diff macs2_callpeak.xml @ 59:ea526bc73f8a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 30858afbdbe0223d07d2936a8469295bcbeda786

--- a/macs2_callpeak.xml	Mon Aug 06 10:41:13 2018 -0400
+++ b/macs2_callpeak.xml	Mon Oct 15 06:48:49 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="macs2_callpeak" name="MACS2 callpeak" version="@VERSION_STRING@.4" profile="17.09">
+<tool id="macs2_callpeak" name="MACS2 callpeak" version="@VERSION_STRING@.5" profile="17.09">
     <description>Call peaks from alignment results</description>
     <macros>
         <import>macs2_macros.xml</import>
@@ -45,6 +45,7 @@
 
         $advanced_options.nolambda
         $advanced_options.to_large
+        $advanced_options.spmr
 
         #if $advanced_options.ratio:
             --ratio $advanced_options.ratio
@@ -219,6 +220,9 @@
                     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. (--to-large). Default: No"/>
                 <param name="nolambda" type="boolean" truevalue="--nolambda" falsevalue="" checked="False" optional="True"
                     label="Use fixed background lambda as local lambda for every peak region" help="up to 9X more time consuming (--nolambda). Default: No"/>
+                <param name="spmr" type="boolean" truevalue="--SPMR" falsevalue="" checked="False" optional="True"
+                    label="Save signal per million reads for fragment pileup profiles"
+                    help="Requires 'Scores in bedGraph files (--bdg)' output to be selected. (--SPMR). Default: No"/>
                 <param name="ratio" type="float" optional="True"
                     label="When set, use a custom scaling ratio of ChIP/control (e.g. calculated using NCIS) for linear scaling"
                     help="(--ratio) Default: ignore"/>