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annotate snvtocnv.xml @ 2:e0724d649885 draft default tip

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 116f2555558a283190cd1dd60ee25b359bcda51e
author artbio
date Fri, 20 May 2022 17:07:54 +0000
parents d2833cfb3f08
children
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2
e0724d649885 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 116f2555558a283190cd1dd60ee25b359bcda51e
artbio
parents: 1
diff changeset
1 <tool id="snvtocnv" name="Infer CNVs from SNVs" version="3.0.0+galaxy1">
0
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
artbio
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2 <description>
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
artbio
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3 </description>
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
artbio
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4 <macros>
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
artbio
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diff changeset
5 <import>macro.xml</import>
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
artbio
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6 </macros>
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
artbio
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7 <requirements>
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
artbio
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diff changeset
8 <requirement type="package" version="3.0.0">sequenza-utils</requirement>
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
artbio
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diff changeset
9 <requirement type="package" version="3.0.0">r-sequenza</requirement>
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
artbio
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diff changeset
10 <requirement type="package" version="1.6.6">r-optparse</requirement>
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
artbio
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11 <requirement type="package" version="1.24.0">bioconductor-biocparallel</requirement>
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
artbio
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diff changeset
12 <requirement type="package" version="1.3.0">r-tidyverse</requirement>
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
artbio
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13 <requirement type="package" version="2021a=he74cb21_0">tzdata</requirement>
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
artbio
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14 </requirements>
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
artbio
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diff changeset
15 <stdio>
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
artbio
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16 <exit_code range="1:" level="fatal" description="Error occured" />
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
artbio
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17 </stdio>
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
artbio
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18 <command detect_errors="exit_code"><![CDATA[
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
artbio
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19 @pipefail@
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
artbio
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20 sequenza-utils snp2seqz -v '$input_snvs' -gc $refwig -o sample.seqz.gz &&
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
artbio
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21 sequenza-utils seqz_binning --seqz sample.seqz.gz -w 50 -o '$wiggle' &&
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
artbio
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22 Rscript $__tool_directory__/segmentation_sequenza.R
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
artbio
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23 -i '$wiggle'
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
artbio
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diff changeset
24 -s sample
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
artbio
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25 -O test &&
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
artbio
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26 Rscript $__tool_directory__/sequenza_to_hrdtools_input.R
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
artbio
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27 -i test/sample_segments.txt
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
artbio
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diff changeset
28 -s test/sample_alternative_solutions.txt
1
d2833cfb3f08 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit aa1b68e64cbbdcdd9167134ec2ea61a151333688
artbio
parents: 0
diff changeset
29 -o '$cnvs' &&
d2833cfb3f08 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit aa1b68e64cbbdcdd9167134ec2ea61a151333688
artbio
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30 ls test
0
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
artbio
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31 ]]></command>
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
artbio
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32 <inputs>
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
artbio
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33 <param name="refwig" type="data" format="txt" label="GC wigle of reference genome"/>
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
artbio
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34 <param name="input_snvs" type="data" format="vcf" label="SNVs to process in a vcf file"/>
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
artbio
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diff changeset
35 </inputs>
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
artbio
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diff changeset
36 <outputs>
2
e0724d649885 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 116f2555558a283190cd1dd60ee25b359bcda51e
artbio
parents: 1
diff changeset
37 <data name="wiggle" format="wig" label="binned wiggle" />
e0724d649885 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 116f2555558a283190cd1dd60ee25b359bcda51e
artbio
parents: 1
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38 <data name="sample_segment" format="tabular" label="sample segments" from_work_dir="test/sample_segments.txt" />
e0724d649885 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 116f2555558a283190cd1dd60ee25b359bcda51e
artbio
parents: 1
diff changeset
39 <data name="alt_solutions" format="tabular" label="alternate solutions" from_work_dir="test/sample_alternative_solutions.txt" />
0
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
artbio
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40 <data name="cnvs" format="tabular" label="Annotated CNVs" />
1
d2833cfb3f08 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit aa1b68e64cbbdcdd9167134ec2ea61a151333688
artbio
parents: 0
diff changeset
41 <data name="chrom_depths" format="pdf" label="Chromosomes sequencing depth" from_work_dir="test/sample_chromosome_depths.pdf"/>
d2833cfb3f08 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit aa1b68e64cbbdcdd9167134ec2ea61a151333688
artbio
parents: 0
diff changeset
42 <data name="chrom_view" format="pdf" label="Chromosomes views" from_work_dir="test/sample_chromosome_view.pdf"/>
d2833cfb3f08 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit aa1b68e64cbbdcdd9167134ec2ea61a151333688
artbio
parents: 0
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43 <data name="genome_view" format="pdf" label="Genome view" from_work_dir="test/sample_genome_view.pdf"/>
d2833cfb3f08 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit aa1b68e64cbbdcdd9167134ec2ea61a151333688
artbio
parents: 0
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44 <data name="model_fit" format="pdf" label="Cellularity and Diploidy model" from_work_dir="test/sample_model_fit.pdf"/>
d2833cfb3f08 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit aa1b68e64cbbdcdd9167134ec2ea61a151333688
artbio
parents: 0
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45 <data name="CN_histo" format="pdf" label="Copy Numbers histogram" from_work_dir="test/sample_CN_bars.pdf"/>
0
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
artbio
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46 </outputs>
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
artbio
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47 <tests>
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
artbio
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48 <test>
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
artbio
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49 <param name="input_snvs" value="hg19_chr22.vcf" ftype="vcf" />
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
artbio
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50 <param name="refwig" value="hg19.GCref.txt" />
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
artbio
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51 <output name="cnvs" file="hg19.cnv.tab" ftype="tabular" />
1
d2833cfb3f08 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit aa1b68e64cbbdcdd9167134ec2ea61a151333688
artbio
parents: 0
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52 <output name="chrom_depths" ftype="pdf" file="hg19_chrom_depths.pdf"/>
d2833cfb3f08 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit aa1b68e64cbbdcdd9167134ec2ea61a151333688
artbio
parents: 0
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53 <output name="chrom_view" ftype="pdf" file="hg19_chrom_view.pdf"/>
d2833cfb3f08 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit aa1b68e64cbbdcdd9167134ec2ea61a151333688
artbio
parents: 0
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54 <output name="genome_view" ftype="pdf" file="hg19_genome_view.pdf"/>
d2833cfb3f08 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit aa1b68e64cbbdcdd9167134ec2ea61a151333688
artbio
parents: 0
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55 <output name="model_fit" ftype="pdf" file="hg19_model.pdf"/>
d2833cfb3f08 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit aa1b68e64cbbdcdd9167134ec2ea61a151333688
artbio
parents: 0
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56 <output name="CN_histo" ftype="pdf" file="hg19_CN_histo.pdf"/>
0
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
artbio
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57 </test>
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
artbio
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58 <test>
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
artbio
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59 <param name="input_snvs" value="hg38_chr22.vcf" ftype="vcf" />
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
artbio
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60 <param name="refwig" value="hg38.GCref.txt" />
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
artbio
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61 <output name="cnvs" file="hg38.cnv.tab" ftype="tabular" />
1
d2833cfb3f08 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit aa1b68e64cbbdcdd9167134ec2ea61a151333688
artbio
parents: 0
diff changeset
62 <output name="chrom_depths" ftype="pdf" file="hg38_chrom_depths.pdf"/>
d2833cfb3f08 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit aa1b68e64cbbdcdd9167134ec2ea61a151333688
artbio
parents: 0
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63 <output name="chrom_view" ftype="pdf" file="hg38_chrom_view.pdf"/>
d2833cfb3f08 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit aa1b68e64cbbdcdd9167134ec2ea61a151333688
artbio
parents: 0
diff changeset
64 <output name="genome_view" ftype="pdf" file="hg38_genome_view.pdf"/>
d2833cfb3f08 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit aa1b68e64cbbdcdd9167134ec2ea61a151333688
artbio
parents: 0
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65 <output name="model_fit" ftype="pdf" file="hg38_model.pdf"/>
d2833cfb3f08 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit aa1b68e64cbbdcdd9167134ec2ea61a151333688
artbio
parents: 0
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66 <output name="CN_histo" ftype="pdf" file="hg38_CN_histo.pdf"/>
0
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
artbio
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67 </test>
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
artbio
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68 </tests>
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
artbio
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69 <help>
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
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70
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
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71 snvtocnv
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
artbio
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72 ============================
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
artbio
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73
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
artbio
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74 Analyze genomic sequencing data from paired normal-tumor samples, including
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
artbio
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75 cellularity and ploidy estimation; mutation and copy number (allele-specific and total
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
artbio
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76 copy number) detection, quantification and visualization.
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
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77
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
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78
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
artbio
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79 Inputs
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
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80 --------
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
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81
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
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82 A GC wigle of genome index generated with the tool "create GC_wiggle of reference genome"
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
artbio
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83 available from this galaxy wrapper
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
artbio
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84
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
artbio
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85 A vcf file of somatic *single* nucleotide variations observed in a tumor sample
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
artbio
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86
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
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87
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
artbio
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88 </help>
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
artbio
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89 <citations>
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
artbio
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90 <citation type="doi">10.1093/annonc/mdu479</citation>
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
artbio
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91 </citations>
b77d7a0a45e8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
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92 </tool>