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comparison freebayes.xml @ 3:72bdc513a54a

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Fixed functional test and added required test files Fixed version number of tool to match supported freebayes version
author Lance Parsons <lparsons@princeton.edu>
date Thu, 22 Dec 2011 14:09:55 -0500
parents c70c9dc2efb7
children 0df882474701
comparison
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2:c70c9dc2efb7 3:72bdc513a54a
159 <outputs> 159 <outputs>
160 <data format="vcf" name="output" metadata_source="bamfile" /> 160 <data format="vcf" name="output" metadata_source="bamfile" />
161 </outputs> 161 </outputs>
162 <tests> 162 <tests>
163 <test> 163 <test>
164 <param name="reference" ftype="fasta" value="mosaik_test_ref.fasta"/> 164 <param name="refGenomeSource" value="history"/>
165 <param name="ownFile" ftype="fasta" value="mosaik_test_ref.fasta"/>
165 <param name="bamfile" ftype="bam" value="freebayes_in.bam"/> 166 <param name="bamfile" ftype="bam" value="freebayes_in.bam"/>
166 <param name="source_select" value="pre_set"/> 167 <param name="source_select" value="pre_set"/>
167 <output name="output" file="freebayes_out.vcf" lines_diff="4"/> 168 <output name="output" file="freebayes_princeton_out.vcf" lines_diff="4"/>
168 </test> 169 </test>
169 </tests> 170 </tests>
170 <help> 171 <help>
171 This tool uses `Freebayes`__ to call SNPS given a reference sequence and a BAM alignment file. 172 This tool uses `Freebayes`__ to call SNPS given a reference sequence and a BAM alignment file.
172 173