Commit 828180a1 authored by JCabral's avatar JCabral

adding test files and fixing up the command call for snp_matrix

parent 23d3b4ad
......@@ -25,6 +25,8 @@
</stdio>
<tests>
<test>
<param name="tabfile" value="filter-stats-in.tsv" />
<output name="out" file="filter-stats-out.tabular" />
</test>
</tests>
......
#Chromosome Position Status Reference query B
chr 5 valid A T A
chr 10 filtered-coverage A G -
Chromosome Genomes
chr ALL B query
Total number of N's and -'s 1 1 0
Total percent of N's and -'s 50.00 50.00 0.00
>A
CCCGCTCGCCACGCTTTGGCCATAGTGCTGCCTTCTACGATGTGTAAACCGTGCAACTTAATGCCATCGGTGCCTACCTT
CAGTACTTGCTGTAACGTGGTGAGGTTTTCAGTGCGCTCTTCACCGGGTAACCCAACAATCAAGTGAGTACACACTTTGA
TACCTAACGCTCTAGCTTTGGCAGTGATCTCTGCGTAGCAGGCAAAATCGTGCCCGCGGTTAATGCGTTTTAAAGTCTGG
>B
CCCGCTCGCCACGCTTTGGCCATAGTGCTGCCTTCTACGATGTGTAAACCGTGCAACTTAATGCCATCGGTGCCTACCTT
CAGTACTTGCTGTAACGTGGTGAGGTTTTCAGTGCGCTCTTCACCGGGTAACCCAACAATCAAGTGAGTACACACTTTGA
TACCTAACGCTCTAGCTTTGGCAGTGATCTCTGCGTAGCAGGCAAAATCGTGCCCGCGGTTAATGCGTTTTAAAGTCTGG
......@@ -6,7 +6,7 @@
</requirements>
<command interpreter="perl">
/\$SCRIPTS/snp_matrix.pl $phylip
/\$VCF2PSEUDO/snp_matrix.pl $phylip
-o $csv
</command>
<inputs>
......@@ -19,8 +19,8 @@
</stdio>
<tests>
<test>
<param name="phylip" value="pseudoalign-3.phy"/>
<output name="csv" file="pseudoalign-3.phy.out"/>
<param name="phylip" value="pseudoalign-13.phy"/>
<output name="csv" file="pseudoalign-13.phy.out"/>
</test>
</tests>
......
5 3
'a' AAY
'b' AAA
'c' AAA
'd' TAA
'e' NGG
strain a e b c d
a 0 1 0 0 0
e 1 0 1 1 1
b 0 1 0 0 0
c 0 1 0 0 0
d 0 1 0 0 0
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