# HG changeset patch
# User iuc
# Date 1556228945 14400
# Node ID 424aefbd777784c987361274e9fcd6de5f361a77
# Parent  495a4173006ff341f3d3f7edad46a4187f924b80
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e90e79e18362561d0060d2c162f1938feebdbc29

diff -r 495a4173006f -r 424aefbd7777 macs2_callpeak.xml
--- a/macs2_callpeak.xml	Tue Oct 16 10:31:14 2018 -0400
+++ b/macs2_callpeak.xml	Thu Apr 25 17:49:05 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="macs2_callpeak" name="MACS2 callpeak" version="@VERSION_STRING@.5" profile="17.09">
+<tool id="macs2_callpeak" name="MACS2 callpeak" version="@VERSION_STRING@.6" profile="17.09">
     <description>Call peaks from alignment results</description>
     <macros>
         <import>macs2_macros.xml</import>
@@ -138,10 +138,10 @@
                 <option value="Yes">Yes</option>
             </param>
             <when value="No" >
-                <param name="input_treatment_file" argument="-t" type="data" format="bam,sam,bed" label="ChIP-Seq Treatment File" />
+                <param name="input_treatment_file" argument="-t" type="data" format="bam,bed" label="ChIP-Seq Treatment File" />
             </when>
             <when value="Yes">
-                <param name="input_treatment_file" argument="-t" type="data" format="bam,sam,bed" multiple="true" label="ChIP-Seq Treatment File" />
+                <param name="input_treatment_file" argument="-t" type="data" format="bam,bed" multiple="true" label="ChIP-Seq Treatment File" />
             </when>
         </conditional>
 
@@ -157,10 +157,10 @@
                         <option value="Yes">Yes</option>
                     </param>
                     <when value="No" >
-                        <param name="input_control_file" argument="-c" type="data" format="bam,sam,bed" label="ChIP-Seq Control File" />
+                        <param name="input_control_file" argument="-c" type="data" format="bam,bed" label="ChIP-Seq Control File" />
                     </when>
                     <when value="Yes">
-                        <param name="input_control_file" argument="-c" type="data" format="bam,sam,bed" multiple="true" label="ChIP-Seq Control File" />
+                        <param name="input_control_file" argument="-c" type="data" format="bam,bed" multiple="true" label="ChIP-Seq Control File" />
                     </when>
                 </conditional>
             </when>
diff -r 495a4173006f -r 424aefbd7777 macs2_filterdup.xml
--- a/macs2_filterdup.xml	Tue Oct 16 10:31:14 2018 -0400
+++ b/macs2_filterdup.xml	Thu Apr 25 17:49:05 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="macs2_filterdup" name="MACS2 filterdup" version="@VERSION_STRING@.0">
+<tool id="macs2_filterdup" name="MACS2 filterdup" version="@VERSION_STRING@.1">
     <description>Remove duplicate reads at the same position</description>
     <macros>
         <import>macs2_macros.xml</import>
@@ -23,7 +23,7 @@
     ]]>
     </command>
     <inputs>
-        <param name="infile" type="data" format="sam,bam,bed" label="Sequencing alignment file" />
+        <param name="infile" type="data" format="bam,bed" label="Sequencing alignment file" />
         <expand macro="conditional_effective_genome_size" />
         <expand macro="tag_size" />
         <param name="pvalue" type="text" value="1e-5" label="Pvalue cutoff for binomial distribution test" help="Default=1e-5 (--pvalue)" />
diff -r 495a4173006f -r 424aefbd7777 macs2_predictd.xml
--- a/macs2_predictd.xml	Tue Oct 16 10:31:14 2018 -0400
+++ b/macs2_predictd.xml	Thu Apr 25 17:49:05 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="macs2_predictd" name="MACS2 predictd" version="@VERSION_STRING@.0">
+<tool id="macs2_predictd" name="MACS2 predictd" version="@VERSION_STRING@.1">
     <description>Predict 'd' or fragment size from alignment results</description>
     <macros>
         <import>macs2_macros.xml</import>
@@ -26,7 +26,7 @@
         Rscript predictd
     ]]></command>
     <inputs>
-        <param name="infiles" type="data" format="bam,sam,bed" multiple="True"
+        <param name="infiles" type="data" format="bam,bed" multiple="True"
                label="ChIP-seq alignment file"
                help="If multiple files are given, then they will all be read and combined. Note that pair-end data is not supposed to work with this command. (-i)" />
         <expand macro="conditional_effective_genome_size" />
diff -r 495a4173006f -r 424aefbd7777 macs2_randsample.xml
--- a/macs2_randsample.xml	Tue Oct 16 10:31:14 2018 -0400
+++ b/macs2_randsample.xml	Thu Apr 25 17:49:05 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="macs2_randsample" name="MACS2 randsample" version="@VERSION_STRING@.0">
+<tool id="macs2_randsample" name="MACS2 randsample" version="@VERSION_STRING@.1">
     <description>Randomly sample number or percentage of total reads</description>
     <macros>
         <import>macs2_macros.xml</import>
@@ -24,7 +24,7 @@
         #end if
         ]]></command>
     <inputs>
-        <param name="infile" type="data" format="sam,bam,bed" label="Sequencing alignment file" />
+        <param name="infile" type="data" format="bam,bed" label="Sequencing alignment file" />
         <expand macro="tag_size" />
         <conditional name="method_options">
             <param name="method_options_selector" type="select" label="Select action to be performed">
diff -r 495a4173006f -r 424aefbd7777 macs2_refinepeak.xml
--- a/macs2_refinepeak.xml	Tue Oct 16 10:31:14 2018 -0400
+++ b/macs2_refinepeak.xml	Thu Apr 25 17:49:05 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="macs2_refinepeak" name="MACS2 refinepeak" version="@VERSION_STRING@.0">
+<tool id="macs2_refinepeak" name="MACS2 refinepeak" version="@VERSION_STRING@.1">
     <description>Refine peak summits and give scores measuring balance of forward- backward tags (Experimental)</description>
     <macros>
         <import>macs2_macros.xml</import>
@@ -17,7 +17,7 @@
             --ofile '${ outfile }'
     ]]></command>
     <inputs>
-        <param name="infile" type="data" format="sam,bam,bed" label="Sequencing alignment file" />
+        <param name="infile" type="data" format="bam,bed" label="Sequencing alignment file" />
         <param name="bed_infile" type="data" format="bed" label="Candidate peak file in BED format" />
         <param name="cutoff" type="float" label="Cutoff" value="5.0" help="default: 5.0 (--cutoff)"/>
         <param name="winsize" type="integer" value="200" label="Scan window size on both side of the summit" help="default: 200bp (--window-size)" />