Mercurial > repos > estrain > srst2v2
changeset 10:a3e5181b3b81 draft
Uploaded
| author | estrain |
|---|---|
| date | Mon, 27 May 2019 20:05:33 -0400 |
| parents | c86195daec93 |
| children | 2bd184a17d85 |
| files | srst2v2.xml |
| diffstat | 1 files changed, 5 insertions(+), 2 deletions(-) [+] |
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--- a/srst2v2.xml Mon May 27 19:54:31 2019 -0400 +++ b/srst2v2.xml Mon May 27 20:05:33 2019 -0400 @@ -15,6 +15,7 @@ ln -s $paired_conditional.fastq1 sample_1.fastq; ln -s $paired_conditional.fastq2 sample_2.fastq; #end if + #set fname=$paired_conditional.fastq1.name #else if $paired_conditional.sPaired == "paired_coll" #if $paired_conditional.coll.forward.is_of_type("fastq.gz") zcat $paired_conditional.coll.forward > sample_1.fastq; @@ -26,6 +27,7 @@ ln -s $paired_conditional.coll.forward sample_1.fastq; ln -s $paired_conditional.coll.reverse sample_2.fastq; #end if + #set fname=$paired_conditional.coll.forward.name #else if $paired_conditional.sPaired == "single" #if $paired_conditional.fastq1.is_of_type("fastq.gz") zcat $paired_conditional.fastq1 > sample_1.fastq; @@ -34,6 +36,7 @@ #else ln -s $paired_conditional.fastq1 sample_1.fastq; #end if + #set fname=$paired_conditional.fastq1.name #end if srst2 @@ -96,10 +99,10 @@ --other "'-p \${GALAXY_SLOTS:-1}'" #end if - ; cat *results.txt | sed /sample/${name}/ > results.txt + ; cat *results.txt | sed /sample/${fname}/ > results.txt #if $job_type.job == "mlst" - ; python $__tool_directory__/scoreProfiles.py --mlst_definitions $job_type.mlst_definitions --profile_cov $job_type.profile_cov --profile_max_mismatch $job_type.profile_max_mismatch --output srst2.pscores ; cat srst2.pscores | sed s/sample/${name}/ > srst2.pscores + ; python $__tool_directory__/scoreProfiles.py --mlst_definitions $job_type.mlst_definitions --profile_cov $job_type.profile_cov --profile_max_mismatch $job_type.profile_max_mismatch --output srst2.pscores ; cat srst2.pscores | sed s/sample/${fname}/ > srst2.pscores #end if ]]></command>