diff csaw.xml @ 2:ed929b85b051 draft

Uploaded

--- a/csaw.xml	Mon Dec 11 10:03:46 2017 -0500
+++ b/csaw.xml	Mon Dec 18 10:58:39 2017 -0500
@@ -1,22 +1,43 @@
 <tool id="CSAW" name="CSAW" version="0.1.0">
+  
+  <requirements>
+    <requirement type="package" version="1.12.0">bioconductor-csaw</requirement>
+    <requirement type="package" version="1.20.0">r-getopt</requirement>
+    <requirement type="package" version="1.10.4">r-data.table</requirement>
+    <requirement type="package" version="1.2.0">r-stringr</requirement>
+    <requirement type="package" version="1.12.0">bioconductor-biocparallel</requirement>
+<requirement type="package" version="1.8.0">bioconductor-summarizedexperiment</requirement>
+<requirement type="package" version="2.38.0">bioconductor-biobase</requirement>
+<requirement type="package" version="1.30.0">bioconductor-genomicranges</requirement>
+<requirement type="package" version="1.14.0">bioconductor-genomeinfodb</requirement>
+<requirement type="package" version="2.12.0">bioconductor-iranges</requirement>
+<requirement type="package" version="0.16.0">bioconductor-s4vectors</requirement>
+<requirement type="package" version="0.24.0">bioconductor-biocgenerics</requirement>
+  </requirements>
+  
   <command detect_errors="exit_code"><![CDATA[
 Rscript $__tool_directory__/csaw.R $inputs $output
     ]]></command>
+  
   <inputs>
     <param type="data" name="inputs" format="bam" multiple="True" />
   </inputs>
+
   <outputs>
     <data name="output" format="txt" />
   </outputs>
+  
   <tests>
     <test>
       <param name="inputs" value="ENCFF027UTM.bam,ENCFF027UTM_1.bam"/>
       <output name="output" file="csaw_results"/>
     </test>
   </tests>
+  
   <help><![CDATA[
         Write the tool help section here.
     ]]></help>
+  
   <citations>
     <citation type="bibtex">
       @misc{github01_mismatch_removal,