Mercurial > repos > estrain > confindr
changeset 2:d255724fda82 draft
Uploaded
| author | estrain |
|---|---|
| date | Sat, 20 Oct 2018 20:22:02 -0400 |
| parents | 9771170b8e25 |
| children | 2734daba664f |
| files | confindr.xml |
| diffstat | 1 files changed, 7 insertions(+), 36 deletions(-) [+] |
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--- a/confindr.xml Sat Oct 20 18:26:37 2018 -0400 +++ b/confindr.xml Sat Oct 20 20:22:02 2018 -0400 @@ -1,33 +1,17 @@ -<tool id="confindr" name="confindr" label="Detect sequence contamination using rMLST" version="0.1.1"> +<tool id="confindr" name="confindr" label="Detect sequence contamination using rMLST" version="0.1.2"> <requirements> <requirement type="package" version="0.4.3">confindr</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ - mkdir in out db; + mkdir in out; #if $jobtype.select == "fastq_single" - #set outname1 = $jobtype.fastq1.name - ln -s $jobtype.fastq1 in/$outname1; + perl $__tool_directory__/makein.pl in $jobtype.fastq1 $jobtype.fastq1.name; #else if $jobtype.select == "fastq_fr" - #set outname1 = $jobtype.fastq1.name - #set outname2 = $jobtype.fastq2.name - ln -s $jobtype.fastq1 in/$outname1; - ln -s $jobtype.fastq2 in/$outname2; + perl $__tool_directory__/makein.pl in $jobtype.fastq1 $jobtype.fastq1.name $jobtype.fastq2 $jobtype.fastq2.name; #else if $jobtype.select == "fastq_pair" - #set outname1 = $jobtype.coll.name - #set outname2 = $jobtype.coll.name - ln -s $jobtype.coll.forward in/$jobtype.coll.forward.name; - ln -s $jobtype.coll.reverse in/$jobtype.coll.reverse.name; - #end if - #if $database.select=="local" - ln -s $database.db_profiles db/profiles.txt; - ln -s $database.refseq db/refseq.msh; - ln -s $database.rmlst db/rMLST_combined.fasta; - ln -s $database.gene db/gene_allele.txt; + perl $__tool_directory__/makein.pl in $jobtype.coll.forward $jobtype.coll.forward.name $jobtype.coll.reverse $jobtype.coll.reverse.name; #end if confindr.py -i in -o out - #if $database.select=="local" - -d db - #end if #if $options.select=="advanced" #if $options.threads -t $options.threads @@ -47,6 +31,7 @@ #else if $options.select=="basic" -t \${GALAXY_SLOTS:-1} #end if + ; sed 's/\,/\t/g' out/confindr_report.csv > confindr_report.tab; ]]></command> <inputs> <conditional name="jobtype"> @@ -66,20 +51,6 @@ <param name="coll" label="Paired FASTQ" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" collection_type="paired" /> </when> </conditional> - <conditional name="database"> - <param name="select" type="select" label="Database: Local or Download"> - <option value="local">Local</option> - <option value="download">Download</option> - </param> - <when value="local"> - <param name="db_profiles" type="data" format="txt" label="Datebase profiles (profiles.txt)" value=""/> - <param name="refseq" type="data" format="binary" label="RefSeq Mash (refseq.msh)" value=""/> - <param name="rmlst" type="data" format="fasta" label="rMLST FASTA (rMLST_combined.fasta)" value=""/> - <param name="gene" type="data" format="txt" label="Gene Allele File (gene_allele.txt)" value=""/> - </when> - <when value="download"> - </when> - </conditional> <conditional name="options"> <param name="select" type="select" label="Basic or Advanced Settings"> <option value="basic">Basic</option> @@ -103,7 +74,7 @@ </conditional> </inputs> <outputs> - <data name="output" label="${tool.name} on ${on_string}" format="tabular" from_work_dir="out/confindr_report.csv" /> + <data name="output" type="data" label="${tool.name} on ${on_string}" format="tabular" from_work_dir="confindr_report.tab" /> </outputs> <help><![CDATA[ For local databases the confinder database files can be downloaded from figshare in .tar.gz format (https://ndownloader.figshare.com/files/1186426).