diff macs2_callpeak.xml @ 3:6d4babad010f draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316

--- a/macs2_callpeak.xml	Mon Oct 12 11:24:39 2015 -0400
+++ b/macs2_callpeak.xml	Wed Jan 27 15:23:25 2016 -0500
@@ -4,8 +4,7 @@
         <import>macs2_macros.xml</import>
     </macros>
     <expand macro="requirements">
-        <requirement type="package" version="3.0.1">R_3_0_1</requirement>
-        <requirement type="package" version="4.1.0">gnu_awk</requirement>
+        <requirement type="package" version="3.1.2">R</requirement>
         <requirement type="set_environment">MACS2_SCRIPT_PATH</requirement>
     </expand>
     <expand macro="stdio" />
@@ -79,9 +78,9 @@
         #end if
 
         2> $temp_stderr)
-        #if 'peaks_bed' in str($outputs).split(','):
+        #if 'peaks_tabular' in str($outputs).split(','):
             &amp;&amp;
-            awk '$2-=1' MACS2_peaks.xls | awk '!/^#/' | awk -v OFS='\t' '$1=$1' | tail -n+3  > "${ output_bed }"
+            cp MACS2_peaks.xls "${ output_tabular }"
         #end if
 
         ## run R to create pdf from model script
@@ -152,7 +151,7 @@
         </conditional>
 
         <param name="outputs" type="select" display="checkboxes" multiple="True" label="Outputs" help="PDF only created when model is build">
-            <option value="peaks_bed" selected="True">Peaks as BED file</option>
+            <option value="peaks_tabular" selected="True">Peaks as tabular file</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>
@@ -202,8 +201,8 @@
     </inputs>
     <outputs>
         <!--callpeaks output-->
-        <data name="output_bed" format="bed" label="${tool.name} on ${on_string} (Peaks in BED format)">
-            <filter>'peaks_bed' in outputs</filter>
+        <data name="output_tabular" format="tabular" label="${tool.name} on ${on_string} (Peaks in tabular format)">
+            <filter>'peaks_tabular' in outputs</filter>
         </data>
         <data name="output_broadpeaks" format="bed" from_work_dir="MACS2_peaks.broadPeak" label="${tool.name} on ${on_string} (broad Peaks)">
             <filter>
@@ -213,7 +212,7 @@
             ))
             </filter>
         </data>
-        <data name="output_gappedpeaks" format="tabular" from_work_dir="MACS2_peaks.gappedPeak" label="${tool.name} on ${on_string} (gapped Peaks)">
+        <data name="output_gappedpeaks" format="bed" from_work_dir="MACS2_peaks.gappedPeak" label="${tool.name} on ${on_string} (gapped Peaks)">
             <filter>
             ((
               advanced_options['advanced_options_selector'] == "on" and
@@ -221,7 +220,7 @@
             ))
             </filter>
         </data>
-        <data name="output_narrowpeaks" format="tabular" from_work_dir="MACS2_peaks.narrowPeak" label="${tool.name} on ${on_string} (narrow Peaks)">
+        <data name="output_narrowpeaks" format="bed" from_work_dir="MACS2_peaks.narrowPeak" label="${tool.name} on ${on_string} (narrow Peaks)">
             <filter>
             (
               advanced_options['advanced_options_selector'] == "off" or
@@ -259,12 +258,12 @@
             <param name="cutoff_options_selector" value="qvalue"/>
             <param name="qvalue" value="0.05"/>
             <param name="band_width" value="300"/>
-            <param name="outputs" value="peaks_bed,bdg"/>
+            <param name="outputs" value="peaks_tabular,bdg"/>
             <param name="effective_genome_size_options_selector" value="user_defined" />
             <param name="gsize" value="3300000000" />
             <output name="output_control_lambda" compare="contains" file="callpeak_control_part.bdg"/>
             <output name="output_treat_pileup" compare="contains" file="callpeak_treatment_part.bdg"/>
-            <output name="output_bed" compare="contains" file="callpeak_part.bed"/>
+            <output name="output_tabular" compare="contains" file="callpeak_part.tabular"/>
             <output name="output_summits" compare="contains" file="callpeak_summits_part.bed"/>
         </test>
         <test>