diff macs21_wrapper.xml @ 2:15889783e759 draft

Fix bugs in tool operation and update dependencies.

--- a/macs21_wrapper.xml	Thu Jan 29 11:11:21 2015 -0500
+++ b/macs21_wrapper.xml	Thu Feb 12 08:29:07 2015 -0500
@@ -1,7 +1,7 @@
-<tool id="macs2_1_peakcalling" name="MACS2.1.0" version="2.1.0-1">
+<tool id="macs2_1_peakcalling" name="MACS2.1.0" version="2.1.0-2">
   <requirements>
     <requirement type="package" version="2.7">python</requirement>
-    <requirement type="package" version="1.8.1">numpy</requirement>
+    <requirement type="package" version="1.9">numpy</requirement>
     <requirement type="package" version="2.1.0.20140616">macs2</requirement>
   </requirements>
   <description>Model-based Analysis of ChIP-Seq</description>
@@ -49,13 +49,15 @@
           --pvalue=$major_command.pq_options.pvalue
        #end if
        ##
+       ## Bedgraph options
+       #if $major_command.bdg_options.bdg == True
+          -B $major_command.bdg_options.spmr
+       #end if
+       ##
        ## Advanced options
        #if str($major_command.advanced_options.advanced_options_selector) == 'on'
           --mfold $major_command.advanced_options.mfoldlo $major_command.advanced_options.mfoldhi
           $major_command.advanced_options.nolambda
-	  #if $major_command.bdg_options.bdg == True
-             -B $major_command.bdg_options.spmr
-	  #end if
           $major_command.advanced_options.call_summits
           #if str($major_command.advanced_options.keep_duplicates.keep_dup) == ''
              --keep-dup $major_command.advanced_options.keep_duplicates.maximum_tags
@@ -64,7 +66,7 @@
           #end if
        #else
           ## Defaults if advanced options not set
-          --mfold 5 50 --keep-dup 1
+          --mfold 10 30 --keep-dup 1
        #end if
        ##
        ## Output files
@@ -82,8 +84,12 @@
        ##
        ## Bedgraph outputs
        #if str($major_command.bdg_options.bdg) == 'True'
-          --output-pileup $output_treat_pileup_file 
+          --output-pileup=$output_treat_pileup_file 
           --output-lambda-bedgraph=$output_lambda_bedgraph_file
+	  #if str($major_command.bdg_options.make_bigwig) == 'True'
+             --output-bigwig=$output_bigwig_file
+             --length=$GALAXY_DATA_INDEX_DIR/shared/ucsc/chrom/${major_command.input_chipseq_file1.dbkey}.len
+	  #end if
        #end if
        ##
        ## XLS/interval output
@@ -153,13 +159,17 @@
 
 	<conditional name="bdg_options">
 	  <param name="bdg"
-		 label="Save fragment pileup, control lambda, -log10pvalue/qvalue in bedGraph"
+		 label="Save treatment and control lambda pileups in bedGraph"
 		 type="boolean" truevalue="-B" falsevalue="" checked="False" />
 	  <when value="-B">
 	    <param name="spmr"
 		   type="boolean" truevalue="--SPMR" falsevalue="" checked="False"
 		   label="Save signal per million reads for fragment pileup profiles"
 		   help="(--SPMR)" />
+	    <param name="make_bigwig" type="boolean" checked="True"
+		   truevalue="True" falsevalue=""
+		   label="Also generate bigWig file from bedGraph"
+		   help="bigWig file can used in subsequent analyses e.g. CEAS" />
 	  </when>
 	  <when value="">
 	    <!-- Display nothing -->
@@ -300,6 +310,12 @@
       <filter>major_command['bdg_options']['bdg'] is True</filter>
       <filter>major_command['major_command_selector'] == 'callpeak'</filter>
     </data>
+    <data name="output_bigwig_file" format="bigwig"
+	  label="${tool.name}: callpeak on ${on_string} (treat pileup: bigWig)">
+      <filter>major_command['major_command_selector'] == 'callpeak'</filter>
+      <filter>major_command['bdg_options']['bdg'] is True</filter>
+      <filter>major_command['bdg_options']['make_bigwig'] is True</filter>
+    </data>
     <!--bdgcmp output-->
     <data name="output_bdgcmp_file" format="bdg"
 	  label="${tool.name}: bdgcmp on ${on_string} (bdg)">