Mercurial > repos > jpetteng > ectyper

comparison ecoli_serotyping/ectyper.xml @ 4:e07f3859a242 draft

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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?">