# HG changeset patch
# User iuc
# Date 1539600529 14400
# Node ID ea526bc73f8a42bf3b62e970a736dcf0dc37ded3
# Parent  567665ed8cdbf15146e5b7a5a0e5bf9a635e0766
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 30858afbdbe0223d07d2936a8469295bcbeda786

diff -r 567665ed8cdb -r ea526bc73f8a macs2_callpeak.xml
--- 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"/>
diff -r 567665ed8cdb -r ea526bc73f8a macs2_predictd.xml
--- a/macs2_predictd.xml	Mon Aug 06 10:41:13 2018 -0400
+++ b/macs2_predictd.xml	Mon Oct 15 06:48:49 2018 -0400
@@ -48,7 +48,11 @@
             <param name="band_width" value="300"/>
             <param name="lower" value="5"/>
             <param name="upper" value="50"/>
-            <output name="outfile" file="predictd_on_ChIP_200K_and_Control_200K.txt" lines_diff="2"/>
+            <output name="outfile">
+                <assert_contents>
+                    <has_line line="# predicted fragment length is 284 bps" />
+                </assert_contents>
+            </output>
             <output name="outfile_image" file="predictd_on_ChIP_200K_and_Control_200K.pdf" compare="sim_size"/>
         </test>
     </tests>
diff -r 567665ed8cdb -r ea526bc73f8a test-data/predictd_on_ChIP_200K_and_Control_200K.txt
--- a/test-data/predictd_on_ChIP_200K_and_Control_200K.txt	Mon Aug 06 10:41:13 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,17 +0,0 @@
-# read alignment files...
-# read treatment tags...
-Detected format is
-Detected format is
-tag size is determined as 86 bps
-# tag size = 86
-# total tags in alignment file
-# Build Peak Model...
-#2 looking for paired plus/minus strand peaks...
-#2 number of paired peaks
-start model_add_line...
-start X-correlation...
-end of X-cor
-# finished!
-# predicted fragment length is 284 bps
-# alternative fragment length(s) may be 284 bps
-# Generate R script for model