diff muse_call.xml @ 5:723755ec06be draft

Uploaded

--- a/muse_call.xml	Thu Oct 25 04:45:32 2018 -0400
+++ b/muse_call.xml	Fri Sep 20 08:22:09 2019 -0400
@@ -3,6 +3,7 @@
   <requirements>
         <requirement type="package" version="1.0.rc" >muse</requirement>
         <requirement type="package" version="1.7">samtools</requirement>
+        <requirement type="package" version="1.0" >openssl</requirement>
   </requirements>
   <macros>
     <import>muse_macros.xml</import>
@@ -10,7 +11,7 @@
   <command> <![CDATA[
     ##creation of the bam indexes and execution of the MuSE call command with all the advanced options
   
-   	samtools index $input2 2> log && samtools index $input3 2>log && 
+   	samtools index $input2 2> $log && samtools index $input3 2> $log && 
         
         MuSE call -O variant_call
          #if $reference_source.reference_source_selector == "history"
@@ -27,7 +28,9 @@
     #end if
     #if $positions
       -l $positions
-    #end if]]>
+    #end if
+    2> $log  
+    ]]>
   </command>
   <inputs>
     <expand macro="reference_loc"/>
@@ -38,6 +41,7 @@
   </inputs>
   <outputs>
     <data format="txt" name="output" from_work_dir="variant_call.MuSE.txt" label="${tool.name} on ${on_string}"/>
+    <data format="txt" name="log" label="${tool.name} on ${on_string} log"/>
   </outputs>
   <tests>
       <test>