# HG changeset patch
# User pjbriggs
# Date 1469541261 14400
# Node ID f346287fe52c28e083a924b7fe4492f812d8c34f
# Parent  062311890289aedddc8087fda2a76a17851b758a
Uploaded

diff -r 062311890289 -r f346287fe52c README.rst
--- a/README.rst	Mon Jun 15 08:32:55 2015 -0400
+++ b/README.rst	Tue Jul 26 09:54:21 2016 -0400
@@ -59,6 +59,8 @@
 ========== ======================================================================
 Version    Changes
 ---------- ----------------------------------------------------------------------
+2.1.0-5    - User must explicitly specify the format for the inputs (to allow
+             for paired-end data)
 2.1.0-4    - Remove 'bdgcmp' functionality.
 2.1.0-3    - Add tool tests
 2.1.0-2    - Add option to create bigWig file from bedGraphs; fix bug with -B
diff -r 062311890289 -r f346287fe52c macs21_wrapper.xml
--- a/macs21_wrapper.xml	Mon Jun 15 08:32:55 2015 -0400
+++ b/macs21_wrapper.xml	Tue Jul 26 09:54:21 2016 -0400
@@ -1,4 +1,4 @@
-<tool id="macs2_1_peakcalling" name="MACS2.1.0" version="2.1.0-4">
+<tool id="macs2_1_peakcalling" name="MACS2.1.0" version="2.1.0-5">
   <description>Model-based Analysis of ChIP-Seq: peak calling</description>
   <requirements>
     <requirement type="package" version="2.7">python</requirement>
@@ -19,7 +19,7 @@
        -c $input_control_file1
     #end if
     ##
-    --format=$input_chipseq_file1.extension
+    --format=$format
     --name="$experiment_name"
     --bw=$bw
     ##
@@ -114,6 +114,15 @@
 	       value="0.1" help="default: 0.1 (--broad-cutoff)"/>
       </when>
     </conditional>
+    <param name="format" type="select" label="Format of input read data"
+	   help="Specify the format of the input data and whether or not it is paired end (--format)">
+      <option value="BAMPE" selected="true">BAM (paired-end)</option>
+      <option value="BAM">BAM (single-end)</option>
+      <option value="BEDPE">BED (paired-end)</option>
+      <option value="BED">BED (single-end)</option>
+      <option value="SAMPE">SAM (paired-end)</option>
+      <option value="SAM">SAM (single-end)</option>
+    </param>
     <param name="input_chipseq_file1" type="data" format="bed,sam,bam"
 	   label="ChIP-seq read file" />
     <param name="input_control_file1" type="data" format="bed,sam,bam" optional="True"
@@ -270,6 +279,7 @@
       <!-- Inputs -->
       <param name="experiment_name" value="test_MACS2.1.0" />
       <param name="broad_regions" value="" />
+      <param name="format" value="BED" />
       <param name="input_chipseq_file1" value="test_region_IP.bed" dbkey="galGal3"
 	     ftype="bed" />
       <param name="input_control_file1" value="test_region_Input.bed"
@@ -308,6 +318,7 @@
       <!-- Inputs -->
       <param name="experiment_name" value="test_MACS2.1.0" />
       <param name="broad_regions" value="" />
+      <param name="format" value="BED" />
       <param name="input_chipseq_file1" value="test_region_IP.bed" dbkey="galGal3"
 	     ftype="bed" />
       <param name="input_control_file1" value="test_region_Input.bed"
diff -r 062311890289 -r f346287fe52c tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Jun 15 08:32:55 2015 -0400
+++ b/tool_dependencies.xml	Tue Jul 26 09:54:21 2016 -0400
@@ -2,10 +2,10 @@
 <tool_dependency>
   <!-- Dependencies from main/test toolsheds -->
   <package name="numpy" version="1.9">
-    <repository changeset_revision="43cb426cb05d" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="1e2b7e63dec2" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
   </package>
   <package name="R" version="3.1.2">
-    <repository changeset_revision="41f43a2064ba" name="package_r_3_1_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="1ca39eb16186" name="package_r_3_1_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
   </package>
   <!-- Subset of UCSC tools -->
   <package name="ucsc_tools_for_macs21" version="1.0">
@@ -45,20 +45,12 @@
               <action type="download_by_url">https://pypi.python.org/packages/source/M/MACS2/MACS2-2.1.0.20140616.tar.gz</action>
 	      <!-- Install environment for main & test toolsheds -->
               <action type="set_environment_for_install">
-		<repository changeset_revision="43cb426cb05d" name="package_numpy_1_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
+		<repository changeset_revision="1e2b7e63dec2" name="package_numpy_1_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
 		  <package name="numpy" version="1.9" />
 		</repository>
-		<repository changeset_revision="4778b172b895" name="package_atlas_3_10" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
-		  <package name="atlas" version="3.10.2" />
-		</repository>
 	      </action>
               <action type="make_directory">$INSTALL_DIR/lib/python</action>
               <action type="shell_command">
-		echo PWD is: ;
-		pwd ;
-		echo PYTHONPATH is $PYTHONPATH ;
-		python -c "import numpy" ;
-		echo About to do the operations: ;
                 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; 
                 python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
               </action>