# HG changeset patch
# User iuc
# Date 1660119823 0
# Node ID 33b8c5eedc04de689ec5adf814f78945713fa228
# Parent  08780101bc36cbd6f92e295a1e364e6402bcdba3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intervene commit bf6d77a84f796430a6b4530209d0f21e1d40d25a

diff -r 08780101bc36 -r 33b8c5eedc04 intervene_pairwise.xml
--- a/intervene_pairwise.xml	Mon Jul 05 11:24:59 2021 +0000
+++ b/intervene_pairwise.xml	Wed Aug 10 08:23:43 2022 +0000
@@ -1,5 +1,8 @@
-<tool id="intervene_pairwise" name="Pairwise intersection" version="@TOOL_VERSION@">
+<tool id="intervene_pairwise" name="Pairwise intersection" version="@TOOL_VERSION@+galaxy1">
     <description>and heatmap for genomic intervals</description>
+    <xrefs>
+        <xref type="bio.tools">intervene</xref>
+    </xrefs>
     <macros>
         <import>macros.xml</import>
     </macros>
@@ -68,6 +71,7 @@
             <expand macro="quote_sanitizer"/>
         </param>
         <expand macro="figure_params"/>
+        <param name="out_matrix" type="boolean" truevalue="true" falsevalue="false" label="Output the intervene matrix file?"/>
     </inputs>
     <outputs>
         <data name="plot" format="pdf" label="Pairwise plot on ${on_string}" from_work_dir="results/Intervene_pairwise.plot">
@@ -77,11 +81,16 @@
                 </action>
             </actions>
         </data>
+        <data name="matrix" format="txt" label="Matrix on ${on_string}" from_work_dir="results/Intervene_pairwise_frac_matrix.txt">
+            <filter>out_matrix</filter>
+        </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="2">
             <param name="input" value="a.bed,b.bed,c.bed"/>
+            <param name="out_matrix" value="true"/>
             <output name="plot" value="bed_pairwise.pdf" compare="sim_size"/>
+            <output name="matrix" value="matrix.txt" />
         </test>
     </tests>
     <help><![CDATA[
diff -r 08780101bc36 -r 33b8c5eedc04 intervene_upset.xml
--- a/intervene_upset.xml	Mon Jul 05 11:24:59 2021 +0000
+++ b/intervene_upset.xml	Wed Aug 10 08:23:43 2022 +0000
@@ -1,5 +1,8 @@
 <tool id="intervene_upset" name="UpSet diagram" version="@TOOL_VERSION@">
     <description>of intersection of genomic regions or list sets</description>
+    <xrefs>
+        <xref type="bio.tools">intervene</xref>
+    </xrefs>
     <macros>
         <import>macros.xml</import>
     </macros>
diff -r 08780101bc36 -r 33b8c5eedc04 test-data/matrix.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/matrix.txt	Wed Aug 10 08:23:43 2022 +0000
@@ -0,0 +1,4 @@
+	a.bed	b.bed	c.bed
+a.bed	1.0	0.75	0.875
+b.bed	1.0	1.0	0.8333333333333334
+c.bed	1.0	0.7142857142857143	1.0