Mercurial > repos > nml > quasitools
diff callntvar.xml @ 7:dcd43b402eb3 draft
planemo upload for repository https://github.com/phac-nml/quasitools commit ce3f1b19e7e110ff47365c672bc6fa17cce0a314
author | nml |
---|---|
date | Fri, 23 Nov 2018 15:43:16 -0500 |
parents | b69e898b8109 |
children | 9def47f3c1e4 |
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--- a/callntvar.xml Fri Oct 12 09:16:03 2018 -0400 +++ b/callntvar.xml Fri Nov 23 15:43:16 2018 -0500 @@ -1,7 +1,7 @@ -<tool id="callntvar" name="Nucleotide Variants" version="0.4.2"> +<tool id="callntvar" name="Nucleotide Variants" version="0.5.1"> <description>Identifies nucleotide variants</description> <requirements> - <requirement type="package" version="0.4.2">quasitools</requirement> + <requirement type="package" version="0.5.1">quasitools</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ @@ -18,7 +18,7 @@ <inputs> <param name="input_bam" type="data" format="bam" optional="false" label="Bam file" /> <param name="ref_file" type="data" format="fasta" optional="false" label="Reference file" /> - <param name="error_rate" type="float" optional="true" min="0" max="1" value="0.01" label="Error rate" help="Estimated sequencing error rate. Defaults to 0.01."/> + <param name="error_rate" type="float" optional="true" min="0" max="1" value="0.0021" label="Error rate" help="Estimated sequencing error rate. Defaults to 0.0021."/> </inputs> <outputs> <data format="vcf" name="output" from_work_dir="output.vcf" /> @@ -30,7 +30,9 @@ <output name="output" > <assert_contents> <has_text_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO"/> - <has_text_matching expression="hxb2_pol\s606\s.\sa\sc\s69\sPASS\sDP=157;AC=12;AF=0.0764" /> + <has_text_matching expression="hxb2_pol\s606\s.\sa\sc\s100\sPASS\sDP=157;AC=12;AF=0.0764" /> + <has_text_matching expression="hxb2_pol\s812\s.\sg\sa\s58\sPASS\sDP=634;AC=10;AF=0.0158" /> + <has_text_matching expression="hxb2_pol\s2278\s.\sc\st\s54\sPASS\sDP=557;AC=9;AF=0.0162" /> </assert_contents> </output> </test> @@ -44,5 +46,13 @@ ]]></help> <citations> + <citation type="bibtex"> + @misc{GitHubquasitoolscallntvar, + title = {quasitools callntvar}, + publisher = {phac-nml}, + journal = {GitHub repository}, + url = {https://github.com/phac-nml/quasitools}, + } + </citation> </citations> </tool>