type) == "base_recalibrator"
+                #set $pattern = "#:GATKTable:Arguments:Recalibration"
+                @LN_2_FILES@
+            #end if
+        #end for
+    ]]></token>
+    <xml name="gatk_form">
+        <repeat name="output" title="GATK output" min="1">
+            <param name="type" type="select" label="Type of GATK output?">
+                <option value="varianteval">Variant eval file</option>
+                <option value="base_recalibrator">Base recalibrator file</option>
+            </param>
+            <param name="input" type="data" format="txt" multiple="true" label="GATK output"/>
+        </repeat>
+    </xml>
+    <!-- add here your test files and tests, the more stringent the better -->
+    <xml name="gatk_test">
+        <test expect_num_outputs="3">
+            <repeat name="results">
+                <conditional name="software_cond">
+                    <param name="software" value="gatk"/>
+                    <repeat name="output">
+                        <param name="type" value="base_recalibrator"/>
+                        <param name="input" value="gatk_BaseRecalibrator.txt"/>
+                    </repeat>
+                    <repeat name="output">
+                        <param name="type" value="varianteval"/>
+                        <param name="input" value="gatk_varianteval.txt"/>
+                    </repeat>
+                </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="gatk_varianteval_variant_plot"/>
+                </assert_contents>
+            </output>
+            <output name="stats">
+                <assert_contents>
+                    <has_text text="gatk_varianteval_txt"/>
+                    <has_n_lines n="2"/>
+                    <has_n_columns n="3"/>
+                </assert_contents>
+            </output>
+            <output_collection name="plots" type="list" count="4"/>
+        </test>
+    </xml>
+</macros>