Mercurial > repos > artbio > lumpy_smoove
annotate lumpy_smoove.xml @ 4:49da975ba395 draft
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
author | artbio |
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date | Thu, 27 Aug 2020 17:14:25 -0400 |
parents | 65b400409455 |
children | bd4135caa3fa |
rev | line source |
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4
49da975ba395
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
artbio
parents:
3
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1 <tool id="lumpy_smoove" name="lumpy_smoove" version="0.6.0"> |
0
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
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2 <description>find structural variants using the smoove workflow</description> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
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3 <macros> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
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4 <import>macro_lumpy_smoove.xml</import> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
changeset
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5 </macros> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
changeset
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6 <requirements> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
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7 <requirement type="package" version="0.2.5">smoove</requirement> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
changeset
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8 </requirements> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
changeset
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9 <stdio> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
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10 <exit_code range="1:" level="fatal" description="Tool exception" /> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
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11 </stdio> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
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12 <command detect_errors="exit_code"><![CDATA[ |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
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13 @pipefail@ |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
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14 @set_fasta_index@ |
4
49da975ba395
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
artbio
parents:
3
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15 #if $set_plan.plan_choice=='pair': |
49da975ba395
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
artbio
parents:
3
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16 ln -s $set_plan.normal_bam normal.bam && |
49da975ba395
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
artbio
parents:
3
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17 ln -f -s $set_plan.normal_bam.metadata.bam_index normal.bam.bai && |
49da975ba395
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
artbio
parents:
3
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18 ln -s $set_plan.tumor_bam tumor.bam && |
49da975ba395
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
artbio
parents:
3
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19 ln -f -s $set_plan.tumor_bam.metadata.bam_index tumor.bam.bai && |
49da975ba395
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
artbio
parents:
3
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20 #else |
49da975ba395
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
artbio
parents:
3
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21 ln -s $set_plan.single_bam single.bam && |
49da975ba395
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
artbio
parents:
3
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22 ln -f -s $set_plan.single_bam.metadata.bam_index single.bam.bai && |
49da975ba395
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
artbio
parents:
3
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23 #end if |
3
65b400409455
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
artbio
parents:
2
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24 |
65b400409455
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
artbio
parents:
2
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25 smoove call --name output |
0
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
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26 #if $set_exclusion.choices=="yes": |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
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27 --exclude $bedmask |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
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28 #end if |
3
65b400409455
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
artbio
parents:
2
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29 --fasta reference.fa |
65b400409455
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
artbio
parents:
2
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30 --processes \${GALAXY_SLOTS:-4} |
65b400409455
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
artbio
parents:
2
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31 --genotype |
65b400409455
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
artbio
parents:
2
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32 #if $prpos=="no": |
65b400409455
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
artbio
parents:
2
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33 --removepr |
65b400409455
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
artbio
parents:
2
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34 #end if |
4
49da975ba395
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
artbio
parents:
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35 *.bam && |
3
65b400409455
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
artbio
parents:
2
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36 ls -latr && |
65b400409455
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
artbio
parents:
2
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37 gunzip output-smoove.genotyped.vcf.gz |
0
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
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38 |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
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39 ]]></command> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
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40 <inputs> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
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41 <expand macro="reference_source_conditional" /> |
4
49da975ba395
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
artbio
parents:
3
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42 <conditional name="set_plan"> |
49da975ba395
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
artbio
parents:
3
diff
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43 <param name="plan_choice" type="select" label="Analyse a single Bam or a pair of Bam (eg normal/tumor)" display="radio"> |
49da975ba395
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
artbio
parents:
3
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44 <option value="pair" selected="true">A pair of Bam files</option> |
49da975ba395
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
artbio
parents:
3
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45 <option value="single">A single Bam</option> |
49da975ba395
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
artbio
parents:
3
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46 </param> |
49da975ba395
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
artbio
parents:
3
diff
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47 <when value="pair"> |
49da975ba395
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
artbio
parents:
3
diff
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48 <param format="bam" name="normal_bam" type="data" label="BAM alignment from the normal sample"/> |
49da975ba395
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
artbio
parents:
3
diff
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49 <param format="bam" name="tumor_bam" type="data" label="BAM alignment from the tumor sample"/> |
49da975ba395
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
artbio
parents:
3
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50 </when> |
49da975ba395
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
artbio
parents:
3
diff
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51 <when value="single"> |
49da975ba395
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
artbio
parents:
3
diff
changeset
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52 <param format="bam" name="single_bam" type="data" label="BAM alignment from a single sample"/> |
49da975ba395
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
artbio
parents:
3
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53 </when> |
49da975ba395
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
artbio
parents:
3
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54 </conditional> |
49da975ba395
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
artbio
parents:
3
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55 |
49da975ba395
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
artbio
parents:
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56 |
0
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
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57 <conditional name="set_exclusion"> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
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58 <param name="choices" type="select" label="exclude regions with a bed file" display="radio"> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
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59 <option value="no" selected="true">No</option> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
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60 <option value="yes">Yes</option> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
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61 </param> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
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62 <when value="yes"> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
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63 <param format="bed" name="bedmask" type="data" label="BED regions to be excluded for the analysis"/> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
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64 </when> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
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65 <when value="no"> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
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66 </when> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
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67 </conditional> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
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68 <param name="prpos" type="select" label="include the PRPOS probabilities in INFO tags" display="radio"> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
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69 <option value="no" selected="true">No</option> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
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70 <option value="yes">Yes</option> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
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71 </param> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
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72 </inputs> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
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73 |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
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74 <outputs> |
3
65b400409455
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
artbio
parents:
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75 <data format="vcf" name="vcf_call" label="lumpy-smoove Variant Calling" from_work_dir="./output-smoove.genotyped.vcf" /> |
0
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
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76 </outputs> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
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77 |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
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78 <tests> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
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79 <test> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
changeset
|
80 <param name="reference_source_selector" value="history" /> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
changeset
|
81 <param name="ref_file" value="chrI-ce11.fa"/> |
3
65b400409455
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
artbio
parents:
2
diff
changeset
|
82 <param name="normal_bam" value="celegans_RG_1.bam"/> |
65b400409455
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
artbio
parents:
2
diff
changeset
|
83 <param name="tumor_bam" value="celegans_RG_2.bam"/> |
0
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
changeset
|
84 <param name="choices" value="yes"/> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
changeset
|
85 <param name="bedmask" value="exclude.bed"/> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
changeset
|
86 <param name="prpos" value="no"/> |
4
49da975ba395
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
artbio
parents:
3
diff
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|
87 <output name="vcf_call" ftype="vcf" file="result-1.vcf" lines_diff="8"/> |
0
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
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|
88 </test> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
changeset
|
89 <test> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
changeset
|
90 <param name="reference_source_selector" value="history" /> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
changeset
|
91 <param name="ref_file" value="chrI-ce11.fa"/> |
3
65b400409455
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
artbio
parents:
2
diff
changeset
|
92 <param name="normal_bam" value="celegans_RG_1.bam"/> |
65b400409455
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
artbio
parents:
2
diff
changeset
|
93 <param name="tumor_bam" value="celegans_RG_2.bam"/> |
0
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
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|
94 <param name="choices" value="no"/> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
changeset
|
95 <param name="prpos" value="no"/> |
4
49da975ba395
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
artbio
parents:
3
diff
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|
96 <output name="vcf_call" ftype="vcf" file="result-2.vcf" lines_diff="8"/> |
0
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
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|
97 </test> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
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98 <test> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
changeset
|
99 <param name="reference_source_selector" value="history" /> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
changeset
|
100 <param name="ref_file" value="chrI-ce11.fa"/> |
3
65b400409455
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
artbio
parents:
2
diff
changeset
|
101 <param name="normal_bam" value="celegans_RG_2.bam"/> |
65b400409455
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
artbio
parents:
2
diff
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|
102 <param name="tumor_bam" value="celegans_RG_1.bam"/> |
0
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
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|
103 <param name="choices" value="no"/> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
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|
104 <param name="prpos" value="no"/> |
4
49da975ba395
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
artbio
parents:
3
diff
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|
105 <output name="vcf_call" ftype="vcf" file="result-3.vcf" lines_diff="8"/> |
0
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
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|
106 </test> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
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|
107 <test> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
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|
108 <param name="reference_source_selector" value="history" /> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
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|
109 <param name="ref_file" value="chrI-ce11.fa"/> |
3
65b400409455
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
artbio
parents:
2
diff
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|
110 <param name="normal_bam" value="celegans_RG_1.bam"/> |
65b400409455
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
artbio
parents:
2
diff
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|
111 <param name="tumor_bam" value="celegans_RG_2.bam"/> |
0
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
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|
112 <param name="choices" value="no"/> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
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|
113 <param name="prpos" value="yes"/> |
4
49da975ba395
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
artbio
parents:
3
diff
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|
114 <output name="vcf_call" ftype="vcf" file="result-4.vcf" lines_diff="8"/> |
0
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
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|
115 </test> |
4
49da975ba395
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
artbio
parents:
3
diff
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|
116 <test> |
49da975ba395
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
artbio
parents:
3
diff
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|
117 <param name="reference_source_selector" value="history" /> |
49da975ba395
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
artbio
parents:
3
diff
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|
118 <param name="plan_choice" value="single" /> |
49da975ba395
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
artbio
parents:
3
diff
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|
119 <param name="ref_file" value="chrI-ce11.fa"/> |
49da975ba395
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
artbio
parents:
3
diff
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|
120 <param name="single_bam" value="celegans_RG_1.bam"/> |
49da975ba395
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
artbio
parents:
3
diff
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|
121 <param name="choices" value="no"/> |
49da975ba395
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
artbio
parents:
3
diff
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|
122 <param name="prpos" value="no"/> |
49da975ba395
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
artbio
parents:
3
diff
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|
123 <output name="vcf_call" ftype="vcf" file="result-5.vcf" lines_diff="8"/> |
49da975ba395
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
artbio
parents:
3
diff
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|
124 </test> |
0
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
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|
125 </tests> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
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126 |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
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127 <help> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
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128 **smoove** simplifies and speeds calling and genotyping SVs for short reads. It also improves |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
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129 specificity by removing many spurious alignment signals that are indicative of low-level |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
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130 noise and often contribute to spurious calls. |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
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131 |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
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132 There is a blog-post describing smoove in more detail |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
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133 here: https://brentp.github.io/post/smoove/ |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
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134 |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
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|
135 Currently, this Galaxy tool only wraps smoove for 2 samples (bam normal and tumor inputs), |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
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|
136 which translates in the command line:: |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
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137 |
3
65b400409455
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
artbio
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2
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|
138 <![CDATA[smoove call --name my-cohort --exclude $bed --fasta $fasta -p $threads --genotype [--removepr] /path/to/*.bam]]> |
0
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
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139 |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
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140 |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
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|
141 the --exclude $bed is highly recommended as it can be used to ignore reads that overlap |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
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142 problematic regions. |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
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143 |
3
65b400409455
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
artbio
parents:
2
diff
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|
144 A good set of regions for GRCh37 can be found here_ |
65b400409455
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
artbio
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145 |
65b400409455
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
artbio
parents:
2
diff
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|
146 .. _here: https://github.com/hall-lab/speedseq/blob/master/annotations/ceph18.b37.lumpy.exclude.2014-01-15.bed |
65b400409455
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
artbio
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|
147 |
0
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
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148 |
3
65b400409455
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
artbio
parents:
2
diff
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|
149 And a good set for GRCh38 can be found there_ |
65b400409455
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
artbio
parents:
2
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|
150 |
65b400409455
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
artbio
parents:
2
diff
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|
151 .. _there: https://github.com/hall-lab/speedseq/blob/master/annotations/exclude.cnvnator_100bp.GRCh38.20170403.bed |
65b400409455
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
artbio
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|
152 |
0
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
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|
153 |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
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|
154 smoove will:: |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
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|
155 |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
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|
156 1. parallelize calls to lumpy_filter to extract split and discordant reads required by lumpy |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
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|
157 |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
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|
158 2. further filter lumpy_filter calls to remove high-coverage, spurious regions and user-specified chroms like 'hs37d5'; |
ee8fc44b1655
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159 it will also remove reads that we've found are likely spurious signals. after this, it will |
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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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160 remove singleton reads (where the mate was removed by one of the previous filters) |
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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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161 from the discordant bams. This makes lumpy much faster and less memory-hungry. |
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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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162 |
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163 3. calculate per-sample metrics for mean, standard deviation, and distribution of insert |
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164 size as required by lumpy. |
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165 |
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166 4. stream output of lumpy directly into multiple svtyper processes for parallel-by-region |
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167 genotyping while lumpy is still running. |
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168 |
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169 5. sort, compress, and index final VCF (but this galaxy wrapper is uncompression the gzip_vcf output) |
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170 |
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171 **Input(s)** |
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172 |
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173 * BAM files: Either a pair of Bam files (e.g. normal vs tumor sample) or a single Bam file. |
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174 Only BAM alignments produced by BWA-mem have been tested with this tool |
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175 |
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176 .. class:: warningmark |
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177 |
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178 It is mandatory for proper run of svtyper that **BAM files contain read group information**, |
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179 ie the @RG tag is present and filled in each BAM file |
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180 |
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181 |
3
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182 * A bed file describing the regions to exclude from the analysis |
65b400409455
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183 * Additional options*: refer to smoove GitHub repository_ and the lumpy publication (doi 10.1186/gb-2014-15-6-r84) |
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184 |
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185 .. _repository: https://github.com/brentp/smoove |
ee8fc44b1655
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186 |
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187 |
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188 Options:: |
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189 |
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190 <![CDATA[ |
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191 |
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192 smoove calls several programs. Those with 'Y' are found on your $PATH. Only those with '*' are required. |
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193 |
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194 [Y] bgzip [ sort -> (compress) -> index ] |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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195 [Y] gsort [(sort) -> compress -> index ] |
ee8fc44b1655
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196 [Y] tabix [ sort -> compress -> (index)] |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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197 [Y] lumpy |
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198 [Y] lumpy_filter |
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199 [Y] samtools |
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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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200 [Y] svtyper |
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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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201 [Y] mosdepth [extra filtering of split and discordant files for better scaling] |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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202 |
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203 [Y] duphold [(optional) annotate calls with depth changes] |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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204 [Y] svtools [only needed for large cohorts]. |
ee8fc44b1655
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205 |
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206 Available sub-commands are below. Each can be run with -h for additional help. |
ee8fc44b1655
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207 |
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208 call : call lumpy (and optionally svtyper) |
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209 merge : merge and sort (using svtools) calls from multiple samples |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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210 genotype : parallelize svtyper on an input VCF |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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211 paste : square final calls from multiple samples (each with same number of variants) |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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212 plot-counts : plot counts of split, discordant reads before, after smoove filtering |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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213 annotate : annotate a VCF with gene and quality of SV call |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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214 hipstr : run hipSTR in parallel |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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215 cnvnator : run cnvnator in parallel |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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216 duphold : run duphold in parallel (this can be done by adding a flag to call or genotype) |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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217 ]]> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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218 </help> |
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219 |
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220 <citations> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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221 <citation type="doi">10.1186/gb-2014-15-6-r84</citation> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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222 </citations> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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223 </tool> |