Mercurial > repos > iuc > bcftools_annotate
annotate bcftools_annotate.xml @ 17:8a2e296c07ef draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
| author | iuc |
|---|---|
| date | Tue, 20 Sep 2022 12:53:07 +0000 |
| parents | 2958e3b49ad4 |
| children |
| rev | line source |
|---|---|
|
0
e58e34d48868
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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1 <?xml version='1.0' encoding='utf-8'?> |
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17
8a2e296c07ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents:
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2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
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0
e58e34d48868
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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3 <description>Annotate and edit VCF/BCF files</description> |
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e58e34d48868
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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4 <macros> |
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e58e34d48868
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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5 <token name="@EXECUTABLE@">annotate</token> |
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e58e34d48868
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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6 <import>macros.xml</import> |
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e58e34d48868
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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7 </macros> |
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14
4f7a47e3857c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit af43d9cf6824f88726900857116f333ff4cdd336"
iuc
parents:
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8 <expand macro="bio_tools" /> |
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e58e34d48868
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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9 <expand macro="requirements" /> |
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e58e34d48868
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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10 <expand macro="version_command" /> |
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e58e34d48868
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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11 <command detect_errors="aggressive"><![CDATA[ |
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e58e34d48868
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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12 @PREPARE_ENV@ |
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e58e34d48868
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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13 @PREPARE_INPUT_FILE@ |
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e58e34d48868
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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14 #set $annotation_file = None |
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e58e34d48868
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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15 #set $annotation_hdr = None |
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e58e34d48868
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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16 #set $section = $sec_annofile |
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12c14f97429b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e
iuc
parents:
0
diff
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17 #if $section.annofile.anno_fmt == 'vcf': |
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9
a80ec64f9101
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 942ca2971ae6a72e548fde6186c6408a1e236653
iuc
parents:
8
diff
changeset
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18 #if $section.annofile.annotations.is_of_type('vcf') |
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a80ec64f9101
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 942ca2971ae6a72e548fde6186c6408a1e236653
iuc
parents:
8
diff
changeset
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19 #set $annotation_file = 'annotations.vcf.gz' |
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15
2958e3b49ad4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ccc967cdce26379110361f8dea521bade23f8612"
iuc
parents:
14
diff
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20 bgzip -c '$section.annofile.annotations' > $annotation_file && |
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9
a80ec64f9101
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 942ca2971ae6a72e548fde6186c6408a1e236653
iuc
parents:
8
diff
changeset
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21 bcftools index $annotation_file && |
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a80ec64f9101
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 942ca2971ae6a72e548fde6186c6408a1e236653
iuc
parents:
8
diff
changeset
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22 #elif $section.annofile.annotations.is_of_type('bcf') |
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a80ec64f9101
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 942ca2971ae6a72e548fde6186c6408a1e236653
iuc
parents:
8
diff
changeset
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23 #set $annotation_file = 'annotations.bcf' |
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a80ec64f9101
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 942ca2971ae6a72e548fde6186c6408a1e236653
iuc
parents:
8
diff
changeset
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24 ln -s '$section.annofile.annotations' $annotation_file && |
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a80ec64f9101
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 942ca2971ae6a72e548fde6186c6408a1e236653
iuc
parents:
8
diff
changeset
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25 #if $section.annofile.annotations.metadata.bcf_index: |
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a80ec64f9101
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 942ca2971ae6a72e548fde6186c6408a1e236653
iuc
parents:
8
diff
changeset
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26 ln -s '${section.annofile.annotations.metadata.bcf_index}' ${annotation_file}.csi && |
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a80ec64f9101
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 942ca2971ae6a72e548fde6186c6408a1e236653
iuc
parents:
8
diff
changeset
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27 #else |
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a80ec64f9101
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 942ca2971ae6a72e548fde6186c6408a1e236653
iuc
parents:
8
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28 bcftools index $annotation_file && |
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a80ec64f9101
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 942ca2971ae6a72e548fde6186c6408a1e236653
iuc
parents:
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29 #end if |
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a80ec64f9101
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 942ca2971ae6a72e548fde6186c6408a1e236653
iuc
parents:
8
diff
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30 #end if |
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0
e58e34d48868
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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31 #elif $section.annofile.anno_fmt == 'tab': |
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12c14f97429b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e
iuc
parents:
0
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32 #if $section.annofile.annotations.is_of_type('bed') |
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0
e58e34d48868
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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33 #set $annotation_file = 'annotations.bed.gz' |
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15
2958e3b49ad4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ccc967cdce26379110361f8dea521bade23f8612"
iuc
parents:
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diff
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34 bgzip -c '$section.annofile.annotations' > $annotation_file && |
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0
e58e34d48868
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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35 tabix -s 1 -b 2 -e 3 $annotation_file && |
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e58e34d48868
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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36 #else: |
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e58e34d48868
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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37 #set $annotation_file = 'annotations.tab.gz' |
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15
2958e3b49ad4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ccc967cdce26379110361f8dea521bade23f8612"
iuc
parents:
14
diff
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38 bgzip -c '$section.annofile.annotations' > $annotation_file && |
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0
e58e34d48868
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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39 tabix -s 1 -b 2 -e 2 $annotation_file && |
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e58e34d48868
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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40 #end if |
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e58e34d48868
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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41 #if $section.annofile.header_file: |
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e58e34d48868
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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42 #set $annotation_hdr = $section.annofile.header_file |
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e58e34d48868
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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43 #elif $section.annofile.header_lines: |
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e58e34d48868
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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44 #set $annotation_hdr = 'annotation.hdr' |
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15
2958e3b49ad4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ccc967cdce26379110361f8dea521bade23f8612"
iuc
parents:
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45 grep '^\#\#INFO' '${hdr_file}' > $annotation_hdr && |
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0
e58e34d48868
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
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46 #end if |
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e58e34d48868
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
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47 #end if |
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5
eb782a60fc53
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
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48 #set $section = $sec_restrict |
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0
e58e34d48868
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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49 |
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e58e34d48868
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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50 bcftools @EXECUTABLE@ |
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5
eb782a60fc53
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
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51 @PREPARE_REGIONS_FILE@ |
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0
e58e34d48868
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
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52 |
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e58e34d48868
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
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53 #set $section = $sec_annofile |
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e58e34d48868
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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54 @COLUMNS@ |
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e58e34d48868
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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55 #if $annotation_file: |
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15
2958e3b49ad4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ccc967cdce26379110361f8dea521bade23f8612"
iuc
parents:
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56 --annotations '${annotation_file}' |
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0
e58e34d48868
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
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57 #end if |
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e58e34d48868
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
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58 #if $annotation_hdr: |
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15
2958e3b49ad4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ccc967cdce26379110361f8dea521bade23f8612"
iuc
parents:
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59 --header-lines '${annotation_hdr}' |
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0
e58e34d48868
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
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60 #end if |
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e58e34d48868
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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61 |
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e58e34d48868
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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62 #if $section.set_id: |
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2958e3b49ad4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ccc967cdce26379110361f8dea521bade23f8612"
iuc
parents:
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63 --set-id '${section.set_id}' |
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0
e58e34d48868
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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64 #end if |
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e58e34d48868
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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65 #if $section.mark_sites: |
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15
2958e3b49ad4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ccc967cdce26379110361f8dea521bade23f8612"
iuc
parents:
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66 --mark-sites '${section.mark_sites}' |
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0
e58e34d48868
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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67 #end if |
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17
8a2e296c07ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents:
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68 #if $section.min_overlap |
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8a2e296c07ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents:
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69 --min-overlap '$section.min_overlap' |
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8a2e296c07ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents:
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70 #end if |
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0
e58e34d48868
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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71 |
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e58e34d48868
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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72 #set $section = $sec_annotate |
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e58e34d48868
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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73 #if $section.rename_chrs: |
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2958e3b49ad4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ccc967cdce26379110361f8dea521bade23f8612"
iuc
parents:
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74 --rename-chrs '${section.rename_chrs}' |
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0
e58e34d48868
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
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75 #end if |
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e58e34d48868
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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76 #if $section.remove: |
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2958e3b49ad4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ccc967cdce26379110361f8dea521bade23f8612"
iuc
parents:
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77 --remove '${section.remove}' |
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0
e58e34d48868
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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78 #end if |
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17
8a2e296c07ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents:
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79 #if $section.rename_annots |
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8a2e296c07ef
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80 --rename-annots '$section.rename_annots' |
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81 #end if |
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82 |
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83 |
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84 ## Default section |
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85 #set $section = $sec_restrict |
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86 @INCLUDE@ |
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87 @EXCLUDE@ |
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88 @COLLAPSE@ |
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89 @REGIONS@ |
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90 @SAMPLES@ |
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91 |
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92 @OUTPUT_TYPE@ |
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93 @THREADS@ |
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94 |
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95 ## Primary Input/Outputs |
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96 @INPUT_FILE@ |
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97 > '$output_file' |
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98 ]]> |
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99 </command> |
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100 <configfiles> |
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101 <configfile name="hdr_file"><![CDATA[#slurp |
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102 #if $sec_annofile.annofile.anno_fmt == 'tab' and str($sec_annofile.annofile.header_lines) != '': |
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103 $sec_annofile.annofile.header_lines.__str__.strip()#slurp |
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104 #end if]]></configfile> |
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105 </configfiles> |
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106 <inputs> |
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107 <expand macro="macro_input" /> |
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108 <section name="sec_annofile" expanded="false" title="Add Annotations"> |
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109 <expand macro="macro_columns" /> |
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110 <conditional name="annofile"> |
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111 <param name="anno_fmt" type="select" label="Annotations File"> |
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112 <option value="none">None</option> |
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113 <option value="vcf">From a VCF/BCF file</option> |
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114 <option value="tab">From a BED or tab-delimited file</option> |
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115 </param> |
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116 <when value="none"/> |
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117 <when value="vcf"> |
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118 <param name="annotations" type="data" format="vcf,bcf" label="Annotations VCF"/> |
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119 </when> |
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120 <when value="tab"> |
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121 <param name="annotations" type="data" format="tabular,bed" label="Annotations"> |
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122 <help><![CDATA[ |
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123 BED, or a tab-delimited file with mandatory columns CHROM, POS (or, alternatively, FROM and TO), |
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124 optional columns REF and ALT, and arbitrary number of annotation columns. |
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125 Note that in case of tab-delimited file, the coordinates POS, FROM and TO are one-based and inclusive. |
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126 ]]></help> |
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127 </param> |
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128 <param name="header_file" type="data" format="txt" label="Header Lines File" optional="true" help="lines which should be appended to the VCF header" /> |
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129 <param name="header_lines" type="text" area="true" label="Header Lines" optional="true" help="lines which should be appended to the VCF header" > |
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130 <help><![CDATA[ |
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131 ##INFO=<ID=NUMERIC_TAG,Number=1,Type=Integer,Description="Example header line"> |
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132 ##INFO=<ID=STRING_TAG,Number=1,Type=String,Description="Yet another header line"> |
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133 ]]></help> |
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134 <sanitizer sanitize="False"/> |
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135 </param> |
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136 </when> |
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137 </conditional> |
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138 <param argument="--mark-sites" type="text" value="" label="Mark Sites TAG" |
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139 help="add INFO/TAG flag to sites which are ("+") or are not ("-") listed in the annotations file" /> |
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140 <param argument="--min-overlap" type="text" value="" label="Minimum required overlap of intersecting regions" optional="true" help="Minimum overlap required as a fraction of the variant in the annotation -a file (ANN), in the target VCF file (:VCF), or both for reciprocal overlap (ANN:VCF). By default overlaps of arbitrary length are sufficient."> |
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141 <sanitizer invalid_char=""> |
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142 <valid initial="string.digits"> |
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143 <add value=":" /> |
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144 <add value="." /> |
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145 </valid> |
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146 </sanitizer> |
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147 <validator type="regex">[0-9.:]+</validator> |
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148 </param> |
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149 <param argument="--set-id" type="text" value="" optional="true" label="Set Id"> |
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150 <help>Assign ID on the fly using the given format. |
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151 By default all existing IDs are replaced. |
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152 If the format string is preceded by "+", only missing IDs will be set. |
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153 For example: '%CHROM\_%POS\_%REF\_%FIRST_ALT' |
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154 </help> |
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155 <sanitizer sanitize="False"/> |
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156 <validator type="regex" message="">^([+]?(%[A-Z_]+)(\\_%[A-Z_]+)*)?$</validator> |
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157 </param> |
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158 </section> |
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159 <section name="sec_annotate" expanded="false" title="Change Annotations"> |
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160 <param argument="--remove" type="text" value="" label="Remove annotations" optional="true"> |
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161 <help><![CDATA[ |
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162 List of annotations to remove. |
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163 Use "FILTER" to remove all filters or "FILTER/SomeFilter" to remove a specific filter. |
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164 Similarly, "INFO" can be used to remove all INFO tags and "FORMAT" to remove all FORMAT tags except GT. |
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165 To remove all INFO tags except "FOO" and "BAR", use "^INFO/FOO,INFO/BAR" (and similarly for FORMAT and FILTER). |
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166 "INFO" can be abbreviated to "INF" and "FORMAT" to "FMT". |
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167 ]]></help> |
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168 <validator type="regex" message="">^(\^?[A-Z]+(/\w+)?(,\^?[A-Z]+(/\w+)?)*)?$</validator> |
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169 </param> |
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170 <param argument="--rename-chrs" type="data" format="tabular" label="Rename CHROM" optional="true" |
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171 help="rename chromosomes according to the map in file, with old_name new_name pairs separated by whitespaces, each on a separate line." /> |
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172 <param argument="--rename-annots" type="data" format="tabular" optional="true" label="Rename annotations" help="TYPE/old\tnew, where TYPE is one of FILTER,INFO,FORMAT" /> |
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173 </section> |
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174 <section name="sec_restrict" expanded="false" title="Restrict to"> |
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175 <expand macro="macro_include" /> |
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176 <expand macro="macro_exclude" /> |
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177 <expand macro="macro_collapse" /> |
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8
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178 <expand macro="macro_restrict" /> |
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179 <expand macro="macro_samples" /> |
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180 </section> |
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181 <expand macro="macro_select_output_type" /> |
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182 </inputs> |
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183 <outputs> |
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184 <expand macro="macro_vcf_output"/> |
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185 </outputs> |
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186 <tests> |
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187 <test> |
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188 <param name="input_file" ftype="vcf" value="annotate.vcf" /> |
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189 <param name="anno_fmt" value="tab" /> |
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190 <param name="annotations" value="annotate.tab" /> |
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191 <param name="header_file" value="annotate.hdr" /> |
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192 <param name="columns" value="CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL" /> |
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193 <param name="output_type" value="v" /> |
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194 <output name="output_file"> |
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195 <assert_contents> |
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196 <has_text text="snp_3000150" /> |
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197 </assert_contents> |
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198 </output> |
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199 </test> |
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200 <test> |
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201 <param name="input_file" ftype="vcf" value="annotate.vcf" /> |
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202 <section name="sec_annofile"> |
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203 <param name="columns" value="CHROM,FROM,TO,T_STR" /> |
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204 <conditional name="annofile"> |
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205 <param name="anno_fmt" value="tab" /> |
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206 <param name="annotations" value="annotate2.tab" /> |
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207 <param name="header_file" value="annotate.hdr" /> |
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208 </conditional> |
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209 <param name="set_id" value="%CHROM\_%POS\_%REF\_%FIRST_ALT" /> |
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210 </section> |
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211 <param name="output_type" value="v" /> |
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212 <output name="output_file"> |
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213 <assert_contents> |
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214 <has_text text="T_STR=region_3000150_3106154" /> |
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215 <has_text text="1_3062915_GTTT_G" /> |
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216 </assert_contents> |
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217 </output> |
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218 </test> |
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219 <test> |
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220 <param name="input_file" ftype="vcf" value="annotate.vcf" /> |
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221 <param name="anno_fmt" value="vcf" /> |
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222 <param name="annotations" value="annots.vcf" /> |
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223 <param name="columns" value="STR,ID,QUAL,FILTER" /> |
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224 <param name="output_type" value="v" /> |
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225 <output name="output_file"> |
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226 <assert_contents> |
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227 <has_text text="idIndel" /> |
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228 <has_text text="STR=testSNP" /> |
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229 </assert_contents> |
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230 </output> |
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231 </test> |
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232 <test> |
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9
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233 <param name="input_file" ftype="vcf" value="annotate.vcf" /> |
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234 <param name="anno_fmt" value="vcf" /> |
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235 <param name="annotations" value="annots.bcf" /> |
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236 <param name="columns" value="STR,ID,QUAL,FILTER" /> |
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237 <param name="output_type" value="v" /> |
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238 <output name="output_file"> |
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239 <assert_contents> |
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240 <has_text text="idIndel" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 942ca2971ae6a72e548fde6186c6408a1e236653
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241 <has_text text="STR=testSNP" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 942ca2971ae6a72e548fde6186c6408a1e236653
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242 </assert_contents> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 942ca2971ae6a72e548fde6186c6408a1e236653
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243 </output> |
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244 </test> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 942ca2971ae6a72e548fde6186c6408a1e236653
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245 <test> |
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0
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246 <param name="input_file" ftype="vcf" value="annotate2.vcf" /> |
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247 <param name="anno_fmt" value="vcf" /> |
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248 <param name="annotations" value="annots2.vcf" /> |
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249 <param name="columns" value="ID,QUAL,FILTER,INFO,FMT" /> |
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250 <param name="output_type" value="v" /> |
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251 <output name="output_file"> |
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252 <assert_contents> |
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253 <has_text text="q99" /> |
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254 <has_text text="FLAG;IINT=88,99;IFLT=8.8,9.9;ISTR=888,999" /> |
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255 </assert_contents> |
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256 </output> |
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257 </test> |
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258 <test> |
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259 <param name="input_file" ftype="vcf" value="annotate2.vcf" /> |
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260 <param name="anno_fmt" value="vcf" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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261 <param name="annotations" value="annots2.vcf" /> |
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262 <param name="columns" value="ID,QUAL,FILTER,INFO,FMT" /> |
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263 <param name="samples" value="A" /> |
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264 <param name="output_type" value="v" /> |
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265 <output name="output_file"> |
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266 <assert_contents> |
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267 <has_text text="q11" /> |
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268 <has_text text="FLAG;IINT=88,99;IFLT=8.8,9.9;ISTR=888,999" /> |
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269 </assert_contents> |
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270 </output> |
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271 </test> |
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272 <test> |
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273 <param name="input_file" ftype="vcf" value="annotate3.vcf" /> |
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274 <param name="anno_fmt" value="none" /> |
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275 <param name="remove" value="ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL" /> |
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276 <param name="output_type" value="v" /> |
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277 <output name="output_file"> |
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278 <assert_contents> |
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279 <not_has_text text="fltY" /> |
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280 </assert_contents> |
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281 </output> |
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282 </test> |
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283 <test> |
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284 <param name="input_file" ftype="vcf" value="annotate3.vcf" /> |
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285 <param name="anno_fmt" value="none" /> |
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286 <param name="remove" value="FORMAT" /> |
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287 <param name="output_type" value="v" /> |
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288 <output name="output_file"> |
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289 <assert_contents> |
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290 <not_has_text text="GT:X:PL:Y:AA" /> |
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291 </assert_contents> |
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292 </output> |
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293 </test> |
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17
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294 <!-- Test region overlap option --> |
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295 <test> |
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296 <param name="input_file" ftype="vcf" value="annotate3.vcf" /> |
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297 <param name="anno_fmt" value="none" /> |
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298 <param name="remove" value="FORMAT" /> |
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299 <param name="output_type" value="v" /> |
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300 <section name="sec_restrict"> |
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301 <param name="regions_overlap" value="1"/> |
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302 </section> |
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303 <output name="output_file"> |
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304 <assert_contents> |
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305 <not_has_text text="GT:X:PL:Y:AA" /> |
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306 </assert_contents> |
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307 </output> |
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308 <assert_command> |
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309 <has_text text="--regions-overlap" /> |
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310 </assert_command> |
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311 </test> |
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312 <!-- Test min overlap option --> |
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313 <test> |
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314 <param name="input_file" ftype="vcf" value="annotate3.vcf" /> |
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315 <param name="anno_fmt" value="none" /> |
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316 <param name="remove" value="FORMAT" /> |
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317 <param name="output_type" value="v" /> |
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318 <section name="sec_annofile"> |
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319 <param name="min_overlap" value="0.5"/> |
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320 </section> |
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321 <output name="output_file"> |
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322 <assert_contents> |
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323 <not_has_text text="GT:X:PL:Y:AA" /> |
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324 </assert_contents> |
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325 </output> |
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326 <assert_command> |
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327 <has_text text="--min-overlap" /> |
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328 </assert_command> |
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329 </test> |
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330 </tests> |
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331 <help><![CDATA[ |
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332 ================================== |
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333 bcftools @EXECUTABLE@ |
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334 ================================== |
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335 |
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336 Annotate and edit VCF/BCF files. |
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337 |
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338 Examples: |
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339 |
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340 # Remove three fields |
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341 bcftools annotate -x ID,INFO/DP,FORMAT/DP file.vcf.gz |
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342 |
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343 # Remove all INFO fields and all FORMAT fields except for GT and PL |
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344 bcftools annotate -x INFO,^FORMAT/GT,FORMAT/PL file.vcf |
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345 |
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346 # Add ID, QUAL and INFO/TAG, not replacing TAG if already present |
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347 bcftools annotate -a src.bcf -c ID,QUAL,+TAG dst.bcf |
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348 |
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349 # Carry over all INFO and FORMAT annotations except FORMAT/GT |
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350 bcftools annotate -a src.bcf -c INFO,^FORMAT/GT dst.bcf |
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351 |
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352 # Annotate from a tab-delimited file with six columns (the fifth is ignored), |
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353 # first indexing with tabix. The coordinates are 1-based. |
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354 tabix -s1 -b2 -e2 annots.tab.gz |
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355 bcftools annotate -a annots.tab.gz -h annots.hdr -c CHROM,POS,REF,ALT,-,TAG file.vcf |
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356 |
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357 # Annotate from a tab-delimited file with regions (1-based coordinates, inclusive) |
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358 tabix -s1 -b2 -e3 annots.tab.gz |
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359 bcftools annotate -a annots.tab.gz -h annots.hdr -c CHROM,FROM,TO,TAG inut.vcf |
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360 |
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361 # Annotate from a bed file (0-based coordinates, half-closed, half-open intervals) |
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362 bcftools annotate -a annots.bed.gz -h annots.hdr -c CHROM,FROM,TO,TAG input.vcf |
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363 |
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364 @REGIONS_HELP@ |
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365 @EXPRESSIONS_HELP@ |
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366 |
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367 @BCFTOOLS_MANPAGE@#@EXECUTABLE@ |
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368 |
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369 @BCFTOOLS_WIKI@ |
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370 ]]> |
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371 </help> |
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372 <expand macro="citations" /> |
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373 </tool> |