diff macs2_callpeak.xml @ 20:f63ccb331626 draft

Uploaded

--- 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
-        &&
-        cat $temp_stderr 2>&1
+        ;
+        exit_code_for_galaxy=\$?;
+        cat $temp_stderr 2>&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>