Mercurial > repos > iuc > bcftools_annotate
annotate bcftools_annotate.xml @ 26:bba9853e1fdc draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
| author | iuc |
|---|---|
| date | Tue, 02 Dec 2025 07:55:02 +0000 |
| parents | 65d418d476a5 |
| children |
| rev | line source |
|---|---|
|
0
045dc7e32f84
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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19
65d418d476a5
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
045dc7e32f84
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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045dc7e32f84
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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045dc7e32f84
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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045dc7e32f84
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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045dc7e32f84
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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16
a974b56e4c43
"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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0
045dc7e32f84
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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045dc7e32f84
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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045dc7e32f84
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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045dc7e32f84
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_INPUT_FILE@ |
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045dc7e32f84
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 #set $annotation_file = None |
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045dc7e32f84
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_hdr = None |
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045dc7e32f84
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 $section = $sec_annofile |
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2
67c573d9c1ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 5725fea947162618d77de7b8011d18b2f16c7094
iuc
parents:
0
diff
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16 #if $section.annofile.anno_fmt == 'vcf': |
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365022dae1c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 942ca2971ae6a72e548fde6186c6408a1e236653
iuc
parents:
9
diff
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17 #if $section.annofile.annotations.is_of_type('vcf') |
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365022dae1c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 942ca2971ae6a72e548fde6186c6408a1e236653
iuc
parents:
9
diff
changeset
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18 #set $annotation_file = 'annotations.vcf.gz' |
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17
28647eee857d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ccc967cdce26379110361f8dea521bade23f8612"
iuc
parents:
16
diff
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19 bgzip -c '$section.annofile.annotations' > $annotation_file && |
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10
365022dae1c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 942ca2971ae6a72e548fde6186c6408a1e236653
iuc
parents:
9
diff
changeset
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20 bcftools index $annotation_file && |
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365022dae1c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 942ca2971ae6a72e548fde6186c6408a1e236653
iuc
parents:
9
diff
changeset
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21 #elif $section.annofile.annotations.is_of_type('bcf') |
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365022dae1c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 942ca2971ae6a72e548fde6186c6408a1e236653
iuc
parents:
9
diff
changeset
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22 #set $annotation_file = 'annotations.bcf' |
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365022dae1c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 942ca2971ae6a72e548fde6186c6408a1e236653
iuc
parents:
9
diff
changeset
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23 ln -s '$section.annofile.annotations' $annotation_file && |
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365022dae1c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 942ca2971ae6a72e548fde6186c6408a1e236653
iuc
parents:
9
diff
changeset
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24 #if $section.annofile.annotations.metadata.bcf_index: |
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365022dae1c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 942ca2971ae6a72e548fde6186c6408a1e236653
iuc
parents:
9
diff
changeset
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25 ln -s '${section.annofile.annotations.metadata.bcf_index}' ${annotation_file}.csi && |
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365022dae1c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 942ca2971ae6a72e548fde6186c6408a1e236653
iuc
parents:
9
diff
changeset
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26 #else |
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365022dae1c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 942ca2971ae6a72e548fde6186c6408a1e236653
iuc
parents:
9
diff
changeset
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27 bcftools index $annotation_file && |
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365022dae1c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 942ca2971ae6a72e548fde6186c6408a1e236653
iuc
parents:
9
diff
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28 #end if |
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365022dae1c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 942ca2971ae6a72e548fde6186c6408a1e236653
iuc
parents:
9
diff
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29 #end if |
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0
045dc7e32f84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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30 #elif $section.annofile.anno_fmt == 'tab': |
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2
67c573d9c1ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 5725fea947162618d77de7b8011d18b2f16c7094
iuc
parents:
0
diff
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31 #if $section.annofile.annotations.is_of_type('bed') |
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0
045dc7e32f84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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32 #set $annotation_file = 'annotations.bed.gz' |
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17
28647eee857d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ccc967cdce26379110361f8dea521bade23f8612"
iuc
parents:
16
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33 bgzip -c '$section.annofile.annotations' > $annotation_file && |
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0
045dc7e32f84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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34 tabix -s 1 -b 2 -e 3 $annotation_file && |
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045dc7e32f84
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 #else: |
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045dc7e32f84
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 #set $annotation_file = 'annotations.tab.gz' |
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17
28647eee857d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ccc967cdce26379110361f8dea521bade23f8612"
iuc
parents:
16
diff
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37 bgzip -c '$section.annofile.annotations' > $annotation_file && |
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0
045dc7e32f84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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38 tabix -s 1 -b 2 -e 2 $annotation_file && |
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045dc7e32f84
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 #end if |
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045dc7e32f84
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 #if $section.annofile.header_file: |
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045dc7e32f84
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 #set $annotation_hdr = $section.annofile.header_file |
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045dc7e32f84
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 #elif $section.annofile.header_lines: |
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045dc7e32f84
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 #set $annotation_hdr = 'annotation.hdr' |
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17
28647eee857d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ccc967cdce26379110361f8dea521bade23f8612"
iuc
parents:
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diff
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44 grep '^\#\#INFO' '${hdr_file}' > $annotation_hdr && |
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0
045dc7e32f84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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45 #end if |
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045dc7e32f84
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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5
2dda35928193
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
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47 #set $section = $sec_restrict |
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0
045dc7e32f84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
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48 |
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045dc7e32f84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
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49 bcftools @EXECUTABLE@ |
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5
2dda35928193
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
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50 @PREPARE_REGIONS_FILE@ |
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0
045dc7e32f84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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51 |
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045dc7e32f84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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52 #set $section = $sec_annofile |
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045dc7e32f84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
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53 @COLUMNS@ |
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045dc7e32f84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
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54 #if $annotation_file: |
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17
28647eee857d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ccc967cdce26379110361f8dea521bade23f8612"
iuc
parents:
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55 --annotations '${annotation_file}' |
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0
045dc7e32f84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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56 #end if |
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045dc7e32f84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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57 #if $annotation_hdr: |
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17
28647eee857d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ccc967cdce26379110361f8dea521bade23f8612"
iuc
parents:
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58 --header-lines '${annotation_hdr}' |
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0
045dc7e32f84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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59 #end if |
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045dc7e32f84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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60 |
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045dc7e32f84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
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61 #if $section.set_id: |
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28647eee857d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ccc967cdce26379110361f8dea521bade23f8612"
iuc
parents:
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62 --set-id '${section.set_id}' |
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0
045dc7e32f84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
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63 #end if |
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045dc7e32f84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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64 #if $section.mark_sites: |
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28647eee857d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ccc967cdce26379110361f8dea521bade23f8612"
iuc
parents:
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65 --mark-sites '${section.mark_sites}' |
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0
045dc7e32f84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
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66 #end if |
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19
65d418d476a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents:
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67 #if $section.min_overlap |
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65d418d476a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents:
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68 --min-overlap '$section.min_overlap' |
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65d418d476a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents:
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69 #end if |
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0
045dc7e32f84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
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70 |
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045dc7e32f84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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71 #set $section = $sec_annotate |
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045dc7e32f84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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72 #if $section.rename_chrs: |
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28647eee857d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ccc967cdce26379110361f8dea521bade23f8612"
iuc
parents:
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73 --rename-chrs '${section.rename_chrs}' |
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0
045dc7e32f84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
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74 #end if |
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045dc7e32f84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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75 #if $section.remove: |
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28647eee857d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ccc967cdce26379110361f8dea521bade23f8612"
iuc
parents:
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76 --remove '${section.remove}' |
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0
045dc7e32f84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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77 #end if |
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19
65d418d476a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents:
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78 #if $section.rename_annots |
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65d418d476a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents:
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79 --rename-annots '$section.rename_annots' |
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65d418d476a5
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80 #end if |
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81 |
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82 |
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83 ## Default section |
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84 #set $section = $sec_restrict |
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85 @INCLUDE@ |
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86 @EXCLUDE@ |
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87 @COLLAPSE@ |
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88 @REGIONS@ |
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89 @SAMPLES@ |
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90 |
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91 @OUTPUT_TYPE@ |
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92 @THREADS@ |
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93 |
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94 ## Primary Input/Outputs |
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95 @INPUT_FILE@ |
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96 > '$output_file' |
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97 ]]> |
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98 </command> |
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99 <configfiles> |
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100 <configfile name="hdr_file"><![CDATA[#slurp |
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101 #if $sec_annofile.annofile.anno_fmt == 'tab' and str($sec_annofile.annofile.header_lines) != '': |
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102 $sec_annofile.annofile.header_lines.__str__.strip()#slurp |
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103 #end if]]></configfile> |
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104 </configfiles> |
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105 <inputs> |
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106 <expand macro="macro_input" /> |
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107 <section name="sec_annofile" expanded="false" title="Add Annotations"> |
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108 <expand macro="macro_columns" /> |
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109 <conditional name="annofile"> |
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110 <param name="anno_fmt" type="select" label="Annotations File"> |
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111 <option value="none">None</option> |
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112 <option value="vcf">From a VCF/BCF file</option> |
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113 <option value="tab">From a BED or tab-delimited file</option> |
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114 </param> |
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115 <when value="none"/> |
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116 <when value="vcf"> |
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10
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117 <param name="annotations" type="data" format="vcf,bcf" label="Annotations VCF"/> |
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118 </when> |
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119 <when value="tab"> |
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120 <param name="annotations" type="data" format="tabular,bed" label="Annotations"> |
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121 <help><![CDATA[ |
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122 BED, or a tab-delimited file with mandatory columns CHROM, POS (or, alternatively, FROM and TO), |
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123 optional columns REF and ALT, and arbitrary number of annotation columns. |
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124 Note that in case of tab-delimited file, the coordinates POS, FROM and TO are one-based and inclusive. |
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125 ]]></help> |
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126 </param> |
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127 <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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128 <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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129 <help><![CDATA[ |
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130 ##INFO=<ID=NUMERIC_TAG,Number=1,Type=Integer,Description="Example header line"> |
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131 ##INFO=<ID=STRING_TAG,Number=1,Type=String,Description="Yet another header line"> |
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132 ]]></help> |
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133 <sanitizer sanitize="False"/> |
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134 </param> |
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135 </when> |
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136 </conditional> |
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137 <param argument="--mark-sites" type="text" value="" label="Mark Sites TAG" |
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138 help="add INFO/TAG flag to sites which are ("+") or are not ("-") listed in the annotations file" /> |
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19
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139 <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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140 <sanitizer invalid_char=""> |
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141 <valid initial="string.digits"> |
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142 <add value=":" /> |
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143 <add value="." /> |
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144 </valid> |
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145 </sanitizer> |
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146 <validator type="regex">[0-9.:]+</validator> |
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147 </param> |
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148 <param argument="--set-id" type="text" value="" optional="true" label="Set Id"> |
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149 <help>Assign ID on the fly using the given format. |
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150 By default all existing IDs are replaced. |
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151 If the format string is preceded by "+", only missing IDs will be set. |
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152 For example: '%CHROM\_%POS\_%REF\_%FIRST_ALT' |
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153 </help> |
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154 <sanitizer sanitize="False"/> |
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155 <validator type="regex" message="">^([+]?(%[A-Z_]+)(\\_%[A-Z_]+)*)?$</validator> |
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156 </param> |
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157 </section> |
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158 <section name="sec_annotate" expanded="false" title="Change Annotations"> |
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159 <param argument="--remove" type="text" value="" label="Remove annotations" optional="true"> |
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160 <help><![CDATA[ |
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161 List of annotations to remove. |
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162 Use "FILTER" to remove all filters or "FILTER/SomeFilter" to remove a specific filter. |
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163 Similarly, "INFO" can be used to remove all INFO tags and "FORMAT" to remove all FORMAT tags except GT. |
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164 To remove all INFO tags except "FOO" and "BAR", use "^INFO/FOO,INFO/BAR" (and similarly for FORMAT and FILTER). |
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165 "INFO" can be abbreviated to "INF" and "FORMAT" to "FMT". |
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166 ]]></help> |
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167 <validator type="regex" message="">^(\^?[A-Z]+(/\w+)?(,\^?[A-Z]+(/\w+)?)*)?$</validator> |
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168 </param> |
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169 <param argument="--rename-chrs" type="data" format="tabular" label="Rename CHROM" optional="true" |
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170 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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171 <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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172 </section> |
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173 <section name="sec_restrict" expanded="false" title="Restrict to"> |
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174 <expand macro="macro_include" /> |
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175 <expand macro="macro_exclude" /> |
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176 <expand macro="macro_collapse" /> |
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177 <expand macro="macro_region_restrict" /> |
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178 <expand macro="macro_samples" /> |
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179 </section> |
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180 <expand macro="macro_select_output_type" /> |
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181 </inputs> |
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182 <outputs> |
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183 <expand macro="macro_vcf_output"/> |
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184 </outputs> |
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185 <tests> |
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186 <test> |
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187 <param name="input_file" ftype="vcf" value="annotate.vcf" /> |
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188 <section name="sec_annofile"> |
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189 <conditional name="annofile"> |
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190 <param name="anno_fmt" value="tab" /> |
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191 <param name="annotations" value="annotate.tab" /> |
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192 <param name="header_file" value="annotate.hdr" /> |
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193 </conditional> |
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194 <param name="columns" value="CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL" /> |
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195 </section> |
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196 <param name="output_type" value="v" /> |
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197 <output name="output_file"> |
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198 <assert_contents> |
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199 <has_text text="snp_3000150" /> |
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200 </assert_contents> |
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201 </output> |
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202 </test> |
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203 <test> |
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204 <param name="input_file" ftype="vcf" value="annotate.vcf" /> |
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205 <section name="sec_annofile"> |
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206 <param name="columns" value="CHROM,FROM,TO,T_STR" /> |
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207 <conditional name="annofile"> |
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208 <param name="anno_fmt" value="tab" /> |
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209 <param name="annotations" value="annotate2.tab" /> |
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210 <param name="header_file" value="annotate.hdr" /> |
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211 </conditional> |
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212 <param name="set_id" value="%CHROM\_%POS\_%REF\_%FIRST_ALT" /> |
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213 </section> |
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214 <param name="output_type" value="v" /> |
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215 <output name="output_file"> |
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216 <assert_contents> |
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217 <has_text text="T_STR=region_3000150_3106154" /> |
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218 <has_text text="1_3062915_GTTT_G" /> |
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219 </assert_contents> |
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220 </output> |
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221 </test> |
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222 <test> |
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223 <param name="input_file" ftype="vcf" value="annotate.vcf" /> |
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224 <section name="sec_annofile"> |
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225 <conditional name="annofile"> |
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226 <param name="anno_fmt" value="vcf" /> |
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227 <param name="annotations" value="annots.vcf" /> |
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228 </conditional> |
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229 <param name="columns" value="STR,ID,QUAL,FILTER" /> |
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230 </section> |
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231 <param name="output_type" value="v" /> |
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232 <output name="output_file"> |
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233 <assert_contents> |
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234 <has_text text="idIndel" /> |
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235 <has_text text="STR=testSNP" /> |
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236 </assert_contents> |
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237 </output> |
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238 </test> |
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239 <test> |
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240 <param name="input_file" ftype="vcf" value="annotate.vcf" /> |
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26
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
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241 <section name="sec_annofile"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
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242 <conditional name="annofile"> |
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bba9853e1fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
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243 <param name="anno_fmt" value="vcf" /> |
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bba9853e1fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
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244 <param name="annotations" value="annots.bcf" /> |
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bba9853e1fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
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245 </conditional> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
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246 <param name="columns" value="STR,ID,QUAL,FILTER" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
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247 </section> |
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10
365022dae1c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 942ca2971ae6a72e548fde6186c6408a1e236653
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248 <param name="output_type" value="v" /> |
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365022dae1c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 942ca2971ae6a72e548fde6186c6408a1e236653
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249 <output name="output_file"> |
|
365022dae1c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 942ca2971ae6a72e548fde6186c6408a1e236653
iuc
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250 <assert_contents> |
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365022dae1c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 942ca2971ae6a72e548fde6186c6408a1e236653
iuc
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251 <has_text text="idIndel" /> |
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365022dae1c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 942ca2971ae6a72e548fde6186c6408a1e236653
iuc
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252 <has_text text="STR=testSNP" /> |
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365022dae1c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 942ca2971ae6a72e548fde6186c6408a1e236653
iuc
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253 </assert_contents> |
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365022dae1c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 942ca2971ae6a72e548fde6186c6408a1e236653
iuc
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254 </output> |
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365022dae1c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 942ca2971ae6a72e548fde6186c6408a1e236653
iuc
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255 </test> |
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365022dae1c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 942ca2971ae6a72e548fde6186c6408a1e236653
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256 <test> |
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0
045dc7e32f84
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257 <param name="input_file" ftype="vcf" value="annotate2.vcf" /> |
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26
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258 <section name="sec_annofile"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
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259 <conditional name="annofile"> |
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bba9853e1fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
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260 <param name="anno_fmt" value="vcf" /> |
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bba9853e1fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
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261 <param name="annotations" value="annots2.vcf" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
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262 </conditional> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
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263 <param name="columns" value="ID,QUAL,FILTER,INFO,FMT" /> |
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bba9853e1fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
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264 </section> |
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0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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265 <param name="output_type" value="v" /> |
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045dc7e32f84
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266 <output name="output_file"> |
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045dc7e32f84
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267 <assert_contents> |
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268 <has_text text="q99" /> |
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269 <has_text text="FLAG;IINT=88,99;IFLT=8.8,9.9;ISTR=888,999" /> |
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270 </assert_contents> |
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271 </output> |
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272 </test> |
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273 <test> |
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274 <param name="input_file" ftype="vcf" value="annotate2.vcf" /> |
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26
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
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275 <section name="sec_annofile"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
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276 <conditional name="annofile"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
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277 <param name="anno_fmt" value="vcf" /> |
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bba9853e1fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
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278 <param name="annotations" value="annots2.vcf" /> |
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bba9853e1fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
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279 </conditional> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
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280 <param name="columns" value="ID,QUAL,FILTER,INFO,FMT" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
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281 </section> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
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282 <section name="sec_restrict"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
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283 <param name="samples" value="A" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
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284 </section> |
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0
045dc7e32f84
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285 <param name="output_type" value="v" /> |
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045dc7e32f84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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286 <output name="output_file"> |
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287 <assert_contents> |
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288 <has_text text="q11" /> |
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289 <has_text text="FLAG;IINT=88,99;IFLT=8.8,9.9;ISTR=888,999" /> |
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290 </assert_contents> |
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291 </output> |
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292 </test> |
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293 <test> |
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294 <param name="input_file" ftype="vcf" value="annotate3.vcf" /> |
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26
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295 <section name="sec_annofile"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
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296 <conditional name="annofile"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
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297 <param name="anno_fmt" value="none" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
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298 </conditional> |
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299 </section> |
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300 <section name="sec_annotate"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
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301 <param name="remove" value="ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
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302 </section> |
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0
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303 <param name="output_type" value="v" /> |
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304 <output name="output_file"> |
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305 <assert_contents> |
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306 <not_has_text text="fltY" /> |
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307 </assert_contents> |
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308 </output> |
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309 </test> |
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310 <test> |
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311 <param name="input_file" ftype="vcf" value="annotate3.vcf" /> |
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26
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312 <section name="sec_annofile"> |
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313 <conditional name="annofile"> |
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314 <param name="anno_fmt" value="none" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
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315 </conditional> |
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316 </section> |
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317 <section name="sec_annotate"> |
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318 <param name="remove" value="FORMAT" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
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319 </section> |
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0
045dc7e32f84
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320 <param name="output_type" value="v" /> |
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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 </test> |
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327 <!-- Test region overlap option --> |
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328 <test> |
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329 <param name="input_file" ftype="vcf" value="annotate3.vcf" /> |
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330 <section name="sec_annofile"> |
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331 <conditional name="annofile"> |
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332 <param name="anno_fmt" value="none" /> |
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333 </conditional> |
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334 </section> |
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335 <section name="sec_annotate"> |
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336 <param name="remove" value="FORMAT" /> |
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337 </section> |
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338 <param name="output_type" value="v" /> |
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339 <section name="sec_restrict"> |
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26
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340 <conditional name="regions"> |
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341 <param name="regions_src" value="regions" /> |
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342 <repeat name="region_specs"> |
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343 <param name="chrom" value="1" /> |
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344 </repeat> |
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345 </conditional> |
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346 </section> |
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347 <output name="output_file"> |
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348 <assert_contents> |
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349 <not_has_text text="GT:X:PL:Y:AA" /> |
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350 </assert_contents> |
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351 </output> |
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352 <assert_command> |
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353 <has_text text="--regions-overlap" /> |
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354 </assert_command> |
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355 </test> |
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356 <!-- Test min overlap option --> |
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357 <test> |
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358 <param name="input_file" ftype="vcf" value="annotate3.vcf" /> |
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359 <section name="sec_annofile"> |
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26
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360 <conditional name="annofile"> |
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361 <param name="anno_fmt" value="none" /> |
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362 </conditional> |
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19
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363 <param name="min_overlap" value="0.5"/> |
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364 </section> |
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26
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365 <section name="sec_annotate"> |
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366 <param name="remove" value="FORMAT" /> |
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367 </section> |
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368 <param name="output_type" value="v" /> |
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369 <output name="output_file"> |
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370 <assert_contents> |
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371 <not_has_text text="GT:X:PL:Y:AA" /> |
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372 </assert_contents> |
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373 </output> |
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374 <assert_command> |
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375 <has_text text="--min-overlap" /> |
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376 </assert_command> |
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377 </test> |
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0
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378 </tests> |
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379 <help><![CDATA[ |
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380 ================================== |
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381 bcftools @EXECUTABLE@ |
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382 ================================== |
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383 |
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384 Annotate and edit VCF/BCF files. |
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385 |
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386 Examples: |
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387 |
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388 # Remove three fields |
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389 bcftools annotate -x ID,INFO/DP,FORMAT/DP file.vcf.gz |
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390 |
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391 # Remove all INFO fields and all FORMAT fields except for GT and PL |
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392 bcftools annotate -x INFO,^FORMAT/GT,FORMAT/PL file.vcf |
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393 |
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394 # Add ID, QUAL and INFO/TAG, not replacing TAG if already present |
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395 bcftools annotate -a src.bcf -c ID,QUAL,+TAG dst.bcf |
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396 |
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397 # Carry over all INFO and FORMAT annotations except FORMAT/GT |
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398 bcftools annotate -a src.bcf -c INFO,^FORMAT/GT dst.bcf |
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399 |
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400 # Annotate from a tab-delimited file with six columns (the fifth is ignored), |
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401 # first indexing with tabix. The coordinates are 1-based. |
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402 tabix -s1 -b2 -e2 annots.tab.gz |
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403 bcftools annotate -a annots.tab.gz -h annots.hdr -c CHROM,POS,REF,ALT,-,TAG file.vcf |
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404 |
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045dc7e32f84
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405 # Annotate from a tab-delimited file with regions (1-based coordinates, inclusive) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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406 tabix -s1 -b2 -e3 annots.tab.gz |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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407 bcftools annotate -a annots.tab.gz -h annots.hdr -c CHROM,FROM,TO,TAG inut.vcf |
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408 |
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045dc7e32f84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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409 # Annotate from a bed file (0-based coordinates, half-closed, half-open intervals) |
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045dc7e32f84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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410 bcftools annotate -a annots.bed.gz -h annots.hdr -c CHROM,FROM,TO,TAG input.vcf |
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411 |
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412 @REGIONS_HELP@ |
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413 @EXPRESSIONS_HELP@ |
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414 |
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415 @BCFTOOLS_MANPAGE@#@EXECUTABLE@ |
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416 |
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26
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417 @BCFTOOLS_HOWTOS@ |
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418 ]]> |
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419 </help> |
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420 <expand macro="citations" /> |
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421 </tool> |