diff macs2_macros.xml @ 18:640d3af5d833 draft

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

--- a/macs2_macros.xml	Thu Apr 25 17:49:05 2019 -0400
+++ b/macs2_macros.xml	Sat Apr 02 21:37:38 2022 +0000
@@ -1,14 +1,18 @@
 <macros>
-    <token name="@VERSION_STRING@">2.1.1.20160309</token>
-
+    <token name="@TOOL_VERSION@">2.2.7.1</token>
+    <token name="@VERSION_SUFFIX@">0</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="@VERSION_STRING@">macs2</requirement>
+            <requirement type="package" version="@TOOL_VERSION@">macs2</requirement>
             <requirement type="package" version="3.4">r-base</requirement>
             <yield />
         </requirements>
     </xml>
-
+    <xml name="bio_tools">
+        <xrefs>
+            <xref type="bio.tools">macs</xref>
+        </xrefs>
+    </xml>
     <token name="@home_dir@"><![CDATA[
         export PYTHON_EGG_CACHE=`pwd` &&
     ]]></token>
@@ -54,7 +58,8 @@
     </xml>
 
     <xml name="mfold_options">
-        <section name="mfold" title="Mfold settings" expanded="True" help="Select the regions within MFOLD range of highconfidence enrichment ratio against background to build model. Fold-enrichment in regions must be lower than upper limit, and higher than the lower limit. Default is 5 for lower and 50 for upper (--mfold)" >
+        <section name="mfold" title="Mfold settings" expanded="True" 
+            help="Select the regions within MFOLD range of highconfidence enrichment ratio against background to build model. Fold-enrichment in regions must be lower than upper limit, and higher than the lower limit. Default is 5 for lower and 50 for upper" >
             <param name="lower" type="integer" value="5" label="Set lower mfold bound" />
             <param name="upper" type="integer" value="50" label="Set upper mfold bound" />
         </section>
@@ -72,13 +77,24 @@
         #end if
     </token>
 
+    <xml name="buffer_size">
+            <param argument="--buffer-size" type="integer" min="0" value="100000" label="Buffer size" 
+                help="Buffer size for incrementally increasing internal array size to store reads alignment information. In most cases, you don't have to change this parameter.
+                    However, if there are large number of chromosomes/contigs/scaffolds in your alignment, it's recommended to specify a smaller buffer size in order to
+                    decrease memory usage (but it will take longer time to read alignment files)." />
+    </xml>
+
+    <token name="@buffer_size@">
+        --buffer-size $buffer_size
+    </token>
+
     <xml name="version_command">
         <version_command>macs2 --version</version_command>
     </xml>
 
     <xml name="tag_size">
-        <param name="tsize" type="integer" label="Tag size" value="" optional="true"
-               help="This will override the auto detected tag size. Per default that option is deactivated: -1.0 (--tsize)" />
+        <param argument="--tsize" type="integer" label="Tag size" value="" optional="true"
+               help="This will override the auto detected tag size. Per default that option is deactivated: -1.0 " />
     </xml>
     <xml name="band_width">
         <param name="band_width" type="integer" value="300"
@@ -86,6 +102,12 @@
                help=" You can set this parameter as the medium fragment size expected from sonication or size selection. (--bw)" />
     </xml>
 
+    <xml name="fragment_size">
+        <param argument="--d-min" type="integer" value="20"
+            label="Minimum fragment size in basepair"
+            help="Any predicted fragment size less than this will be excluded."/>
+    </xml>
+
     <token name="@tag_size@">
         #if $tsize:
             --tsize '${ tsize }'