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"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_margin_cons_medaka commit cdc887baab41af2b386b1ec7239b55d474c0fff5-dirty"
author dfornika
date Tue, 17 Mar 2020 22:05:59 +0000
parents f52f0a2778f8
children
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47eb99e41bfb "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_margin_cons_medaka commit cdc887baab41af2b386b1ec7239b55d474c0fff5-dirty"
dfornika
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1 <tool id="artic_margin_cons_medaka" name="ARTIC margin_cons_medaka" version="0.1.0-1005a47+galaxy0">
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2 <description>Generate consensus fasta file from a reference fasta, bam alignment and VCF file</description>
7df876ad836a "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_margin_cons_medaka commit c866a76470b72bf5abdc2a88e6bf584c2f2f9b02-dirty"
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3 <requirements>
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4 <requirement type="package" version="0.6.8">pyvcf</requirement>
7df876ad836a "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_margin_cons_medaka commit c866a76470b72bf5abdc2a88e6bf584c2f2f9b02-dirty"
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5 <requirement type="package" version="1.76">biopython</requirement>
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6 <requirement type="package" version="1.9">samtools</requirement>
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7 </requirements>
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8 <command detect_errors="exit_code"><![CDATA[
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9 ln -s '${input_alignment}' '${input_alignment.element_identifier}.bam' &&
be08b76fd78b "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_margin_cons_medaka commit cdc887baab41af2b386b1ec7239b55d474c0fff5-dirty"
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10 samtools index '${input_alignment.element_identifier}.bam' &&
be08b76fd78b "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_margin_cons_medaka commit cdc887baab41af2b386b1ec7239b55d474c0fff5-dirty"
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11 ln -s '${input_variants}' '${input_variants.element_identifier}.vcf' &&
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7df876ad836a "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_margin_cons_medaka commit c866a76470b72bf5abdc2a88e6bf584c2f2f9b02-dirty"
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12 python '${__tool_directory__}/margin_cons_medaka.py'
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13 --depth '${minimum_depth}'
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14 --quality '${minimum_quality}'
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15 '${ref_fasta}'
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16 '${input_variants.element_identifier}.vcf'
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17 '${input_alignment.element_identifier}.bam'
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18 > '${consensus_fasta}'
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19 2> '${report}'
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20 ]]></command>
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21 <inputs>
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22 <param name="ref_fasta" type="data" format="fasta" label="Reference Sequence"/>
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23 <param name="input_alignment" type="data" format="bam" label="Input Alignment"/>
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24 <param name="input_variants" type="data" format="vcf" label="Input Variants"/>
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25 <param name="minimum_depth" type="integer" value="5" min="1" max="500" label="Minimum depth to call a variant"/>
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26 <param name="minimum_quality" type="integer" value="0" min="0" max="100" label="Minimum quality to call a variant"/>
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27 </inputs>
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28 <outputs>
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29 <data name="consensus_fasta" format="fasta" label="${tool.name} on ${on_string}: Consensus (.fasta)" />
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30 <data name="report" format="tabular" label="${tool.name} on ${on_string}: Report" />
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31 </outputs>
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32 <tests>
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33 </tests>
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34 <help><![CDATA[
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35 ]]></help>
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36 <citations>
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37 </citations>
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38 </tool>