Commit 6afc9b98 authored by Philip Mabon's avatar Philip Mabon

Merge branch 'addSnpEff' into 'development'

Add snp eff
parents d09a790d 9191a297
<tool id="filter_unique_basepairs" name="Filter Unique Basepairs" version="1.0.0">
<description>Determines what position in a pseudoalignment file for given number of strains have unique basepairs compared to other strains in the file</description>
<command interpreter="perl">filter_unique_basepairs.pl --tsv $tsv_file --tree $tree_file --clade $clade_output --output $output
#if $valid_flag
--valid false
#end if
#for $f in $vcf_collection.keys# --vcf "$f=$vcf_collection[$f]" #end for#
</command>
<inputs>
<param name="tsv_file" type="data" format="tabular" label="Pseudoalignment-positions file" />
<param name="tree_file" type="data" format="newick" label="Tree file" />
<param name="valid_flag" type="boolean" label="Include non-valid entries" />
<param name="vcf_collection" type="data_collection" label="Filtered VCF" help="" optional="false" collection_type="list" />
<!--repeat name="vcf_files" title="VCF Files">
<param name="vcf" format="vcf" type="data" label="VCF" optional="false"/>
</repeat-->
</inputs>
<outputs>
<data format="tabular" name="output" label="Output.tsv"/>
<data format="newick" name="clade_output" label="Clades.tre"/>
</outputs>
</tool>
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