Mercurial > repos > iuc > delly_filter
annotate filter.xml @ 0:a75e05f20a66 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
author | iuc |
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date | Mon, 28 Sep 2020 07:44:40 +0000 |
parents | |
children | 9919057a466c |
rev | line source |
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0
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
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1 <?xml version="1.0"?> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
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2 <tool id="delly_filter" name="Delly filter" version="@TOOL_VERSION@+galaxy0" profile="18.01"> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
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3 <description>somatic or germline structural variants</description> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
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4 <macros> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
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5 <import>macros.xml</import> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
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6 </macros> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
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7 <expand macro="requirements"/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
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8 <expand macro="version_command"/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
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9 <command detect_errors="exit_code"><![CDATA[ |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
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10 ## initialize |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
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11 #if $samples.is_of_type('vcf') |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
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12 bcftools view -Ob '$samples' > 'sample.bcf.gz' && |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
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13 bcftools index 'sample.bcf.gz' && |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
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14 #else |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
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15 ln -s '${samples}' 'sample.bcf.gz' && |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
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16 ln -s '${samples.metadata.bcf_index}' 'sample.bcf.gz.csi' && |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
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17 #end if |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
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18 |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
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19 ## run |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
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20 delly filter |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
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21 ## generic options |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
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22 --filter $sv.mode_cond.mode_sel |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
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23 --outfile 'result.bcf' |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
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24 --altaf $generic.altaf |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
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25 --minsize $generic.minsize |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
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26 --maxsize $generic.maxsize |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
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27 --ratiogeno $generic.ratiogeno |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
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28 $generic.pass |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
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29 ## somatic options |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
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30 #if $sv.mode_cond.mode_sel == 'somatic' |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
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31 --samples '$sv.mode_cond.samples' |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
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32 --coverage $sv.mode_cond.coverage |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
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33 --controlcontamination $sv.mode_cond.controlcontamination |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
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34 #end if |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
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35 ## germline options |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
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36 #if $sv.mode_cond.mode_sel == 'germline' |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
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37 --gq $sv.mode_cond.gq |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
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38 --rddel $sv.mode_cond.rddel |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
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39 --rddup $sv.mode_cond.rddup |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
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40 #end if |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
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41 ## samples |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
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42 'sample.bcf.gz' ## input |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
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43 |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
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44 ## postprocessing |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
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45 #if 'log' in $oo.out |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
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46 |& tee 'log.txt' |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
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47 #end if |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
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48 #if 'vcf' in $oo.out |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
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49 && test -f 'result.bcf' && bcftools view 'result.bcf' > 'result.vcf' || echo 'No results.' |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
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50 #end if |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
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51 ]]></command> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
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52 <inputs> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
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53 <expand macro="samples" format="bcf,vcf" multiple="false" label="Select file"/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
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54 <section name="generic" title="Generic options" expanded="true"> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
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55 <param argument="--altaf" type="float" value="0.2" min="0.0" max="1.0" label="Set minimum fractional ALT support"/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
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56 <param argument="--minsize" type="integer" value="0" label="Set minimum SV size"/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
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57 <param argument="--maxsize" type="integer" value="500000000" label="Set maximum SV size"/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
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58 <param argument="--ratiogeno" type="float" value="0.75" min="0.0" max="1.0" label="Set minimum fraction of genotyped samples"/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
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59 <param argument="--pass" type="boolean" truevalue="--pass" falsevalue="" label="Filter sites for PASS?"/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
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60 </section> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
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61 <section name="sv" title="SV calling options" expanded="true"> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
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62 <conditional name="mode_cond"> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
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63 <param argument="mode_sel" type="select" label="Select filter mode"> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
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64 <option value="somatic" selected="true">Somatic</option> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
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65 <option value="germline">Germline</option> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
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66 </param> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
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67 <when value="somatic"> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
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68 <param argument="--samples" type="data" format="tabular" label="Select sample file" help="Two-column sample file listing sample name and tumor or control."/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
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69 <param argument="--coverage" type="integer" value="10" label="Set minimum coverage in tumor."/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
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70 <param argument="--controlcontamination" type="float" value="0.0" min="0.0" max="1.0" label="Set maximum fractional ALT support in control"/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
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71 </when> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
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72 <when value="germline"> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
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73 <param argument="--gq" type="integer" value="15" label="Set minimum median GQ for carriers and non-carriers"/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
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74 <param argument="--rddel" type="float" value="0.8" label="Set maximum read-depth ratio of carrier vs. non-carrier for a deletion"/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
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75 <param argument="--rddup" type="float" value="1.2" label="Set minimum read-depth ratio of carrier vs. non-carrier for a duplication"/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
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76 </when> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
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77 </conditional> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
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78 </section> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
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79 <section name="oo" title="Output options"> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
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80 <param name="out" type="select" multiple="true" optional="false" label="Select output file(s)"> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
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81 <option value="bcf" selected="true">BCF</option> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
82 <option value="vcf">VCF</option> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
83 <option value="log">Log</option> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
84 </param> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
85 </section> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
86 </inputs> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
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87 <outputs> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
88 <expand macro="vcf"/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
89 <expand macro="bcf"/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
90 <expand macro="log"/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
91 </outputs> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
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92 <tests> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
93 <!-- #1 default, somatic, bcf --> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
94 <test expect_num_outputs="2"> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
95 <param name="samples" value="call_1.bcf.gz"/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
96 <section name="sv"> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
97 <conditional name="mode_cond"> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
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|
98 <param name="mode_sel" value="somatic"/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
99 <param name="samples" value="samples.tsv"/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
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100 </conditional> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
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|
101 </section> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
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102 <section name="oo"> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
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103 <param name="out" value="vcf,bcf"/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
104 </section> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
105 <output name="out_bcf"> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
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|
106 <assert_contents> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
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|
107 <has_size value="2281" delta="10"/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
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|
108 </assert_contents> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
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|
109 </output> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
110 <output name="out_vcf"> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
111 <assert_contents> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
112 <has_n_lines n="140"/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
113 <has_line line="##fileformat=VCFv4.2"/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
114 <has_line line="#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NORMAL	TUMOR"/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
115 </assert_contents> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
116 </output> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
117 </test> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
118 <!-- #2 somatic, bcf --> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
119 <test expect_num_outputs="3"> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
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|
120 <param name="samples" value="call_1.bcf.gz"/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
121 <section name="generic"> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
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|
122 <param name="altaf" value="0.3"/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
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|
123 <param name="minsize" value="1"/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
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|
124 <param name="maxsize" value="500000001"/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
125 <param name="ratiogeno" value="0.76"/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
126 <param name="pass" value="true"/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
127 </section> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
128 <section name="sv"> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
129 <conditional name="mode_cond"> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
130 <param name="mode_sel" value="somatic"/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
131 <param name="samples" value="samples.tsv"/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
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|
132 <param name="coverage" value="11"/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
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|
133 <param name="controlcontamination" value="0.1"/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
134 </conditional> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
135 </section> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
136 <section name="oo"> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
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|
137 <param name="out" value="vcf,bcf,log"/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
138 </section> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
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|
139 <output name="out_bcf"> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
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|
140 <assert_contents> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
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|
141 <has_size value="2281" delta="10"/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
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|
142 </assert_contents> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
143 </output> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
144 <output name="out_vcf"> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
145 <assert_contents> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
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|
146 <has_n_lines n="140"/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
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|
147 <has_line line="##fileformat=VCFv4.2"/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
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|
148 <has_line line="#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NORMAL	TUMOR"/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
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|
149 </assert_contents> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
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|
150 </output> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
151 <output name="out_log"> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
152 <assert_contents> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
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|
153 <has_text_matching expression=".+Done\."/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
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|
154 </assert_contents> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
155 </output> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
156 </test> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
157 <!-- #3 default, germline, bcf --> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
158 <test expect_num_outputs="2"> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
159 <param name="samples" value="call_1.bcf.gz"/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
160 <section name="sv"> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
161 <conditional name="mode_cond"> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
162 <param name="mode_sel" value="germline"/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
163 </conditional> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
164 </section> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
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|
165 <section name="oo"> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
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|
166 <param name="out" value="vcf,bcf"/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
167 </section> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
168 <output name="out_bcf"> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
169 <assert_contents> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
170 <has_size value="2264" delta="10"/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
171 </assert_contents> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
172 </output> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
173 <output name="out_vcf"> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
174 <assert_contents> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
175 <has_n_lines n="139"/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
176 <has_line line="##fileformat=VCFv4.2"/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
177 <has_line line="#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NORMAL	TUMOR"/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
178 </assert_contents> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
179 </output> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
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180 </test> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
181 <!-- #4 germline, bcf --> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
182 <test expect_num_outputs="3"> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
183 <param name="samples" value="call_1.bcf.gz"/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
184 <section name="generic"> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
185 <param name="altaf" value="0.1"/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
186 <param name="minsize" value="1"/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
187 <param name="maxsize" value="500000001"/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
188 <param name="ratiogeno" value="0.76"/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
189 <param name="pass" value="true"/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
190 </section> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
191 <section name="sv"> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
192 <conditional name="mode_cond"> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
193 <param name="mode_sel" value="germline"/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
194 <param name="gq" value="14"/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
195 <param name="rddel" value="0.7"/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
196 <param name="rddup" value="1.3"/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
197 </conditional> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
198 </section> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
199 <section name="oo"> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
200 <param name="out" value="vcf,bcf,log"/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
201 </section> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
202 <output name="out_bcf"> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
203 <assert_contents> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
204 <has_size value="2264" delta="10"/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
205 </assert_contents> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
206 </output> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
207 <output name="out_vcf"> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
208 <assert_contents> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
209 <has_n_lines n="139"/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
210 <has_line line="##fileformat=VCFv4.2"/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
211 <has_line line="#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NORMAL	TUMOR"/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
212 </assert_contents> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
213 </output> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
214 <output name="out_log"> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
215 <assert_contents> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
216 <has_text_matching expression=".+Done\."/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
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|
217 </assert_contents> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
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|
218 </output> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
219 </test> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
220 <!-- #5 default, somatic, vcf --> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
221 <test expect_num_outputs="2"> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
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|
222 <param name="samples" value="call_1.vcf.gz"/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
223 <section name="sv"> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
224 <conditional name="mode_cond"> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
225 <param name="mode_sel" value="somatic"/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
226 <param name="samples" value="samples.tsv"/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
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|
227 </conditional> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
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|
228 </section> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
229 <section name="oo"> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
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|
230 <param name="out" value="vcf,bcf"/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
231 </section> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
232 <output name="out_bcf"> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
233 <assert_contents> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
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|
234 <has_size value="2440" delta="10"/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
235 </assert_contents> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
236 </output> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
237 <output name="out_vcf"> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
238 <assert_contents> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
239 <has_n_lines n="142"/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
240 <has_line line="##fileformat=VCFv4.2"/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
241 <has_line line="#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NORMAL	TUMOR"/> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
242 </assert_contents> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
243 </output> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
244 </test> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
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|
245 </tests> |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
changeset
|
246 <help><![CDATA[ |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
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|
247 .. class:: infomark |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
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|
248 |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
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|
249 **What it does** |
a75e05f20a66
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff
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|
250 |
a75e05f20a66
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251 @WID@ |
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252 |
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253 Delly *filter* contains workflows for germline and somatic SV calling. |
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254 |
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255 **Input** |
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256 |
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257 *Somatic* filtering requires a called SV input with at least one tumor sample and a matched control sample. In addition, a tab-delimited sample description needs to be provided, in which the first column holds the sample ids (as found in the VCF/BCF input) and the second column specifies either tumor or control. |
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258 |
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259 *Germline* SV calling is done by sample for high-coverage genomes or in small batches for low-coverage genomes. |
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260 |
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261 **Output** |
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262 |
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263 The output is available in BCF and VCF format. |
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264 |
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265 .. class:: infomark |
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266 |
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267 **References** |
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268 |
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269 @REFERENCES@ |
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270 ]]></help> |
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271 <expand macro="citations"/> |
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272 </tool> |