diff macs2_callpeak.xml @ 18:640d3af5d833 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e8307adcc6ee9245fa2bb9ecb6de1cbe008dc2c3"

--- a/macs2_callpeak.xml	Thu Apr 25 17:49:05 2019 -0400
+++ b/macs2_callpeak.xml	Sat Apr 02 21:37:38 2022 +0000
@@ -1,5 +1,6 @@
-<tool id="macs2_callpeak" name="MACS2 callpeak" version="@VERSION_STRING@.6" profile="17.09">
+<tool id="macs2_callpeak" name="MACS2 callpeak" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
     <description>Call peaks from alignment results</description>
+    <expand macro="bio_tools"/>
     <macros>
         <import>macs2_macros.xml</import>
     </macros>
@@ -72,6 +73,8 @@
             --keep-dup '${ advanced_options.keep_dup_options.keep_dup_options_selector }'
         #end if
 
+        --d-min $advanced_options.d_min
+        --buffer-size $advanced_options.buffer_size
 
         ## With --bdg two additional output files will be generated.
         #if "bdg" in str($outputs).split(','):
@@ -246,6 +249,8 @@
                     </when>
                 </conditional>
                 <expand macro="keep_duplicates" />
+                <expand macro="fragment_size"/>
+                <expand macro="buffer_size"/>
         </section>
     </inputs>
     <outputs>
@@ -310,6 +315,10 @@
             <param name="gsize" value="3300000000" />
             <param name="lower" value="5" />
             <param name="upper" value="50" />
+            <assert_command>
+                <has_text text="--buffer-size"/>
+                <has_text text="--d-min"/>
+            </assert_command>
             <output name="output_control_lambda" compare="contains" file="callpeak_control_part.bdg" lines_diff="1"/>
             <output name="output_treat_pileup" compare="contains" file="callpeak_treatment_part.bdg" lines_diff="1"/>
             <output name="output_tabular" compare="contains" file="callpeak_part.tabular" lines_diff="3"/>
@@ -333,7 +342,7 @@
             <param name="gsize" value="3300000000" />
             <param name="lower" value="5" />
             <param name="upper" value="50" />
-            <output name="output_plot" file="magic.pdf" ftype="pdf" compare="contains" />
+            <output name="output_plot" file="magic.pdf" compare="sim_size" ftype="pdf"/>
         </test>
         <!-- Ensure BAMPE works -->
         <test expect_num_outputs="1">