Mercurial > repos > jpetteng > ectyper
comparison ecoli_serotyping/ectyper.xml @ 4:e07f3859a242 draft
Updated xml file to require ectyper itself as it should be available via conda.
| author | jpetteng |
|---|---|
| date | Fri, 05 Jan 2018 10:59:51 -0500 |
| parents | 2b5e95d690c2 |
| children | a202cc394af8 |
comparison
equal
deleted
inserted
replaced
| 3:19b25805275f | 4:e07f3859a242 |
|---|---|
| 1 <tool id="ectyper" name="ectyper" version="2.0"> | 1 <tool id="ectyper" name="ectyper" version="2.0"> |
| 2 <requirements> | 2 <requirements> |
| 3 <requirement type="package" version="3.6.3">python</requirement> | 3 <requirement type="package" version="3.6.3">python</requirement> |
| 4 <requirement type="package">ectyper</requirement> | |
| 4 <requirement type="package">biopython</requirement> | 5 <requirement type="package">biopython</requirement> |
| 5 <requirement type="package">blast</requirement> | 6 <requirement type="package">blast</requirement> |
| 6 <requirement type="package">samtools</requirement> | 7 <requirement type="package">samtools</requirement> |
| 7 <requirement type="package">bcftools</requirement> | 8 <requirement type="package">bcftools</requirement> |
| 8 <requirement type="package">bowtie</requirement> | 9 <requirement type="package">bowtie</requirement> |
| 30 #else if $jobtype.select == "pe" | 31 #else if $jobtype.select == "pe" |
| 31 -m 2 | 32 -m 2 |
| 32 -i sample_1.fastq sample_2.fastq | 33 -i sample_1.fastq sample_2.fastq |
| 33 #end if | 34 #end if |
| 34 -b $maptype.select; | 35 -b $maptype.select; |
| 35 cat SeqSero_result*/Seqsero_result.txt > results.txt; | 36 cat ectyper_result*/ectyper_result.txt > results.txt; |
| 36 | 37 |
| 37 ]]></command> | 38 ]]></command> |
| 38 <inputs> | 39 <inputs> |
| 39 <conditional name="jobtype"> | 40 <conditional name="jobtype"> |
| 40 <param name="select" type="select" label="Assembly or FASTQ Reads?"> | 41 <param name="select" type="select" label="Assembly or FASTQ Reads?"> |