diff macs2_callpeak.xml @ 1:d202e3d663bb draft

Uploaded

--- a/macs2_callpeak.xml	Thu Jan 16 13:31:17 2014 -0500
+++ b/macs2_callpeak.xml	Thu Jan 16 15:44:43 2014 -0500
@@ -1,12 +1,13 @@
 <tool id="macs2_callpeak" name="Call peaks" version="2.0.10.0">
     <description>from alignment results</description>
-    <requirements>
-        <requirement type="python-module">macs2</requirement>
-        <requirement type="python-module">numpy</requirement>
-        <requirement type="package" version="2.0.10.2">macs2</requirement>
-        <requirement type="package" version="1.7.1">numpy</requirement>
+    <expand macro="requirements">
+        <requirement type="package" version="3.0.1">R_3_0_1</requirement>
         <!-- awk and R is missing -->
-    </requirements>
+    </expand>
+    <expand macro="version_command" />
+    <macros>
+        <import>macs2_macros.xml</import>
+    </macros>
     <command>
         #set $temp_stderr = 'macs2_stderr'
         macs2 callpeak
@@ -21,14 +22,10 @@
         #for $ifile in $input_treatment_file:
             --format='$ifile.ext.upper()'
         #end for
-        
-        #if $effective_genome_size_options.effective_genome_size_options_selector == 'user_defined':
-            --gsize $effective_genome_size_options.gsize
-        #else:
-            --gsize $effective_genome_size_options.effective_genome_size_options_selector
-        #end if
 
-        --bw='$bw'
+        @effective_genome_size@
+
+        --bw='$band_width'
 
         ##advanced options
         #if str( $advanced_options.advanced_options_selector ) == 'on':
@@ -116,26 +113,15 @@
         #end if
 
         cat $temp_stderr 2>&#38;1
-
     </command>
     <inputs>
         <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" />
 
-        <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="user_defined">User defined</option>
-            </param>
-            <when value="user_defined">
-                <param name="gsize" type="integer" size="12" label="Effective genome size" value=""/>
-            </when>
-        </conditional>
+        <expand macro="conditional_effective_genome_size" />
 
-        <param name="bw" type="integer" label="Band width" value="300" help="(--bw)"/>
+        <param name="band_width" type="integer" value="300" label="Band width for picking regions to compute fragment size"
+            help="This value is only used while building the shifting model." />
         <param name="bdg" type="boolean" truevalue="-B" falsevalue="" checked="False" label="Save fragment pileup, control lambda, -log10pvalue/qvalue in bedGraph" help="Files are located in the html report."/>
 
         <conditional name="pq_options">