Mercurial > repos > jpetteng > ectyper0_1
changeset 5:ec569c3c11e2 draft
Uploaded
| author | jpetteng |
|---|---|
| date | Wed, 10 Jan 2018 11:50:22 -0500 |
| parents | 8ae7b0f14317 |
| children | b35d91bc0ead |
| files | ectyper.xml |
| diffstat | 1 files changed, 6 insertions(+), 14 deletions(-) [+] |
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--- a/ectyper.xml Tue Jan 09 16:13:32 2018 -0500 +++ b/ectyper.xml Wed Jan 10 11:50:22 2018 -0500 @@ -12,7 +12,7 @@ ln -s $jobtype.fastq2 sample_2.fastq; #end if - python $__tool_directory__/bin/ectyper + python $__tool_directory__/bin/ectyper #if $jobtype.select == "asm" -i sample.fasta #else if $jobtype.select == "se" @@ -20,15 +20,9 @@ #else if $jobtype.select == "pe" -i sample_1.fastq sample_2.fastq #end if - - #if $options.percent_identity - -d $options.percent_identity - #end if - - #if $options.percent_length - -l $options.percent_length - #end if - + -d $percent_identity + -l $percent_length + cat ectyper_result*/ectyper_result.txt > results.txt; ]]></command> @@ -51,10 +45,8 @@ </when> </conditional> - <conditional name="options"> - <param name="percent_identity" type="integer" format="txt" label="Percent identity required for an allele match [default 90]" value="90" /> - <param name="percent_length" type="integer" format="txt" label="Percent length required for an allele match [default 50]" value="50" /> - </conditional> + <param name="percent_identity" type="integer" label="Percent identity required for an allele match [default 90]" value="90" /> + <param name="percent_length" type="integer" label="Percent length required for an allele match [default 50]" value="50" /> </inputs> <outputs>