Mercurial > repos > estrain > srst2v2
changeset 14:5cfca4d5291a draft default tip
Uploaded
author | estrain |
---|---|
date | Tue, 28 May 2019 06:48:00 -0400 |
parents | a2c25a81368b |
children | |
files | srst2v2.xml |
diffstat | 1 files changed, 3 insertions(+), 4 deletions(-) [+] |
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--- a/srst2v2.xml Tue May 28 06:31:14 2019 -0400 +++ b/srst2v2.xml Tue May 28 06:48:00 2019 -0400 @@ -99,6 +99,8 @@ --other "'-p \${GALAXY_SLOTS:-1}'" #end if + ; cat *results.txt | sed s/sample/${fname}/ > cat_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 #end if @@ -176,16 +178,13 @@ </inputs> <outputs> - <data format="tabular" label="SRST2 Results" name="results" from_work_dir="*.txt"/> + <data format="tabular" label="SRST2 Results" name="results" from_work_dir="*cat_results.txt"/> <data format="tabular" label="SRST2 Allele Scores" name="scores" from_work_dir="*.scores"> <filter>job_type['job'] == "mlst"</filter> </data> <data format="tabular" label="SRST2 Profile Scores" name="pscores" from_work_dir="*.pscores"> <filter> job_type['job'] == "mlst"</filter> </data> - <data format="tabular" label="SRST2 Predicted Alleles" name="alleles" from_work_dir="*results.txt"> - <filter> job_type['job'] == "mlst"</filter> - </data> <data format="tabular" label="SRST2 Gene Scores" name="gscores" from_work_dir="*.scores"> <filter>job_type['job'] == "gene"</filter> </data>