diff macs2_callpeak.xml @ 19:86e2413cf3f8 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 7bd4238efae0d755b6a0dfff8daa43a228f18d96

--- a/macs2_callpeak.xml	Sat Apr 02 21:37:38 2022 +0000
+++ b/macs2_callpeak.xml	Mon Oct 16 13:18:37 2023 +0000
@@ -1,9 +1,9 @@
 <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"/>
+    <description>Call peaks from alignment results</description> 
     <macros>
         <import>macs2_macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements">
     </expand>
     <expand macro="stdio" />
@@ -218,7 +218,7 @@
         </param>
 
         <section name="advanced_options" title="Advanced Options">
-                <param name="to_large" argument="--to-large" type="boolean" truevalue="--to-large" falsevalue="" checked="false"
+                <param argument="--to-large" type="boolean" truevalue="--to-large" falsevalue="" checked="false"
                     label="When set, scale the small sample up to the bigger sample"
                     help="By default, the bigger dataset will be scaled down towards the smaller dataset, which will lead to smaller p/qvalues and more specific results. Keep in mind that scaling down will bring down background noise more. Default: No"/>
                 <param argument="--nolambda" type="boolean" truevalue="--nolambda" falsevalue="" checked="false"
@@ -244,7 +244,7 @@
                             help="value is either p-value or q-value as specified above (--broad-cutoff)"/>
                     </when>
                     <when value="nobroad">
-                        <param name="call_summits" argument="--call-summits" type="boolean" truevalue="--call-summits" falsevalue="" checked="false"
+                        <param argument="--call-summits" type="boolean" truevalue="--call-summits" falsevalue="" checked="false"
                             label="Use a more sophisticated signal processing approach to find subpeak summits in each enriched peak region"/>
                     </when>
                 </conditional>
@@ -313,8 +313,8 @@
             <param name="outputs" value="peaks_tabular,bdg,html"/>
             <param name="effective_genome_size_options_selector" value="user_defined" />
             <param name="gsize" value="3300000000" />
-            <param name="lower" value="5" />
-            <param name="upper" value="50" />
+            <param name="mfold_lower" value="5" />
+            <param name="mfold_upper" value="50" />
             <assert_command>
                 <has_text text="--buffer-size"/>
                 <has_text text="--d-min"/>
@@ -340,8 +340,8 @@
             <param name="outputs" value="pdf"/>
             <param name="effective_genome_size_options_selector" value="user_defined" />
             <param name="gsize" value="3300000000" />
-            <param name="lower" value="5" />
-            <param name="upper" value="50" />
+            <param name="mfold_lower" value="5" />
+            <param name="mfold_upper" value="50" />
             <output name="output_plot" file="magic.pdf" compare="sim_size" ftype="pdf"/>
         </test>
         <!-- Ensure BAMPE works -->