# HG changeset patch
# User bgruening
# Date 1390323001 18000
# Node ID 97449a3c1f27f8d04bb8de717a97e7e0a67af325
# Parent  a83ea372ddd140c03dc7b491e312b0cea87b9982
Uploaded

diff -r a83ea372ddd1 -r 97449a3c1f27 macs2_macros.xml
--- a/macs2_macros.xml	Thu Jan 16 17:53:00 2014 -0500
+++ b/macs2_macros.xml	Tue Jan 21 11:50:01 2014 -0500
@@ -1,8 +1,6 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="python-module">macs2</requirement>
-            <requirement type="python-module">numpy</requirement>
             <requirement type="package" version="2.0.10.2">macs2</requirement>
             <requirement type="package" version="1.7.1">numpy</requirement>
             <yield />
diff -r a83ea372ddd1 -r 97449a3c1f27 macs2_predict.xml
--- a/macs2_predict.xml	Thu Jan 16 17:53:00 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,66 +0,0 @@
-<tool id="macs2_predict" name="Predict" version="2.0.10.0">
-    <description>d or fragment size from alignment results</description>
-    <expand macro="requirements">
-        <requirement type="package" version="3.0.1">R_3_0_1</requirement>
-    </expand>
-    <expand macro="version_command" />
-    <macros>
-        <import>macs2_macros.xml</import>
-    </macros>
-    <command>
-        macs2 predict
-            -i #echo ','.join($infiles)#
-            --tsize $tsize
-            @effective_genome_size@
-            --bw $band_width
-            --mfold $advanced_options.mfoldlo $advanced_options.mfoldhi
-            &gt; $outfile;
-
-        Rscript predicted_model.R &gt; $outfile_image
-    </command>
-        <expand macro="stdio" />
-    <inputs>
-        <repeat name="infiles" title="ChIP-seq alignment files" min="1" 
-            help="If multiple files are given, then they will all be read and combined. Note that pair-end data is not supposed to work with this command.">
-
-            <param name="infile" type="data" format="bam,sam,bed" multiple="True" optional="True" label="ChIP-seq alignment file" help="-i" />
-        </repeat>
-
-        <expand macro="conditional_effective_genome_size" />
-        <expand macro="tag_size" />
-
-        <param name="band_width" type="integer" value="300" label="Band width for picking regions to compute fragment size"
-            help="This value is only used while building the shifting model. (--bw)" />
-
-        <param name="mfoldlo" type="integer" label="Fold-enrichment lower limit" value="5"
-            help="Select the regions with MFOLD high-confidence enrichment ratio against background to build model (--mfold)"/>
-        <param name="mfoldhi" type="integer" label="Fold-enrichment upper-limit" value="50"
-            help="Select the regions with MFOLD high-confidence enrichment ratio against background to build model (--mfold)"/>
-
-    </inputs>
-
-    <outputs>
-        <data name="outfile" format="txt" label="${tool.name} on ${on_string} - d value" />
-        <data name="outfile_image" format="png" label="${tool.name} on ${on_string} - X-correlation image" />
-    </outputs>
-    <tests>
-        <!--none yet for macs2-->
-    </tests>
-    <help>
-**What it does**
-
-bdgdiff from macs2
-
-
-Note that pair-end data is not supposed to work with this command.
-
-
-------
-
-**Citation**
-
-For the underlying tool, please cite Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137.
-
-Integration of MACS2 with Galaxy performed by Ziru Zhou ( ziruzhou@gmail.com ). Please send your comments/questions to modENCODE DCC at help@modencode.org.
-    </help>
-</tool>
diff -r a83ea372ddd1 -r 97449a3c1f27 macs2_predictd.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macs2_predictd.xml	Tue Jan 21 11:50:01 2014 -0500
@@ -0,0 +1,66 @@
+<tool id="macs2_predict" name="Predict" version="2.0.10.0">
+    <description>d or fragment size from alignment results</description>
+    <expand macro="requirements">
+        <requirement type="package" version="3.0.1">R_3_0_1</requirement>
+    </expand>
+    <expand macro="version_command" />
+    <macros>
+        <import>macs2_macros.xml</import>
+    </macros>
+    <command>
+        macs2 predict
+            -i #echo ','.join($infiles)#
+            --tsize $tsize
+            @effective_genome_size@
+            --bw $band_width
+            --mfold $advanced_options.mfoldlo $advanced_options.mfoldhi
+            &gt; $outfile;
+
+        Rscript predicted_model.R &gt; $outfile_image
+    </command>
+        <expand macro="stdio" />
+    <inputs>
+        <repeat name="infiles" title="ChIP-seq alignment files" min="1" 
+            help="If multiple files are given, then they will all be read and combined. Note that pair-end data is not supposed to work with this command.">
+
+            <param name="infile" type="data" format="bam,sam,bed" multiple="True" optional="True" label="ChIP-seq alignment file" help="-i" />
+        </repeat>
+
+        <expand macro="conditional_effective_genome_size" />
+        <expand macro="tag_size" />
+
+        <param name="band_width" type="integer" value="300" label="Band width for picking regions to compute fragment size"
+            help="This value is only used while building the shifting model. (--bw)" />
+
+        <param name="mfoldlo" type="integer" label="Fold-enrichment lower limit" value="5"
+            help="Select the regions with MFOLD high-confidence enrichment ratio against background to build model (--mfold)"/>
+        <param name="mfoldhi" type="integer" label="Fold-enrichment upper-limit" value="50"
+            help="Select the regions with MFOLD high-confidence enrichment ratio against background to build model (--mfold)"/>
+
+    </inputs>
+
+    <outputs>
+        <data name="outfile" format="txt" label="${tool.name} on ${on_string} - d value" />
+        <data name="outfile_image" format="png" label="${tool.name} on ${on_string} - X-correlation image" />
+    </outputs>
+    <tests>
+        <!--none yet for macs2-->
+    </tests>
+    <help>
+**What it does**
+
+bdgdiff from macs2
+
+
+Note that pair-end data is not supposed to work with this command.
+
+
+------
+
+**Citation**
+
+For the underlying tool, please cite Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137.
+
+Integration of MACS2 with Galaxy performed by Ziru Zhou ( ziruzhou@gmail.com ). Please send your comments/questions to modENCODE DCC at help@modencode.org.
+    </help>
+</tool>
diff -r a83ea372ddd1 -r 97449a3c1f27 tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Jan 16 17:53:00 2014 -0500
+++ b/tool_dependencies.xml	Tue Jan 21 11:50:01 2014 -0500
@@ -7,7 +7,7 @@
        <repository changeset_revision="4b2ef8519550" name="package_scipy_0_12" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="R_3_0_1" version="3.0.1">
-        <repository changeset_revision="0a395bcd7efd" name="package_r_3_0_1" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="1d5b86c2e93d" name="package_r_3_0_1" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="macs2" version="2.0.10.2">
         <install version="1.0">
@@ -24,7 +24,7 @@
                 <action type="make_directory">$INSTALL_DIR/lib/python</action>
                 <action type="shell_command">
                     export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; 
-                    python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $env.INSTALL_DIR/bin
+                    python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
                 </action>
                 <action type="set_environment">
                     <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>