Commit bc949e75 authored by Aaron Petkau's avatar Aaron Petkau

Tests for vcf2pseudoalignment, not quite working yet

parent 4d249478
#Chromosome Position Status Reference v1 v2
ref1 2 valid T A A
ref1 5 filtered-invalid C A N
ref1 7 filtered-coverage G T -
ref2 3 valid A T A
......@@ -52,12 +52,31 @@
<stdio>
<exit_code range="1:" level="fatal" description="Unknown error has occured"/>
</stdio>
<!--tests>
<tests>
<test>
<param name="input" value="fa_gc_content_input.fa"/>
<output name="out_file1" file="fa_gc_content_output.txt"/>
<param name="reference" value="vcf2pseudoalignment.input.1.reference.fasta"/>
<param name="coverage" value="4"/>
<param name="invalid" value="vcf2pseudoalignment.input.1.invalid_positions.tsv"/>
<param name="ambiguous" value="true"/>
<param name="freebayes_collection">
<collection type="list">
<element name="name1" value="vcf2pseudoalignment.input.1.v1.vcf.gz"/>
<element name="name2" value="vcf2pseudoalignment.input.1.v2.vcf.gz"/>
</collection>
</param>
<param name="mpileup_collection">
<collection type="list">
<element name="name1" value="vcf2pseudoalignment.input.1.mpileup.v1.vcf.gz"/>
<element name="name2" value="vcf2pseudoalignment.input.1.mpileup.v2.vcf.gz"/>
</collection>
</param>
<param name="numcpus" value="4"/>
<output name="tabular" file="vcf2pseudoalignment.output.1.positions.tsv"/>
<output name="fasta" file="vcf2pseudoalignment.output.1.expected.fasta"/>
<output name="phylip" file="vcf2pseudoalignment.output.1.expected.phy"/>
</test>
</tests-->
</tests>
<help>
Best metaalignment program ever!
......
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