# HG changeset patch
# User dnbenso
# Date 1643343578 0
# Node ID 86aa445e75d6bae76b12fa1b19b418fcb8b3ca32
# Parent  0a33488ca043afe6fd0f454d484a1b2a25c49bff
Uploaded

diff -r 0a33488ca043 -r 86aa445e75d6 masurca_simple.xml
--- a/masurca_simple.xml	Sun Jan 23 22:08:50 2022 +0000
+++ b/masurca_simple.xml	Fri Jan 28 04:19:38 2022 +0000
@@ -10,13 +10,13 @@
         #set $long = 'false'
         #if $nanopore_input.np_input == "Yes":
             #if $pacbio_input.pb_input == "Yes":
-                cat '$nanopore_input.nano' '$pacbio_input.pacbio' > long.fastq.gz &&
+                cat '$nanopore_input.nano' '$pacbio_input.pacbio' > \$_GALAXY_JOB_TMP_DIR/long.fastq.gz &&
             #else:
-                ln -s '$nanopore_input.nano' long.fastq.gz &&
+                ln -s '$nanopore_input.nano' \$_GALAXY_JOB_TMP_DIR/long.fastq.gz &&
             #end if
             #set $long = 'true'
         #elif $pacbio_input.pb_input == "Yes":
-            ln -s '$pacbio_input.pacbio' long.fastq.gz &&
+            ln -s '$pacbio_input.pacbio' \$_GALAXY_JOB_TMP_DIR/long.fastq.gz &&
             #set $long = 'true'
         #end if
         masurca -t \${GALAXY_SLOTS:-8} -i
@@ -28,7 +28,7 @@
             '$illumina_input.fastq_input1','$illumina_input.fastq_input2'
         #end if
         #if $long == "true":
-            -r long.fastq.gz
+            -r \$_GALAXY_JOB_TMP_DIR/long.fastq.gz
         #end if
     ]]></command>
     <inputs>
@@ -92,7 +92,11 @@
             <conditional name="pacbio_input">
                 <param name="pb_input" value="No" />
             </conditional>
-            <output name="superReads" ftype="fasta" />
+            <output name="superReads" ftype="fasta">
+                <assert_contents>
+                    <has_line_matching expression="^TCCGAAAGTGTTAACTT.*"/>
+                </assert_contents>
+            </output>
         </test>
     </tests>
     <help><![CDATA[