Mercurial > repos > dfornika > ivar_variants_to_vcf

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"planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
author dfornika
date Fri, 05 Jun 2020 05:10:05 +0000
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c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
dfornika
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1 <tool id="ivar_variants_to_vcf" name="iVar Variants to VCF" version="0.1.0">
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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2 <description>Convert iVar tabular variant output to .vcf format</description>
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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3 <requirements />
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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4 <command detect_errors="exit_code"><![CDATA[
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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5 '$__tool_directory__/ivar_variants_to_vcf.py'
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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6 -ma '${min_allele_freq}'
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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7 ${input}
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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8 ${output}
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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9 ]]></command>
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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10 <inputs>
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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11 <param name="input" type="data" format="tabular" />
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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12 <param name="min_allele_freq" type="float" min="0.0" value="0.0" max="1.0" />
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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13 </inputs>
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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14 <outputs>
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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15 <data name="output" label="Variants (VCF)" format="vcf" />
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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16 </outputs>
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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17 <tests>
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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18 <test>
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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19 <param name="input" value="SAMEA6808195-variants.tsv" />
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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20 <param name="min_allele_freq" value="0.5" />
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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21 <output name="output" file="SAMEA6808195-variants.vcf" lines_diff="2"/>
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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22 </test>
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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23 </tests>
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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24 <help><![CDATA[
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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25 ]]></help>
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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26 <citations>
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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27 <citation type="doi">10.5281/zenodo.3872730</citation>
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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28 </citations>
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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29 </tool>