--- a/masurca.xml	Tue Jan 25 03:45:18 2022 +0000
+++ b/masurca.xml	Fri Jan 28 04:20:09 2022 +0000
@@ -10,14 +10,14 @@
         cp $__tool_directory__/default-masurca-config  config.txt &&
         #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
-            sed -i 's|#NANOPORE=INPUTREADLONG|NANOPORE=long.fastq.gz|' config.txt &&
+            sed -i 's|#NANOPORE=INPUTREADLONG|NANOPORE='\$_GALAXY_JOB_TMP_DIR'/long.fastq.gz|' config.txt &&
         #elif $pacbio_input.pb_input == "Yes":
-            ln -s '$pacbio_input.pacbio' long.fastq.gz &&
-            sed -i 's|#PACBIO=INPUTREADLONG|PACBIO=long.fastq.gz|' config.txt &&
+            ln -s '$pacbio_input.pacbio' \$_GALAXY_JOB_TMP_DIR/long.fastq.gz &&
+            sed -i 's|#PACBIO=INPUTREADLONG|PACBIO='\$_GALAXY_JOB_TMP_DIR'/long.fastq.gz|' config.txt &&
         #end if
         #if str( $illumina_input.input_type ) == "single"
             ln -s '$illumina_input.fastq_input1' ill_1.fastq.gz &&
@@ -119,6 +119,9 @@
         <data name="flye_assembly" format="fasta" from_work_dir="flye.mr.*/assembly.fasta" label="${tool.name} on ${on_string}: flye_assembly">
             <filter>flye == True</filter>
         </data>
+        <data name="flye_log" format="txt" from_work_dir="flye.mr.*/flye.log" label="${tool.name} on ${on_string}: flye_log">
+            <filter>flye == True</filter>
+        </data>
     </outputs>
     <tests>
         <test>
@@ -171,14 +174,14 @@
 
 **Input data**
 
-The following types of data are supported::
+The following types of data are supported:
 
   * Illumina paired end (or single end) reads -- MANDATORY. The mean and stdev parameters are the library insert average length and standard deviation. If the standard deviation is not known, set it to approximately 15% of the mean.If the second (reverse) read set is not available, do not specify it and just specify the forward reads. Files must be in fastq format and can be gzipped.
   * PacBio/MinION data are supported. Note that you have to have 50x + coverage in Illumina Paired End reads to use PacBio of Oxford Nanopore MinION data. Supply PacBio or MinION reads in a single fasta or fastq file (can be gzipped).
 
 **Parameters**
 
-The following parameter is mandatory::
+The following parameter is mandatory:
 
   * jellyfish hash size, set this to about 10x the genome size.