Mercurial > repos > artbio > lumpy_smoove
annotate vcf2hrdetect.xml @ 6:ad8853ee9909 draft
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 7d69f5c91e7ec5e252e9728fdfb0f7bcc254bf24"
author | artbio |
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date | Sun, 14 Feb 2021 23:59:42 +0000 |
parents | |
children | b4dec06d8fc6 |
rev | line source |
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6
ad8853ee9909
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 7d69f5c91e7ec5e252e9728fdfb0f7bcc254bf24"
artbio
parents:
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1 <tool id="vcf2hrdetect" name="Convert lumpy-smoove vcf" version="1"> |
ad8853ee9909
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 7d69f5c91e7ec5e252e9728fdfb0f7bcc254bf24"
artbio
parents:
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2 <description>to tabular hrdetect</description> |
ad8853ee9909
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 7d69f5c91e7ec5e252e9728fdfb0f7bcc254bf24"
artbio
parents:
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3 <macros> |
ad8853ee9909
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 7d69f5c91e7ec5e252e9728fdfb0f7bcc254bf24"
artbio
parents:
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4 <import>macro_lumpy_smoove.xml</import> |
ad8853ee9909
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 7d69f5c91e7ec5e252e9728fdfb0f7bcc254bf24"
artbio
parents:
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5 </macros> |
ad8853ee9909
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 7d69f5c91e7ec5e252e9728fdfb0f7bcc254bf24"
artbio
parents:
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6 <stdio> |
ad8853ee9909
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 7d69f5c91e7ec5e252e9728fdfb0f7bcc254bf24"
artbio
parents:
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7 <exit_code range="1:" level="fatal" description="Tool exception" /> |
ad8853ee9909
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 7d69f5c91e7ec5e252e9728fdfb0f7bcc254bf24"
artbio
parents:
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changeset
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8 </stdio> |
ad8853ee9909
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 7d69f5c91e7ec5e252e9728fdfb0f7bcc254bf24"
artbio
parents:
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9 <command detect_errors="exit_code"><![CDATA[ |
ad8853ee9909
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 7d69f5c91e7ec5e252e9728fdfb0f7bcc254bf24"
artbio
parents:
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10 @pipefail@ |
ad8853ee9909
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 7d69f5c91e7ec5e252e9728fdfb0f7bcc254bf24"
artbio
parents:
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11 python '$__tool_directory__'/vcf2hrdetect.py '$lumpy_smoove_vcf' '$hrdetect_tabular' |
ad8853ee9909
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 7d69f5c91e7ec5e252e9728fdfb0f7bcc254bf24"
artbio
parents:
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12 ]]></command> |
ad8853ee9909
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 7d69f5c91e7ec5e252e9728fdfb0f7bcc254bf24"
artbio
parents:
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13 <inputs> |
ad8853ee9909
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 7d69f5c91e7ec5e252e9728fdfb0f7bcc254bf24"
artbio
parents:
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14 <param name="lumpy_smoove_vcf" type="data" format="vcf" label="lumpy-smoove vcf to process"/> |
ad8853ee9909
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 7d69f5c91e7ec5e252e9728fdfb0f7bcc254bf24"
artbio
parents:
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changeset
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15 </inputs> |
ad8853ee9909
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 7d69f5c91e7ec5e252e9728fdfb0f7bcc254bf24"
artbio
parents:
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16 |
ad8853ee9909
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 7d69f5c91e7ec5e252e9728fdfb0f7bcc254bf24"
artbio
parents:
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17 <outputs> |
ad8853ee9909
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 7d69f5c91e7ec5e252e9728fdfb0f7bcc254bf24"
artbio
parents:
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18 <data format="tabular" name="hrdetect_tabular" label="tabular hrdetec SVs" /> |
ad8853ee9909
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 7d69f5c91e7ec5e252e9728fdfb0f7bcc254bf24"
artbio
parents:
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changeset
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19 </outputs> |
ad8853ee9909
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 7d69f5c91e7ec5e252e9728fdfb0f7bcc254bf24"
artbio
parents:
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20 |
ad8853ee9909
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 7d69f5c91e7ec5e252e9728fdfb0f7bcc254bf24"
artbio
parents:
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21 <tests> |
ad8853ee9909
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 7d69f5c91e7ec5e252e9728fdfb0f7bcc254bf24"
artbio
parents:
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22 <test> |
ad8853ee9909
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 7d69f5c91e7ec5e252e9728fdfb0f7bcc254bf24"
artbio
parents:
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23 <param name="lumpy_smoove_vcf" value="test_vcf2hrdetect.vcf" ftype="vcf" /> |
ad8853ee9909
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 7d69f5c91e7ec5e252e9728fdfb0f7bcc254bf24"
artbio
parents:
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changeset
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24 <output name="hrdetect_tabular" file="test_vcf2hrdetect.tab" ftype="tabular" /> |
ad8853ee9909
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 7d69f5c91e7ec5e252e9728fdfb0f7bcc254bf24"
artbio
parents:
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25 </test> |
ad8853ee9909
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 7d69f5c91e7ec5e252e9728fdfb0f7bcc254bf24"
artbio
parents:
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changeset
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26 </tests> |
ad8853ee9909
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 7d69f5c91e7ec5e252e9728fdfb0f7bcc254bf24"
artbio
parents:
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27 <help> |
ad8853ee9909
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 7d69f5c91e7ec5e252e9728fdfb0f7bcc254bf24"
artbio
parents:
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28 **vcf2hrdetect** convert a vcf produced by lumpy-smoove to a somatic_sv.tsv tabular file compatible with |
ad8853ee9909
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 7d69f5c91e7ec5e252e9728fdfb0f7bcc254bf24"
artbio
parents:
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29 the HRDetect pipeline (https://github.com/eyzhao/hrdetect-pipeline/blob/master/data/example/patients/patient1/sample1/somatic_sv.tsv) |
ad8853ee9909
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 7d69f5c91e7ec5e252e9728fdfb0f7bcc254bf24"
artbio
parents:
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30 </help> |
ad8853ee9909
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 7d69f5c91e7ec5e252e9728fdfb0f7bcc254bf24"
artbio
parents:
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31 |
ad8853ee9909
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 7d69f5c91e7ec5e252e9728fdfb0f7bcc254bf24"
artbio
parents:
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32 <citations> |
ad8853ee9909
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 7d69f5c91e7ec5e252e9728fdfb0f7bcc254bf24"
artbio
parents:
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33 <citation type="doi">10.1038/nm.4292</citation> |
ad8853ee9909
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 7d69f5c91e7ec5e252e9728fdfb0f7bcc254bf24"
artbio
parents:
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34 </citations> |
ad8853ee9909
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 7d69f5c91e7ec5e252e9728fdfb0f7bcc254bf24"
artbio
parents:
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35 </tool> |