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comparison call.xml @ 1:c027f82af2fb draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
author iuc
date Thu, 29 Oct 2020 20:47:48 +0000
parents e15927444573
children 680f0aef5e77
comparison
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0:e15927444573 1:c027f82af2fb
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="delly_call" name="Delly call" version="@TOOL_VERSION@+galaxy0" profile="18.01"> 2 <tool id="delly_call" name="Delly call" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="18.01">
3 <description>and genotype structural variants</description> 3 <description>and genotype structural variants</description>
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
8 <expand macro="version_command"/> 8 <expand macro="version_command"/>
9 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
10 ## initialize 10 ## initialize
11 #for $i, $current in enumerate($samples) 11 @BAM@
12 ln -s '${current}' 'sample_${i}.bam' &&
13 ln -s '${current.metadata.bam_index}' 'sample_${i}.bam.bai' &&
14 #end for
15 12
16 ## run 13 ## run
17 delly call 14 delly call
18 ## generic options 15 ## generic options
19 --svtype $generic.svtype 16 --svtype $generic.svtype
25 ## discovery options 22 ## discovery options
26 --map-qual $discovery.mapqual 23 --map-qual $discovery.mapqual
27 --qual-tra $discovery.qualtra 24 --qual-tra $discovery.qualtra
28 --mad-cutoff $discovery.madcutoff 25 --mad-cutoff $discovery.madcutoff
29 --minclip $discovery.minclip 26 --minclip $discovery.minclip
27 --min-clique-size $discovery.mincliquesize
30 --minrefsep $discovery.minrefsep 28 --minrefsep $discovery.minrefsep
31 --maxreadsep $discovery.maxreadsep 29 --maxreadsep $discovery.maxreadsep
32 ## genotyping options 30 ## genotyping options
33 #if $genotyping.vcffile 31 #if $genotyping.vcffile
34 --vcffile '$genotyping.vcffile' 32 --vcffile '$genotyping.vcffile'
41 #for $i, $current in enumerate($samples) 39 #for $i, $current in enumerate($samples)
42 'sample_${i}.bam' 40 'sample_${i}.bam'
43 #end for 41 #end for
44 42
45 ## postprocessing 43 ## postprocessing
46 #if 'log' in $oo.out 44 @LOG@
47 |& tee 'log.txt' 45 @VCF@
48 #end if 46 @DUMP@
49 #if 'vcf' in $oo.out
50 && test -f 'result.bcf' && bcftools view 'result.bcf' > 'result.vcf' || echo 'No results.'
51 #end if
52 #if 'dump' in $oo.out
53 && test -f 'dump.tsv.gz' && bgzip -d 'dump.tsv.gz' || echo 'No dump file.'
54 #end if
55 ]]></command> 47 ]]></command>
56 <inputs> 48 <inputs>
57 <expand macro="samples"/> 49 <expand macro="samples"/>
58 <section name="generic" title="Generic options" expanded="true"> 50 <section name="generic" title="Generic options" expanded="true">
59 <expand macro="svtype"/> 51 <expand macro="svtype"/>
63 <section name="discovery" title="Discovery options" expanded="true"> 55 <section name="discovery" title="Discovery options" expanded="true">
64 <param name="mapqual" type="integer" value="1" label="Set minimum paired-end (PE) mapping quality" help="(--map-qual)"/> 56 <param name="mapqual" type="integer" value="1" label="Set minimum paired-end (PE) mapping quality" help="(--map-qual)"/>
65 <param name="qualtra" type="integer" value="20" label="Set minimum PE quality for translocation" help="(--qual-tra)"/> 57 <param name="qualtra" type="integer" value="20" label="Set minimum PE quality for translocation" help="(--qual-tra)"/>
66 <param name="madcutoff" type="integer" value="9" label="Set insert size cutoff" help="median+s*MAD, deletions only (--mad-cutoff)"/> 58 <param name="madcutoff" type="integer" value="9" label="Set insert size cutoff" help="median+s*MAD, deletions only (--mad-cutoff)"/>
67 <expand macro="minclip"/> 59 <expand macro="minclip"/>
60 <expand macro="mincliquesize"/>
68 <expand macro="minrefsep"/> 61 <expand macro="minrefsep"/>
69 <expand macro="maxreadsep"/> 62 <expand macro="maxreadsep"/>
70 </section> 63 </section>
71 <section name="genotyping" title="Genotyping options" expanded="true"> 64 <section name="genotyping" title="Genotyping options" expanded="true">
72 <expand macro="vcffile"/> 65 <expand macro="vcffile"/>
177 <section name="discovery"> 170 <section name="discovery">
178 <param name="mapqual" value="2"/> 171 <param name="mapqual" value="2"/>
179 <param name="qualtra" value="19"/> 172 <param name="qualtra" value="19"/>
180 <param name="madcutoff" value="8"/> 173 <param name="madcutoff" value="8"/>
181 <param name="minclip" value="24"/> 174 <param name="minclip" value="24"/>
175 <param name="mincliquesize" value="1"/>
182 <param name="minrefsep" value="24"/> 176 <param name="minrefsep" value="24"/>
183 <param name="maxreadsep" value="39"/> 177 <param name="maxreadsep" value="39"/>
184 </section> 178 </section>
185 <section name="genotyping"> 179 <section name="genotyping">
186 <param name="genoqual" value="4"/> 180 <param name="genoqual" value="4"/>
277 271
278 Delly *call* needs a sorted, indexed and duplicate marked BAM file for every input sample. An indexed reference genome is required to identify split-reads. Additionally a VCF/BCF file for genotyping can be applied. 272 Delly *call* needs a sorted, indexed and duplicate marked BAM file for every input sample. An indexed reference genome is required to identify split-reads. Additionally a VCF/BCF file for genotyping can be applied.
279 273
280 **Output** 274 **Output**
281 275
282 The output is available in BCF and VCF format. Additionally a output file for SV-reads is provided. 276 The output is available in BCF and VCF format. Additionally an output file for SV-reads is provided.
283 277
284 .. class:: infomark 278 .. class:: infomark
285 279
286 **References** 280 **References**
287 281