# HG changeset patch
# User iuc
# Date 1390480206 18000
# Node ID 16dc0e3d659bb321392a1f80272dc333708ade53
# Parent  da0a1fcf7fe0deb3250e97e922b92525812cab7e
Uploaded

diff -r da0a1fcf7fe0 -r 16dc0e3d659b macs2_bdgbroadcall.xml
--- a/macs2_bdgbroadcall.xml	Tue Jan 21 13:14:33 2014 -0500
+++ b/macs2_bdgbroadcall.xml	Thu Jan 23 07:30:06 2014 -0500
@@ -1,5 +1,5 @@
-<tool id="macs2_bdgbroadcall" name="Call broad peaks" version="2.0.10.0">
-    <description>from bedGraph</description>
+<tool id="macs2_bdgbroadcall" name="MACS2 bdgbroadcall" version="2.0.10.0">
+    <description>Call broad peaks from bedGraph output</description>
     <expand macro="requirements" />
     <expand macro="version_command" />
     <macros>
diff -r da0a1fcf7fe0 -r 16dc0e3d659b macs2_bdgcmp.xml
--- a/macs2_bdgcmp.xml	Tue Jan 21 13:14:33 2014 -0500
+++ b/macs2_bdgcmp.xml	Thu Jan 23 07:30:06 2014 -0500
@@ -1,5 +1,5 @@
-<tool id="macs2_bdgcmp" name="Deduct noise" version="2.0.10.0">
-    <description>by comparing two signal tracks in bedGraph (bdgcmp)</description>
+<tool id="macs2_bdgcmp" name="MACS2 bdgcmp" version="2.0.10.0">
+    <description>Deduct noise by comparing two signal tracks in bedGraph</description>
     <expand macro="requirements" />
     <expand macro="version_command" />
     <macros>
diff -r da0a1fcf7fe0 -r 16dc0e3d659b macs2_bdgdiff.xml
--- a/macs2_bdgdiff.xml	Tue Jan 21 13:14:33 2014 -0500
+++ b/macs2_bdgdiff.xml	Thu Jan 23 07:30:06 2014 -0500
@@ -1,5 +1,5 @@
-<tool id="macs2_bdgdiff" name="Differential peak detection" version="2.0.10.0">
-    <description>based on paired four bedgraph files</description>
+<tool id="macs2_bdgdiff" name="MACS2 bdgdiff" version="2.0.10.0">
+    <description>Differential peak detection based on paired four bedgraph files</description>
     <expand macro="requirements" />
     <expand macro="version_command" />
     <macros>
diff -r da0a1fcf7fe0 -r 16dc0e3d659b macs2_bdgpeakcall.xml
--- a/macs2_bdgpeakcall.xml	Tue Jan 21 13:14:33 2014 -0500
+++ b/macs2_bdgpeakcall.xml	Thu Jan 23 07:30:06 2014 -0500
@@ -1,5 +1,5 @@
-<tool id="macs2_bdgpeakcall" name="Call peaks" version="2.0.10.0">
-    <description>from bedGraph output</description>
+<tool id="macs2_bdgpeakcall" name="MACS2 bdgpeakcall" version="2.0.10.0">
+    <description>Call peaks from bedGraph output</description>
     <expand macro="requirements" />
     <expand macro="version_command" />
     <macros>
diff -r da0a1fcf7fe0 -r 16dc0e3d659b macs2_callpeak.xml
--- a/macs2_callpeak.xml	Tue Jan 21 13:14:33 2014 -0500
+++ b/macs2_callpeak.xml	Thu Jan 23 07:30:06 2014 -0500
@@ -1,5 +1,5 @@
-<tool id="macs2_callpeak" name="Call peaks" version="2.0.10.0">
-    <description>from alignment results</description>
+<tool id="macs2_callpeak" name="MACS2 callpeak" version="2.0.10.0">
+    <description>Call peaks from alignment results</description>
     <expand macro="requirements">
         <requirement type="package" version="3.0.1">R_3_0_1</requirement>
         <!-- awk and R is missing -->
@@ -62,8 +62,8 @@
 
         ## TODO
         ## run R to create pdf from model script
-        ##if os.path.exists( os.path.join( tmp_dir, "MACS2_PREFIX_model.r" ) ):
-        ##    cmdline = 'Rscript "MACS2_PREFIX_model.r" > "MACS2_PREFIX_model.r.log"' )
+        ##if os.path.exists( os.path.join( tmp_dir, "MACS2_model.r" ) ):
+        ##    cmdline = 'Rscript "MACS2_model.r" > "MACS2_model.r.log"' )
         ##    proc = subprocess.Popen( args=cmdline, shell=True, cwd=tmp_dir )
         ##    proc.wait()
 
@@ -89,7 +89,7 @@
         ##parse xls files to interval files as needed
         ##TODO is in working dir
         #if 'peaks_interval' in str($outputs).split(','):
-            #set $file = os.path.join( $tmp_dir, 'MACS2_PREFIX_peaks.xls' )
+            #set $file = os.path.join( $tmp_dir, 'MACS2_peaks.xls' )
             #if os.path.exists( $file ):
                 echo '#peaks file' > $output_xls_to_interval_peaks_file;
                 awk '$2-=1' $file >> $output_xls_to_interval_peaks_file;
@@ -145,14 +145,13 @@
         </conditional>
 
         <param name="outputs" type="select" display="checkboxes" multiple="True" label="Outputs">
-            <option value="peaks_bed" selected="True">Peaks as bed file</option>
+            <option value="peaks_bed" selected="True">Peaks as BED file</option>
             <option value="html">Summary page (html)</option>
             <option value="narrow">narrow Peaks</option>
             <option value="broad">broad Peaks</option>
             <option value="gapped">gapped Peaks</option>
             <option value="summits" selected="true">summits</option>
             <option value="peaks_interval">Peaks as interval file</option>
-
             <validator type="no_options" message="Please select at least one output file." />
         </param>
 
@@ -181,19 +180,19 @@
     </inputs>
     <outputs>
         <!--callpeaks output-->
-        <data name="output_bed" format="tabular" from_work_dir="MACS2_PREFIX_peaks.xls" label="${tool.name} on ${on_string} (peaks: xls)">
+        <data name="output_bed" format="tabular" from_work_dir="MACS2_peaks.bed" label="${tool.name} on ${on_string} (peaks in BED)">
             <filter>'peaks_bed' in outputs</filter>
         </data>
-        <data name="output_narrowpeaks" format="tabular" from_work_dir="MACS2_PREFIX_peaks.narrowPeak" label="${tool.name} on ${on_string} (narrow Peaks)">
+        <data name="output_narrowpeaks" format="tabular" from_work_dir="MACS2_peaks.encodePeak" label="${tool.name} on ${on_string} (narrow Peaks)">
             <filter>'narrow' in outputs</filter>
         </data>
-        <data name="output_broadpeaks" format="tabular" from_work_dir="MACS2_PREFIX_peaks.broadPeak" label="${tool.name} on ${on_string} (broad Peaks)">
+        <data name="output_broadpeaks" format="tabular" from_work_dir="MACS2_broad_peaks.bed" label="${tool.name} on ${on_string} (broad Peaks)">
             <filter>'broad' in outputs</filter>
         </data>
-        <data name="output_gappedpeaks" format="tabular" from_work_dir="MACS2_PREFIX_peaks.gappedPeak" label="${tool.name} on ${on_string} (gapped Peaks)">
+        <data name="output_gappedpeaks" format="tabular" from_work_dir="MACS2_peaks.gappedPeak" label="${tool.name} on ${on_string} (gapped Peaks)">
             <filter>'gapped' in outputs</filter>
         </data>
-        <data name="output_summits" format="bed" from_work_dir="MACS2_PREFIX_summits.bed" label="${tool.name} on ${on_string} (summits)">
+        <data name="output_summits" format="bed" from_work_dir="MACS2_summits.bed" label="${tool.name} on ${on_string} (summits in BED)">
             <filter>'summits' in outputs</filter>
         </data>
         <data name="output_xls_to_interval_peaks_file" format="interval" label="${tool.name} on ${on_string} (peaks: interval)">
diff -r da0a1fcf7fe0 -r 16dc0e3d659b macs2_filterdup.xml
--- a/macs2_filterdup.xml	Tue Jan 21 13:14:33 2014 -0500
+++ b/macs2_filterdup.xml	Thu Jan 23 07:30:06 2014 -0500
@@ -1,5 +1,5 @@
-<tool id="macs2_filterdup" name="Remove duplicate reads" version="2.0.10.0">
-    <description>at the same position</description>
+<tool id="macs2_filterdup" name="MACS2 filterdup" version="2.0.10.0">
+    <description>Remove duplicate reads at the same position</description>
     <expand macro="requirements" />
     <expand macro="version_command" />
     <macros>
diff -r da0a1fcf7fe0 -r 16dc0e3d659b macs2_predict.xml
--- a/macs2_predict.xml	Tue Jan 21 13:14:33 2014 -0500
+++ b/macs2_predict.xml	Thu Jan 23 07:30:06 2014 -0500
@@ -1,5 +1,5 @@
-<tool id="macs2_predict" name="Predict" version="2.0.10.0">
-    <description>d or fragment size from alignment results</description>
+<tool id="macs2_predict" name="MACS2 predictd" version="2.0.10.0">
+    <description>Predict 'd' or fragment size from alignment results</description>
     <expand macro="requirements">
         <requirement type="package" version="3.0.1">R_3_0_1</requirement>
     </expand>
@@ -8,7 +8,7 @@
         <import>macs2_macros.xml</import>
     </macros>
     <command>
-        macs2 predict
+        macs2 predictd
             -i #echo ','.join($infiles)#
             --tsize $tsize
             @effective_genome_size@
diff -r da0a1fcf7fe0 -r 16dc0e3d659b macs2_randsample.xml
--- a/macs2_randsample.xml	Tue Jan 21 13:14:33 2014 -0500
+++ b/macs2_randsample.xml	Thu Jan 23 07:30:06 2014 -0500
@@ -1,5 +1,5 @@
-<tool id="macs2_randsamoke" name="Randomly sample number or percentage" version="2.0.10.0">
-    <description>of total reads</description>
+<tool id="macs2_randsamoke" name="MACS2" version="2.0.10.0">
+    <description>Randomly sample number or percentage of total reads</description>
     <expand macro="requirements" />
     <expand macro="version_command" />
     <macros>
diff -r da0a1fcf7fe0 -r 16dc0e3d659b macs2_refinepeak.xml
--- a/macs2_refinepeak.xml	Tue Jan 21 13:14:33 2014 -0500
+++ b/macs2_refinepeak.xml	Thu Jan 23 07:30:06 2014 -0500
@@ -1,5 +1,5 @@
-<tool id="macs2_refinepeak" name="Refine peak summits" version="2.0.10.0">
-    <description></description>
+<tool id="macs2_refinepeak" name="MACS2 refinepeak" version="2.0.10.0">
+    <description>Refine peak summits and give scores measuring balance of forward- backward tags (Experimental)</description>
     <expand macro="requirements" />
     <expand macro="version_command" />
     <macros>