Mercurial > repos > estrain > srst2v2
changeset 9:c86195daec93 draft
Uploaded
| author | estrain |
|---|---|
| date | Mon, 27 May 2019 19:54:31 -0400 |
| parents | 3a0554ef7cc2 |
| children | a3e5181b3b81 |
| files | srst2v2.xml |
| diffstat | 1 files changed, 7 insertions(+), 5 deletions(-) [+] |
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--- a/srst2v2.xml Sun May 19 10:00:38 2019 -0400 +++ b/srst2v2.xml Mon May 27 19:54:31 2019 -0400 @@ -96,8 +96,10 @@ --other "'-p \${GALAXY_SLOTS:-1}'" #end if + ; cat *results.txt | sed /sample/${name}/ > 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 + ; 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 #end if ]]></command> @@ -109,14 +111,14 @@ <option value="paired_coll">Paired FASTQ Collection</option> </param> <when value="single"> - <param name="fastq1" type="data" format="fastq,fastqsanger" label="FASTQ file" help="FASTQ" /> + <param name="fastq1" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" label="FASTQ file" help="FASTQ" /> </when> <when value="paired"> - <param name="fastq1" type="data" format="fastq,fastqsanger" label="Forward FASTQ file" help="FASTQ" /> - <param name="fastq2" type="data" format="fastq,fastqsanger" label="Reverse FASTQ file" help="FASTQ" /> + <param name="fastq1" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" label="Forward FASTQ file" help="FASTQ" /> + <param name="fastq2" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" label="Reverse FASTQ file" help="FASTQ" /> </when> <when value="paired_coll"> - <param name="coll" label="Paired FASTQ" type="data_collection" format="fastq,fastqsanger" collection_type="paired" /> + <param name="coll" label="Paired FASTQ" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" collection_type="paired" /> </when> </conditional>