diff macs2_predictd.xml @ 5:beb902da6e5f draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b

--- a/macs2_predictd.xml	Mon Feb 06 02:30:37 2017 -0500
+++ b/macs2_predictd.xml	Sat Apr 08 08:28:57 2017 -0400
@@ -3,40 +3,37 @@
     <macros>
         <import>macs2_macros.xml</import>
     </macros>
-    <expand macro="requirements">
-        <requirement type="package" version="3.1.2">R</requirement>
-        <requirement type="package" version="4.1.0">gnu_awk</requirement>
-    </expand>
+    <expand macro="requirements"/>
     <expand macro="stdio" />
     <expand macro="version_command" />
     <command>
+        <![CDATA[
         macs2 predictd
-            -i ${ ' '.join( map( lambda x:'"%s"' % ( x ), $infiles ) ) }
-            @tag_size@
-            @effective_genome_size@
-            --bw "${ band_width }"
-            --mfold "${ mfoldlo }" "${ mfoldhi }"
 
-            ## remove the timepoint and strip the output
-            2>&amp;1 | awk -F: '{print $4}' | awk '{$1=$1}1'
+        -i ${ ' '.join(["'%s'" % $x for $x in $infiles ]) }
+        @tag_size@
+        @effective_genome_size@
+        --bw '${ band_width }'
+        @mfold_command@
 
-            &gt; "${ outfile }"
+        ## remove the timepoint and strip the output
+        2>&1 | awk -F: '{print $4}' | awk '{$1=$1}1'
 
-        &amp;&amp;
+        > '${ outfile }'
+
+        &&
 
         Rscript predictd
+        ]]>
     </command>
     <inputs>
-        <param name="infiles" type="data" format="bam,sam,bed" multiple="True" label="ChIP-seq alignment file" help="If multiple files are given, then they will all be read and combined. Note that pair-end data is not supposed to work with this command. (-i)" />
+        <param name="infiles" type="data" format="bam,sam,bed" multiple="True"
+               label="ChIP-seq alignment file"
+               help="If multiple files are given, then they will all be read and combined. Note that pair-end data is not supposed to work with this command. (-i)" />
         <expand macro="conditional_effective_genome_size" />
         <expand macro="tag_size" />
         <expand macro="band_width" />
-
-        <param name="mfoldlo" type="integer" label="Fold-enrichment lower limit" value="5"
-            help="Select the regions with MFOLD high-confidence enrichment ratio against background to build model (--mfold)"/>
-        <param name="mfoldhi" type="integer" label="Fold-enrichment upper-limit" value="50"
-            help="Select the regions with MFOLD high-confidence enrichment ratio against background to build model (--mfold)"/>
-
+        <expand macro="mfold_options" />
     </inputs>
 
     <outputs>
@@ -48,24 +45,25 @@
             <param name="infiles" value="Control_200K.bed,ChIP_200K.bed" ftype="bed" />
             <param name="effective_genome_size_options_selector" value="user_defined" />
             <param name="gsize" value="3300000000" />
-            <param name="tsize" value="-1.0"/>
+            <param name="tsize" value=""/>
             <param name="band_width" value="300"/>
-            <param name="mfoldlo" value="5"/>
-            <param name="mfoldhi" value="50"/>
+            <param name="lower" value="5"/>
+            <param name="upper" value="50"/>
             <output name="outfile" file="predictd_on_ChIP_200K_and_Control_200K.txt"/>
             <output name="outfile_image" file="predictd_on_ChIP_200K_and_Control_200K.pdf" compare="sim_size"/>
         </test>
     </tests>
     <help>
+<![CDATA[
 **What it does**
 
-predictd from macs2
-
+This is **predictd** utility from the MACS2_ Package. It predicts the *d* value or fragment size from alignment results.
 
-Note that pair-end data is not supposed to work with this command.
-
+.. _MACS2: https://github.com/taoliu/MACS
 
 @citation@
+]]>
+
     </help>
     <expand macro="citations" />
 </tool>