Mercurial > repos > jpetteng > ectyper0_1
changeset 18:b4fe4085b240 draft
Uploaded
author | jpetteng |
---|---|
date | Wed, 10 Jan 2018 13:33:23 -0500 |
parents | 80b1401a70ef |
children | 445fac787b2a |
files | ectyper.xml |
diffstat | 1 files changed, 12 insertions(+), 4 deletions(-) [+] |
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--- a/ectyper.xml Wed Jan 10 13:22:00 2018 -0500 +++ b/ectyper.xml Wed Jan 10 13:33:23 2018 -0500 @@ -3,14 +3,22 @@ <requirement type="package" version="0.1">ectyper</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ + #if $jobtype.select == "asm" + ln -s $jobtype.draft sample.fasta; + #else if $jobtype.select == "se" + ln -s $jobtype.fastq1 sample_1.fastq; + #else if $jobtype.select == "pe" + ln -s $jobtype.fastq1 sample_1.fastq; + ln -s $jobtype.fastq2 sample_2.fastq; + #end if $__tool_directory__/ectyper #if $jobtype.select == "asm" - -i $draft + -i sample.fasta #else if $jobtype.select == "se" - -i $fastq1 + -i sample_1.fastq #else if $jobtype.select == "pe" - -i $fastq1 $fastq2 + -i sample_1.fastq sample_2.fastq #end if -d $percent_identity -l $percent_length @@ -41,7 +49,7 @@ </inputs> <outputs> - <data format="csv" label="ectyper Results" name="#{tool_input_name}.ectperResults" from_work_dir="*.csv"/> + <data format="csv" label="${input1.name}" name="${input1.name}.ectperResults" from_work_dir="*.csv"/> </outputs> <help><![CDATA[