Mercurial > repos > dnbenso > masurca_simple
changeset 1:86aa445e75d6 draft default tip
Uploaded
| author | dnbenso |
|---|---|
| date | Fri, 28 Jan 2022 04:19:38 +0000 |
| parents | 0a33488ca043 |
| children | |
| files | masurca_simple.xml |
| diffstat | 1 files changed, 9 insertions(+), 5 deletions(-) [+] |
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--- 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[