# HG changeset patch
# User p.lucas
# Date 1557392732 14400
# Node ID d30476d83afead2ae0ab9f35366668871f01ecbb
# Parent  fbac2ea88cf384fcbd3d36df4c72b0509aa13b15
Fix output error

diff -r fbac2ea88cf3 -r d30476d83afe SsuisSerotyping_pipeline.xml
--- a/SsuisSerotyping_pipeline.xml	Thu May 09 04:57:01 2019 -0400
+++ b/SsuisSerotyping_pipeline.xml	Thu May 09 05:05:32 2019 -0400
@@ -68,14 +68,14 @@
         </conditional>
     </inputs>
     <outputs>
-        <data name="output1" format="txt" label="${tool.name} on ${on_string}: Results_FinalResults.txt" />
-        <data name="output2" format="txt" label="${tool.name} on ${on_string}: Results_MLSTResults.txt" />
-        <data name="output3" format="txt" label="${tool.name} on ${on_string}: Results_recN__fullgenes__recN_full__results.txt" />
-        <data name="output4" format="txt" label="${tool.name} on ${on_string}: Results_speciesConfirmation.txt" />
-        <data name="output5" format="txt" label="${tool.name} on ${on_string}: Results_FinalSerotypingResults.txt" />
-        <data name="output6" format="txt" label="${tool.name} on ${on_string}: Results_InitialCapsuleResults.txt" />
-        <data name="output7" format="txt" label="${tool.name} on ${on_string}: Results_VirulenceFactors__fullgenes__Virulence__results.txt" />
-        <data name="output8" format="txt" label="${tool.name} on ${on_string}: Results_VirulenceFactorResults.txt" />
+        <data name="output1" format="txt" label="${tool.name} on ${on_string}: Results_FinalResults.txt" from_work_dir="Results_FinalResults.txt"/>
+        <data name="output2" format="txt" label="${tool.name} on ${on_string}: Results_MLSTResults.txt" from_work_dir="Results_MLSTResults.txt"/>
+        <data name="output3" format="txt" label="${tool.name} on ${on_string}: Results_recN__fullgenes__recN_full__results.txt" from_work_dir="Results_recN__fullgenes__recN_full__results.txt" />
+        <data name="output4" format="txt" label="${tool.name} on ${on_string}: Results_speciesConfirmation.txt" from_work_dir="Results_speciesConfirmation.txt" />
+        <data name="output5" format="txt" label="${tool.name} on ${on_string}: Results_FinalSerotypingResults.txt" from_work_dir="Results_FinalSerotypingResults.txt" />
+        <data name="output6" format="txt" label="${tool.name} on ${on_string}: Results_InitialCapsuleResults.txt" from_work_dir="Results_InitialCapsuleResults.txt" />
+        <data name="output7" format="txt" label="${tool.name} on ${on_string}: Results_VirulenceFactors__fullgenes__Virulence__results.txt" from_work_dir="Results_VirulenceFactors__fullgenes__Virulence__results.txt" />
+        <data name="output8" format="txt" label="${tool.name} on ${on_string}: Results_VirulenceFactorResults.txt" from_work_dir="Results_VirulenceFactorResults.txt" />
     </outputs>
     <tests>
         <test>