# HG changeset patch
# User iuc
# Date 1398291951 14400
# Node ID 05aca18fd8dc064f61c2e41bf1a5da3e5befff97
# Parent  ab352bb83cb2ed51159c98ac3e79cfbc1f828f4c
Uploaded

diff -r ab352bb83cb2 -r 05aca18fd8dc macs2_bdgbroadcall.xml
--- a/macs2_bdgbroadcall.xml	Sat Feb 15 15:50:45 2014 -0500
+++ b/macs2_bdgbroadcall.xml	Wed Apr 23 18:25:51 2014 -0400
@@ -9,14 +9,15 @@
     </macros>
     <command>
         macs2 bdgbroadcall
-            --ifile $infile
-            --cutoff-peak $cutoffpeak
-            --cutoff-link $cutofflink
-            --min-length $minlen
-            --lvl1-max-gap $LVL1MAXGAP
-            --lvl2-max-gap $LVL2MAXGAP
-            --ofile "macs2_bdgbroadcall.bdg";
-        awk '!/^track name/' "macs2_bdgbroadcall.bdg" > $outfile
+            --ifile "${ infile }"
+            --cutoff-peak "${ cutoffpeak }"
+            --cutoff-link "${ cutofflink }"
+            --min-length "${ minlen }"
+            --lvl1-max-gap "${ LVL1MAXGAP }"
+            --lvl2-max-gap "${ LVL2MAXGAP }"
+            --ofile "macs2_bdgbroadcall.bdg"
+        &amp;&amp;
+        awk '!/^track name/' "macs2_bdgbroadcall.bdg" > "${ outfile }"
     </command>
     <expand macro="stdio" />
     <inputs>
diff -r ab352bb83cb2 -r 05aca18fd8dc macs2_bdgcmp.xml
--- a/macs2_bdgcmp.xml	Sat Feb 15 15:50:45 2014 -0500
+++ b/macs2_bdgcmp.xml	Wed Apr 23 18:25:51 2014 -0400
@@ -7,14 +7,14 @@
     </macros>
     <command>
         macs2 bdgcmp
-            -t $infile_treatment
-            -c $infile_control
+            -t "${ infile_treatment }"
+            -c "${ infile_control }"
 
-            -m $bdgcmp_options.bdgcmp_options_selector
+            -m "${ bdgcmp_options.bdgcmp_options_selector }"
             #if str($bdgcmp_options.bdgcmp_options_selector) in ['FE', 'logFE', 'logLR']:
-                -p $bdgcmp_options.pseudocount
+                -p "${ bdgcmp_options.pseudocount }"
             #end if
-            --ofile $outfile
+            -o "${ outfile }"
 
     </command>
     <expand macro="stdio" />
diff -r ab352bb83cb2 -r 05aca18fd8dc macs2_bdgdiff.xml
--- a/macs2_bdgdiff.xml	Sat Feb 15 15:50:45 2014 -0500
+++ b/macs2_bdgdiff.xml	Wed Apr 23 18:25:51 2014 -0400
@@ -7,15 +7,15 @@
     </macros>
     <command>
         macs2 bdgdiff
-            --t1 $infile_pileup_cond1
-            --t2 $infile_pileup_cond2
-            --c1 $infile_control_cond1
-            --c2 $infile_control_cond2
-            --cutoff $cutoff
-            --min-len $minlen
-            --depth1 $depth1
-            --depth2 $depth2
-            --max-gap $maxgap
+            --t1 "${ infile_pileup_cond1 }"
+            --t2 "${ infile_pileup_cond2 }"
+            --c1 "${ infile_control_cond1 }"
+            --c2 "${ infile_control_cond2 }"
+            --cutoff "${ cutoff }"
+            --min-len "${ minlen }"
+            --depth1 "${ depth1 }"
+            --depth2 "${ depth2 }"
+            --max-gap "${ maxgap }"
             --o-prefix MACS2
 
     </command>
diff -r ab352bb83cb2 -r 05aca18fd8dc macs2_bdgpeakcall.xml
--- a/macs2_bdgpeakcall.xml	Sat Feb 15 15:50:45 2014 -0500
+++ b/macs2_bdgpeakcall.xml	Wed Apr 23 18:25:51 2014 -0400
@@ -9,14 +9,15 @@
     </macros>
     <command>
         macs2 bdgpeakcall
-        --ifile $infile
-        --cutoff $cutoff
-        --min-length $minlen
-        --max-gap $maxgap
-        $callsummits
-        $notrackline
-        --ofile "macs2_bdgpeakcall.bdg";
-        awk '!/^track name/' "macs2_bdgpeakcall.bdg" > $outfile
+        --ifile "${ infile }"
+        --cutoff "${ cutoff }"
+        --min-length "${ minlen }"
+        --max-gap "${ maxgap }"
+        ${ callsummits }
+        ${ notrackline }
+        --ofile "macs2_bdgpeakcall.bdg"
+        &amp;&amp;
+        awk '!/^track name/' "macs2_bdgpeakcall.bdg" > "${ outfile }"
     </command>
     <expand macro="stdio" />
     <inputs>
diff -r ab352bb83cb2 -r 05aca18fd8dc macs2_callpeak.xml
--- a/macs2_callpeak.xml	Sat Feb 15 15:50:45 2014 -0500
+++ b/macs2_callpeak.xml	Wed Apr 23 18:25:51 2014 -0400
@@ -12,17 +12,17 @@
     <command>
         #import os
         #set $temp_stderr = 'macs2_stderr'
-        macs2 callpeak
+        (macs2 callpeak
 
             --name "MACS2"
-            -t #echo ' '.join( map(str, $input_treatment_file) )#
+            -t ${ ' '.join( map( lambda x:'"%s"' % ( x ), $input_treatment_file ) ) }
 
-            #if ' '.join( map(str, $input_control_file) ) != 'None':
-                -c #echo ' '.join( map(str, $input_control_file) )#
+            #if str( $input_control_file ) != 'None':
+                -t ${ ' '.join( map( lambda x:'"%s"' % ( x ), $input_control_file ) ) }
             #end if
 
         #for $ifile in $input_treatment_file:
-            --format='$ifile.ext.upper()'
+            --format='${ ifile.ext.upper() }'
         #end for
 
         @effective_genome_size@
@@ -35,7 +35,7 @@
             $advanced_options.call_summits
             #if $advanced_options.broad_options.broad_options_selector == 'broad':
                 --broad
-                --broad-cutoff='$advanced_options.broad_options.broad_cutoff'
+                --broad-cutoff='${ advanced_options.broad_options.broad_cutoff }'
             #end if
         #end if
 
@@ -46,44 +46,48 @@
 
         ## cutoff selection
         #if str( $cutoff_options.cutoff_options_selector ) == 'qvalue':
-            --qvalue $cutoff_options.qvalue
+            --qvalue "${ cutoff_options.qvalue }"
         #elif str( $cutoff_options.cutoff_options_selector ) == 'pvalue':
             #if str($cutoff_options.pvalue).strip() != '':
-                --pvalue $cutoff_options.pvalue
+                --pvalue "${ cutoff_options.pvalue }"
             #end if
         #else:
-            --foldenrichment $cutoff_options.foldenrichment
+            --foldenrichment "${ cutoff_options.foldenrichment }"
         #end if
 
         ## model options
         #if $nomodel_type.nomodel_type_selector == 'nomodel':
             --nomodel
             ##--shiftsize '$nomodel_type.shiftsize'
-            --extsize '$nomodel_type.extsize'
+            --extsize '${ nomodel_type.extsize }'
         #end if
 
-        2> $temp_stderr;
-
+        2> $temp_stderr)
         #if 'peaks_bed' in str($outputs).split(','):
-            awk '$2-=1' MACS2_peaks.xls | awk '!/^#/' | awk -v OFS='\t' '$1=$1' | tail -n+3  > $output_bed;
+            &amp;&amp;
+            awk '$2-=1' MACS2_peaks.xls | awk '!/^#/' | awk -v OFS='\t' '$1=$1' | tail -n+3  > "${ output_bed }"
         #end if
 
         ## run R to create pdf from model script
         #if 'pdf' in str($outputs).split(','):
-            Rscript MACS2_model.r > MACS2_model.r.log;
+            &amp;&amp;
+            Rscript MACS2_model.r > MACS2_model.r.log
         #end if
 
         #if 'html' in str($outputs).split(','):
             ## if output files exists, move them to the extra_files_path and create a html result page linking to them
+            &amp;&amp;
+            (
             count=`ls -1 MACS2* 2>/dev/null | wc -l`;
             if [ \$count != 0 ];
             then 
-                mkdir $output_extra_files.extra_files_path;
-                cp MACS2* $output_extra_files.extra_files_path;
-                python \$MACS2_SCRIPT_PATH/dir2html.py $output_extra_files.extra_files_path $temp_stderr > $output_extra_files;
+                mkdir "${ output_extra_files.extra_files_path }";
+                cp MACS2* "${ output_extra_files.extra_files_path }";
+                python "\$MACS2_SCRIPT_PATH/dir2html.py" "${ output_extra_files.extra_files_path }" $temp_stderr > "${ output_extra_files }";
             fi;
+            )
         #end if
-
+        &amp;&amp;
         cat $temp_stderr 2>&#38;1
     </command>
     <expand macro="stdio" />
diff -r ab352bb83cb2 -r 05aca18fd8dc macs2_filterdup.xml
--- a/macs2_filterdup.xml	Sat Feb 15 15:50:45 2014 -0500
+++ b/macs2_filterdup.xml	Wed Apr 23 18:25:51 2014 -0400
@@ -7,17 +7,17 @@
     </macros>
     <command>
         macs2 filterdup
-            -i $infile
-            -o $outfile
+            -i "${ infile }"
+            -o "${ outfile }"
 
-        --format '$infile.extension.upper()'
+        --format '${ infile.extension.upper() }'
         @effective_genome_size@
         @tag_size@
-        --pvalue $pvalue
+        --pvalue "${ pvalue }"
         #if str( $keep_dup_options.keep_dup_options_selector ) == "user":
-            --keep-dup $keep_dup_options.user_keepdup
+            --keep-dup "${ keep_dup_options.user_keepdup }"
         #else
-            --keep-dup $keep_dup_options.keep_dup_options_selector
+            --keep-dup "${ keep_dup_options.keep_dup_options_selector }"
         #end if
     </command>
     <expand macro="stdio" />
diff -r ab352bb83cb2 -r 05aca18fd8dc macs2_macros.xml
--- a/macs2_macros.xml	Sat Feb 15 15:50:45 2014 -0500
+++ b/macs2_macros.xml	Wed Apr 23 18:25:51 2014 -0400
@@ -11,10 +11,10 @@
     <xml name="conditional_effective_genome_size">
         <conditional name="effective_genome_size_options">
             <param name="effective_genome_size_options_selector" type="select" label="Effective genome size" help="--gsize">
-                <option value="3300000000">Human (3.300.000.000)</option>
-                <option value="3000000000">Mouse (3.000.000.000)</option>
-                <option value="190000000">Fly (190.000.000)</option>
-                <option value="130000000">Worm (130.000.000)</option>
+                <option value="2451960000">Human (2.451.960.000)</option>
+                <option value="2150570000">Mouse (2.150.570.000)</option>
+                <option value="121400000">Fly (121.400.000)</option>
+                <option value="93260000">Worm (93.260.000)</option>
                 <option value="user_defined">User defined</option>
             </param>
             <when value="user_defined">
@@ -25,9 +25,9 @@
 
     <token name="@effective_genome_size@">
         #if $effective_genome_size_options.effective_genome_size_options_selector == 'user_defined':
-            --gsize $effective_genome_size_options.gsize
+            --gsize "${ effective_genome_size_options.gsize }"
         #else:
-            --gsize $effective_genome_size_options.effective_genome_size_options_selector
+            --gsize "${ effective_genome_size_options.effective_genome_size_options_selector }"
         #end if
     </token>
 
@@ -45,7 +45,7 @@
 
     <token name="@tag_size@">
         #if $tsize == -1.0:
-            --tsize $tsize
+            --tsize "${ tsize }"
         #end if
     </token>
 
diff -r ab352bb83cb2 -r 05aca18fd8dc macs2_predictd.xml
--- a/macs2_predictd.xml	Sat Feb 15 15:50:45 2014 -0500
+++ b/macs2_predictd.xml	Wed Apr 23 18:25:51 2014 -0400
@@ -10,18 +10,20 @@
     </macros>
     <command>
         macs2 predictd
-            -i #echo ' '.join( map( str, $infiles) )#
+            -i ${ ' '.join( map( lambda x:'"%s"' % ( x ), $infiles ) ) }
             @tag_size@
             @effective_genome_size@
-            --bw $band_width
-            --mfold $mfoldlo $mfoldhi
+            --bw "${ band_width }"
+            --mfold "${ mfoldlo }" "${ mfoldhi }"
 
             ## remove the timepoint and strip the output
             2>&amp;1 | awk -F: '{print $4}' | awk '{$1=$1}1'
 
-            &gt; $outfile;
+            &gt; "${ outfile }"
+            
+        &amp;&amp;
 
-        Rscript predictd;
+        Rscript predictd
     </command>
     <expand macro="stdio" />
     <inputs>
diff -r ab352bb83cb2 -r 05aca18fd8dc macs2_randsample.xml
--- a/macs2_randsample.xml	Sat Feb 15 15:50:45 2014 -0500
+++ b/macs2_randsample.xml	Wed Apr 23 18:25:51 2014 -0400
@@ -7,16 +7,16 @@
     </macros>
     <command>
         macs2 randsample
-            -t $infile
-            -o $outfile
+            -t "${ infile }"
+            -o "${ outfile }"
 
-        --format '$infile.extension.upper()'
+        --format '${ infile.extension.upper() }'
 
         @tag_size@
         #if $method_options.method_options_selector == 'percentage':
-            --percentage $method_options.percentage
+            --percentage "${ method_options.percentage }"
         #else:
-            --number $method_options.number
+            --number "${ method_options.number }"
         #end if
     </command>
     <expand macro="stdio" />
diff -r ab352bb83cb2 -r 05aca18fd8dc macs2_refinepeak.xml
--- a/macs2_refinepeak.xml	Sat Feb 15 15:50:45 2014 -0500
+++ b/macs2_refinepeak.xml	Wed Apr 23 18:25:51 2014 -0400
@@ -7,12 +7,12 @@
     </macros>
     <command>
         macs2 refinepeak
-            -b $bed_infile
-            -i $infile
-            --format '$infile.extension.upper()'
-            --cutoff $cutoff
-            --window-size $winsize
-            --ofile $outfile
+            -b "${ bed_infile }"
+            -i "${ infile }"
+            --format '${ infile.extension.upper() }'
+            --cutoff "${ cutoff }"
+            --window-size "${ winsize }"
+            --ofile "${ outfile }"
     </command>
     <expand macro="stdio" />
     <inputs>
diff -r ab352bb83cb2 -r 05aca18fd8dc tool_dependencies.xml
--- a/tool_dependencies.xml	Sat Feb 15 15:50:45 2014 -0500
+++ b/tool_dependencies.xml	Wed Apr 23 18:25:51 2014 -0400
@@ -7,7 +7,7 @@
        <repository changeset_revision="4b2ef8519550" name="package_scipy_0_12" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="R_3_0_1" version="3.0.1">
-        <repository changeset_revision="4666f68ad4d5" name="package_r_3_0_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="7302d8de5972" name="package_r_3_0_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="gnu_awk" version="4.1.0">
        <repository changeset_revision="cbe9f1c8c98b" name="package_gnu_awk_4_1_0" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
@@ -35,8 +35,11 @@
                     </repository>
                 </action>
                 <action type="make_directory">$INSTALL_DIR/lib/python</action>
+                <!-- exporting the CFLAGS and CPPFLAGS are due to http://stackoverflow.com/questions/22313407/clang-error-unknown-argument-mno-fused-madd-python-package-installation-fa -->
                 <action type="shell_command">
-                    export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; 
+                    export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;
+                    export CFLAGS=-Qunused-arguments &amp;&amp;
+                    export CPPFLAGS=-Qunused-arguments &amp;&amp;
                     python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
                 </action>
                 <action type="set_environment">