Mercurial > repos > dfornika > uvp

diff uvp.xml @ 3:845a20f1fa5e draft

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"planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/uvp commit 2482e856a9414983c82d94c9f59ff8985574895e-dirty"
author dfornika
date Fri, 11 Oct 2019 19:50:07 -0400
parents 76eefba8e661
children d04a4e171098
line wrap: on
line diff
--- a/uvp.xml	Fri Oct 11 18:28:50 2019 -0400
+++ b/uvp.xml	Fri Oct 11 19:50:07 2019 -0400
@@ -9,19 +9,28 @@
     <version_command>uvp --version</version_command>
     <command detect_errors="exit_code">
         <![CDATA[
+        #if $single_paired.single_paired_selector == 'yes'
+            ln -s '${single_paired.forward_input}' 'R1.fastq.gz' &&
+            ln -s '${single_paired.reverse_input}' 'R2.fastq.gz' &&
+        #elif $single_paired.single_paired_selector == "collection":
+            ln -s '${single_paired.input_pair.forward}' 'R1.fastq.gz' &&
+            ln -s '${single_paired.input_pair.reverse}' 'R2.fastq.gz' &&
+        #else:
+            ln -s '${single_paired.input_sequences}' 'R1.fastq.gz'
+        #endif
         uvp
             --threads \${GALAXY_SLOTS:-1}
             #if $single_paired.single_paired_selector == 'yes'
                 -n '${single_paired.forward_input.element_identifier}'
-                -q '${single_paired.forward_input}' 
-                -q2 '${single_paired.reverse_input}'
+                -q 'R1.fastq.gz'
+                -q2 'R2.fastq.gz'
             #elif $single_paired.single_paired_selector == "collection":
                 -n '${single_paired.input_pair.forward.element_identifier}'
-                -q '${single_paired.input_pair.forward}'
-                -q2 '${single_paired.input_pair.reverse}'
+                -q 'R1.fastq.gz'
+                -q2 'R2.fastq.gz'
             #else:
                 -n '${single_paired.input_sequences.element_identifier}'
-                -q '${single_paired.input_sequences}'
+                -q 'R1.fastq.gz'
             #end if
             --krakendb '${kraken_database.fields.path}'
             -r '${reference}'