Mercurial > repos > jdv > nanopolish

comparison nanopolish_variants.xml @ 9:f1141f6a2d65 draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0ace87b59137f1ed770db97fbb33036e16205edf
author jdv
date Mon, 12 Feb 2018 23:15:26 -0500
parents 32cb27adeb34
children c00a942cfc0b
comparison
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8:b437c0a7ca04 9:f1141f6a2d65
102 <param name="input_bam" value="called.bam" ftype="bam" /> 102 <param name="input_bam" value="called.bam" ftype="bam" />
103 <param name="input_ref" value="ref.fa" ftype="fasta" /> 103 <param name="input_ref" value="ref.fa" ftype="fasta" />
104 <param name="fix_homopolymers" value="True"/> 104 <param name="fix_homopolymers" value="True"/>
105 <output name="out_consensus" file="consensus.hp.fa" compare="diff" /> 105 <output name="out_consensus" file="consensus.hp.fa" compare="diff" />
106 <output name="out_variants" file="consensus.hp.vcf" compare="diff" /> 106 <output name="out_variants" file="consensus.hp.vcf" compare="diff" />
107 <assert_command>
108 <has_text text="--fix-homopolymers" />
109 <not_has_text text="--calculate-all-support" />
110 </assert_command>
107 </test> 111 </test>
108 <!-- test pre-calculated index input --> 112 <!-- test pre-calculated index input, fix-homopolymers command -->
109 <test> 113 <test>
110 <param name="input_reads" value="called.fa" ftype="fasta" /> 114 <param name="input_reads" value="called.fa" ftype="fasta" />
111 <param name="input_fast5" value="test.fast5.tar.gz" ftype="fast5.tar.gz" /> 115 <param name="input_fast5" value="test.fast5.tar.gz" ftype="fast5.tar.gz" />
112 <param name="input_bam" value="called.bam" ftype="bam" /> 116 <param name="input_bam" value="called.bam" ftype="bam" />
113 <param name="input_ref" value="ref.fa" ftype="fasta" /> 117 <param name="input_ref" value="ref.fa" ftype="fasta" />
115 <param name="fix_homopolymers" value="True"/> 119 <param name="fix_homopolymers" value="True"/>
116 <output name="out_consensus" file="consensus.hp.fa" compare="diff" /> 120 <output name="out_consensus" file="consensus.hp.fa" compare="diff" />
117 <output name="out_variants" file="consensus.hp.vcf" compare="diff" /> 121 <output name="out_variants" file="consensus.hp.vcf" compare="diff" />
118 <assert_command> 122 <assert_command>
119 <has_text text="--index" /> 123 <has_text text="--index" />
120 <has_text text="--fix-homopolymers" /> 124 </assert_command>
125 </test>
126 <!-- test calculate-all-support command -->
127 <test>
128 <param name="input_reads" value="called.fa" ftype="fasta" />
129 <param name="input_fast5" value="test.fast5.tar.gz" ftype="fast5.tar.gz" />
130 <param name="input_bam" value="called.bam" ftype="bam" />
131 <param name="input_ref" value="ref.fa" ftype="fasta" />
132 <param name="input_index" value="index.tar" ftype="tar" />
133 <param name="calculate_all_support" value="True"/>
134 <assert_command>
135 <not_has_text text="--fix-homopolymers" />
136 <has_text text="--calculate-all-support" />
121 </assert_command> 137 </assert_command>
122 </test> 138 </test>
123 </tests> 139 </tests>
124 140
125 <!-- ***************************************************************** --> 141 <!-- ***************************************************************** -->