Mercurial > repos > dfornika > artic_align_trim
annotate artic_align_trim.xml @ 3:ba460f482c35 draft
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
author | dfornika |
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date | Tue, 10 Mar 2020 22:35:31 +0000 |
parents | 8bcfa2bb56cd |
children | f09154638542 |
rev | line source |
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0
defebd1f95b9
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
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1 <tool id="artic_align_trim" name="ARTIC align_trim" version="0.1.0+galaxy0"> |
defebd1f95b9
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
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2 <description>Trim aligned reads based on a set of primer loci</description> |
defebd1f95b9
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
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3 <requirements> |
defebd1f95b9
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
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4 <requirement type="package" version="0.15.3">pysam</requirement> |
defebd1f95b9
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
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5 <requirement type="package" version="1.9">samtools</requirement> |
defebd1f95b9
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
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6 </requirements> |
defebd1f95b9
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
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7 <command detect_errors="exit_code"><![CDATA[ |
defebd1f95b9
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
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8 '${__tool_directory__}/align_trim.py' |
defebd1f95b9
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
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9 '${primer_scheme_bedfile}' |
defebd1f95b9
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
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10 --start |
defebd1f95b9
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
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11 --report '${start_trim_report}' |
defebd1f95b9
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
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12 < '${input_alignment}' |
defebd1f95b9
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
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13 2> '${start_trim_err}' | |
defebd1f95b9
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
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14 samtools view -bS - | |
defebd1f95b9
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
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15 samtools sort - -o '${trimmed_sorted_alignment}' |
defebd1f95b9
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
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16 ]]></command> |
defebd1f95b9
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
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17 <inputs> |
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ba460f482c35
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
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18 <param name="input_alignment" type="data" format="bam" label="Input Alignment"/> |
ba460f482c35
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
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19 <param name="primer_scheme_bedfile" type="select" format="bed" label="Primer Scheme"> |
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defebd1f95b9
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
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20 <options from_data_table="primer_scheme_bedfiles"> |
defebd1f95b9
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
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21 <validator type="no_options" message="No primer scheme .bed files are available" /> |
defebd1f95b9
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
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22 </options> |
defebd1f95b9
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
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23 </param> |
defebd1f95b9
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
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24 </inputs> |
defebd1f95b9
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
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25 <outputs> |
defebd1f95b9
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
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26 <data name="start_trim_report" format="txt" label="Alignment Report" /> |
defebd1f95b9
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
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27 <data name="start_trim_err" format="txt" label="Alignment Error Report" /> |
defebd1f95b9
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
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28 <data name="trimmed_sorted_alignment" format="bam" /> |
defebd1f95b9
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
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29 </outputs> |
defebd1f95b9
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
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30 <tests> |
defebd1f95b9
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
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31 </tests> |
defebd1f95b9
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
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32 <help><![CDATA[ |
defebd1f95b9
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
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33 ]]></help> |
defebd1f95b9
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
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34 <citations> |
defebd1f95b9
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
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35 </citations> |
defebd1f95b9
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
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36 </tool> |