# HG changeset patch
# User iuc
# Date 1398978466 14400
# Node ID f63ccb331626a1d3eef7d30fdb3f41fbea1dcd54
# Parent  05aca18fd8dc064f61c2e41bf1a5da3e5befff97
Uploaded

diff -r 05aca18fd8dc -r f63ccb331626 macs2_bdgcmp.xml
--- a/macs2_bdgcmp.xml	Wed Apr 23 18:25:51 2014 -0400
+++ b/macs2_bdgcmp.xml	Thu May 01 17:07:46 2014 -0400
@@ -19,18 +19,18 @@
     </command>
     <expand macro="stdio" />
     <inputs>
+        <param name="infile_treatment" type="data" format="bedgraph" label="Treatment bedGraph file" />
         <param name="infile_control" type="data" format="bedgraph" label="Control bedGraph file" />
-        <param name="infile_treatment" type="data" format="bedgraph" label="Treatment bedGraph file" />
 
         <conditional name="bdgcmp_options">
             <param name="bdgcmp_options_selector" type="select" label="Method to use while calculating a score in any bin by comparing treatment value and control value">
                 <option value="ppois" selected="true">Poisson pvalue (-log10) using control as lambda and treatment as observation (ppois)</option>
                 <option value="qpois">q-value through a BH process for poisson pvalues (qpois)</option>
                 <option value="subtract">subtraction from treatment (subtract)</option>
-                <option value="logFE">log10 fold enrichment (logFR)</option>
+                <option value="logFE">log10 fold enrichment (logFE)</option>
                 <option value="FE">linear scale fold enrichment (FE)</option>
                 <option value="logLR">log10 likelihood between ChIP-enriched model and open chromatin model (logLR)</option>
-                <option value="slogLR">symmetric log10 likelihood between two ChIP-enrichment models and open chromatin model (slogLR)</option>
+                <option value="slogLR">symmetric log10 likelihood between two ChIP-enrichment models (slogLR)</option>
             </param>
             <when value="FE">
                 <param name="pseudocount" type="float" label="Set pseudocount" value="0.0" help="The count will be applied after normalization of sequencing depth. default: 0.0, no pseudocount is applied."/>
diff -r 05aca18fd8dc -r f63ccb331626 macs2_callpeak.xml
--- a/macs2_callpeak.xml	Wed Apr 23 18:25:51 2014 -0400
+++ b/macs2_callpeak.xml	Thu May 01 17:07:46 2014 -0400
@@ -18,11 +18,15 @@
             -t ${ ' '.join( map( lambda x:'"%s"' % ( x ), $input_treatment_file ) ) }
 
             #if str( $input_control_file ) != 'None':
-                -t ${ ' '.join( map( lambda x:'"%s"' % ( x ), $input_control_file ) ) }
+                -c ${ ' '.join( map( lambda x:'"%s"' % ( x ), $input_control_file ) ) }
             #end if
 
-        #for $ifile in $input_treatment_file:
-            --format='${ ifile.ext.upper() }'
+        #for $ifile in $input_treatment_file[0]:
+            #if ${ ifile.ext.upper() } == 'BAM' and ${ bampe }:
+                --format BAMPE
+            #else:
+                --format='${ ifile.ext.upper() }'
+            #end
         #end for
 
         @effective_genome_size@
@@ -37,6 +41,19 @@
                 --broad
                 --broad-cutoff='${ advanced_options.broad_options.broad_cutoff }'
             #end if
+
+            #if $advanced_options.keepdup.keepdup_opt == 'specific':
+                --keep-dup '${ $advanced_options.keepdup.keep_duplicates }'
+            #else
+                --keep-dup '${ $advanced_options.keepdup.keepdup_opt }'
+            #end if
+
+            #if str( $advanced_options.keep_dup_options.keep_dup_options_selector ) == "user":
+                --keep-dup "${ advanced_options.keep_dup_options.user_keepdup }"
+            #else
+                --keep-dup "${ advanced_options.keep_dup_options.keep_dup_options_selector }"
+            #end if
+
         #end if
 
         ## With --bdg two additional output files will be generated.
@@ -87,13 +104,18 @@
             fi;
             )
         #end if
-        &amp;&amp;
-        cat $temp_stderr 2>&#38;1
+        ;
+        exit_code_for_galaxy=\$?;
+        cat $temp_stderr 2&gt;&amp;1;
+        (exit \$exit_code_for_galaxy)
     </command>
     <expand macro="stdio" />
     <inputs>
+        <param name="input_treatment_file" type="data" format="bam,sam,bed" multiple="True" label="ChIP-Seq Treatment File" />
         <param name="input_control_file" type="data" format="bam,sam,bed" multiple="True" optional="True" label="ChIP-Seq Control File" />
-        <param name="input_treatment_file" type="data" format="bam,sam,bed" multiple="True" label="ChIP-Seq Treatment File" />
+
+        <param name="bampe" type="boolean" truevalue="--format BAMPE" falsevalue="" checked="False" label="Are your inputs Paired-end BAM files?"
+            help="The 'Build model step' will be ignored and the real fragments will be used for each template defined by leftmost and rightmost mapping positions. (--format BAMPE)"/>
 
         <expand macro="conditional_effective_genome_size" />
         <expand macro="band_width" />
@@ -133,8 +155,8 @@
 
         <param name="outputs" type="select" display="checkboxes" multiple="True" label="Outputs">
             <option value="peaks_bed" selected="True">Peaks as BED file</option>
-            <option value="narrow">narrow Peaks</option>
-            <option value="summits" selected="true">summits</option>
+            <!--<option value="narrow">narrow Peaks</option>-->
+            <!--<option value="summits" selected="true">summits</option>-->
             <option value="bdg" selected="true">Scores in bedGraph files (--bdg)</option>
             <option value="html">Summary page (html)</option>
             <option value="pdf">Plot in PDF</option>
@@ -147,8 +169,8 @@
                 <option value="on">Display advanced options</option>
             </param>
             <when value="on">
-                <param name="nolambda" type="boolean" truevalue="--nolambda" falsevalue="" checked="False" label="Use fixed background lambda as local lambda for every peak region" help="up to 9X more time consuming (--nolambda)"/>
-                <param name="call_summits" type="boolean" truevalue="--call-summits" falsevalue="" checked="False" label="Use a more sophisticated signal processing approach to find subpeak summits in each enriched peak region" help="(--call-summits)"/>
+                <param name="nolambda" type="boolean" truevalue="--nolambda" falsevalue="" checked="False" 
+                    label="Use fixed background lambda as local lambda for every peak region" help="up to 9X more time consuming (--nolambda)"/>
                 <conditional name="broad_options">
                     <param name="broad_options_selector" type="select"
                         label="Composite broad regions" help="by putting nearby highly enriched regions into a broad region with loose cutoff (--broad)">
@@ -156,10 +178,16 @@
                         <option value="broad">broad regions</option>
                     </param>
                     <when value="broad">
-                        <param name="broad_cutoff" type="float" label="Cutoff for broad region" value="0.1" help="value is either p-value or q-value as specified above (--broad-cutoff)"/>
+                        <param name="broad_cutoff" type="float" label="Cutoff for broad region" value="0.1" 
+                            help="value is either p-value or q-value as specified above (--broad-cutoff)"/>
                     </when>
-                    <when value="nobroad"/>
+                    <when value="nobroad">
+                        <param name="call_summits" type="boolean" truevalue="--call-summits" falsevalue="" checked="False" 
+                            label="Use a more sophisticated signal processing approach to find subpeak summits in each enriched peak region" 
+                            help="(--call-summits)"/>
+                    </when>
                 </conditional>
+                <expand macro="keep_duplicates" />
             </when>
             <when value="off" />
         </conditional>
@@ -169,10 +197,15 @@
         <data name="output_bed" format="bed" label="${tool.name} on ${on_string} (Peaks in BED format)">
             <filter>'peaks_bed' in outputs</filter>
         </data>
-        <data name="output_narrowpeaks" format="tabular" from_work_dir="MACS2_peaks.encodePeak" label="${tool.name} on ${on_string} (narrow Peaks)">
-            <filter>'narrow' in outputs</filter>
+        <data name="output_broadpeaks" format="tabular" from_work_dir="MACS2_peaks.broadPeak" label="${tool.name} on ${on_string} (broad Peaks)">
+            <filter>
+            ((
+              advanced_options['advanced_options_selector'] == "on" and
+              advanced_options['broad_options']['broad_options_selector'] == "broad"
+            ))
+            </filter>
         </data>
-        <data name="output_broadpeaks" format="tabular" from_work_dir="MACS2_broad_peaks.bed" label="${tool.name} on ${on_string} (broad Peaks)">
+        <data name="output_gappedpeaks" format="tabular" from_work_dir="MACS2_peaks.gappedPeak" label="${tool.name} on ${on_string} (gapped Peaks)">
             <filter>
             ((
               advanced_options['advanced_options_selector'] == "on" and
@@ -180,8 +213,21 @@
             ))
             </filter>
         </data>
+        <data name="output_narrowpeaks" format="tabular" from_work_dir="MACS2_peaks.narrowPeak" label="${tool.name} on ${on_string} (narrow Peaks)">
+            <filter>
+            ((
+              advanced_options['advanced_options_selector'] == "on" and
+              advanced_options['broad_options']['broad_options_selector'] == "nobroad"
+            ))
+            </filter>
+        </data>
         <data name="output_summits" format="bed" from_work_dir="MACS2_summits.bed" label="${tool.name} on ${on_string} (summits in BED)">
-            <filter>'summits' in outputs</filter>
+            <filter>
+            ((
+              advanced_options['advanced_options_selector'] == "on" and
+              advanced_options['broad_options']['broad_options_selector'] == "nobroad"
+            ))
+            </filter>
         </data>
         <data name="output_plot" format="pdf" from_work_dir="MACS2_model.pdf" label="${tool.name} on ${on_string} (plot)">
             <filter>'pdf' in outputs</filter>
diff -r 05aca18fd8dc -r f63ccb331626 macs2_filterdup.xml
--- a/macs2_filterdup.xml	Wed Apr 23 18:25:51 2014 -0400
+++ b/macs2_filterdup.xml	Thu May 01 17:07:46 2014 -0400
@@ -27,19 +27,8 @@
         <expand macro="tag_size" />
         <param name="pvalue" type="text" value="1e-5" label="Pvalue cutoff for binomial distribution test" help="default: 1e-5 (--pvalue)" />
 
-        <conditional name="keep_dup_options">
-            <param name="keep_dup_options_selector" type="select" label="controlling behavior of duplicate tags at the exact same location"
-                help="It controls the 'macs2 filterdup' behavior towards duplicate tags at the exact same location (the same coordination and the same strand. The default 'auto') option makes 'macs2 filterdup' calculate the maximum tags at the exact same location based on binomal distribution using given -p as pvalue cutoff; and the 'all' option keeps every tags (useful if you only want to convert formats). If an integer is given, at most this number of tags will be kept at the same location. Default: auto">
-                <option value="auto" selected="true">auto</option>
-                <option value="all">all</option>
-                <option value="user">user defined</option>
-            </param>
-            <when value="user">
-                <param name="user_keepdup" type="integer" value="10" label="Keep at most this number of tags"/>
-            </when>
-            <when value="all"/>
-            <when value="auto"/>
-        </conditional>
+        <expand macro="keep_duplicates" />
+
     </inputs>
     <outputs>
         <data name="outfile" format="bed" label="${tool.name} on ${on_string}" />
diff -r 05aca18fd8dc -r f63ccb331626 macs2_macros.xml
--- a/macs2_macros.xml	Wed Apr 23 18:25:51 2014 -0400
+++ b/macs2_macros.xml	Thu May 01 17:07:46 2014 -0400
@@ -23,6 +23,25 @@
         </conditional>
     </xml>
 
+    <xml name="keep_duplicates">
+        <conditional name="keep_dup_options">
+            <param name="keep_dup_options_selector" type="select" label="How many duplicate tags at the exact same location are allowed?"
+                help="The default 'auto' option calculates the maximum tags at the exact same location based on binomal distribution using 1e-5 as pvalue cutoff. The 'all' option keeps every tags. If an integer is given, at most this number of tags will be kept at the same location. The default is to keep one tag at the same location. (--keep-dup 1)">
+                <option value="1" selected="true">1</option>
+                <option value="all">all</option>
+                <option value="auto">auto</option>
+                <option value="user">user defined</option>
+            </param>
+            <when value="user">
+                <param name="user_keepdup" type="integer" value="1" label="Keep at most this number of tags at the exact same location" 
+                    help=""/>
+            </when>
+            <when value="1" />
+            <when value="all" />
+            <when value="auto" />
+        </conditional>
+    </xml>
+
     <token name="@effective_genome_size@">
         #if $effective_genome_size_options.effective_genome_size_options_selector == 'user_defined':
             --gsize "${ effective_genome_size_options.gsize }"
diff -r 05aca18fd8dc -r f63ccb331626 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Apr 23 18:25:51 2014 -0400
+++ b/tool_dependencies.xml	Thu May 01 17:07:46 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="7302d8de5972" name="package_r_3_0_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="1c0e86a44f73" 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" />