Mercurial > repos > iuc > bcftools_concat
annotate bcftools_concat.xml @ 22:74303445f6bd draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 868f4386992de55d25da197660a43a913a09c8df
author | iuc |
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date | Wed, 14 Aug 2024 16:40:38 +0000 |
parents | 03e0645395d2 |
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rev | line source |
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dda05d07d7d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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1 <?xml version='1.0' encoding='utf-8'?> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
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2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
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dda05d07d7d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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3 <description>Concatenate or combine VCF/BCF files</description> |
dda05d07d7d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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4 <macros> |
dda05d07d7d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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5 <token name="@EXECUTABLE@">concat</token> |
dda05d07d7d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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6 <import>macros.xml</import> |
dda05d07d7d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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7 </macros> |
15
fc47ffec447e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit af43d9cf6824f88726900857116f333ff4cdd336"
iuc
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8 <expand macro="bio_tools" /> |
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dda05d07d7d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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9 <expand macro="requirements" /> |
dda05d07d7d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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10 <expand macro="version_command" /> |
dda05d07d7d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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11 <command detect_errors="aggressive"><![CDATA[ |
dda05d07d7d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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12 @PREPARE_ENV@ |
dda05d07d7d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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13 @PREPARE_INPUT_FILES@ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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14 #set $section = $sec_restrict |
40174941cbda
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
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15 @PREPARE_REGIONS_FILE@ |
40174941cbda
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
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16 |
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dda05d07d7d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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17 bcftools @EXECUTABLE@ |
dda05d07d7d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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18 |
dda05d07d7d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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19 ## Default section |
dda05d07d7d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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20 #set $section = $sec_default |
dda05d07d7d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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21 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e2075caee2ecdc6aed15a356e5328c5ca09cfb13
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22 #if $section.mode.naive == "yes": |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
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23 --naive |
62ca6da715bf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents:
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24 #else: |
62ca6da715bf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents:
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25 #if $section.mode.overlaps.allow_overlaps == 'yes': |
62ca6da715bf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
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26 --allow-overlaps |
62ca6da715bf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
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27 #if $section.mode.overlaps.rm_dups: |
62ca6da715bf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents:
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28 --rm-dups $section.mode.overlaps.rm_dups |
62ca6da715bf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
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29 #end if |
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2d95ed0b720a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e2075caee2ecdc6aed15a356e5328c5ca09cfb13
iuc
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30 #end if |
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62ca6da715bf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
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31 ${section.mode.ligate} |
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03e0645395d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
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32 #if $section.mode.ligate_mode |
03e0645395d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
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33 $section.mode.ligate_mode |
03e0645395d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
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34 #end if |
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dda05d07d7d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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35 #end if |
dda05d07d7d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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36 ${section.compact_PS} |
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62ca6da715bf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
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37 #if str($section.min_PQ): |
62ca6da715bf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
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38 --min-PQ ${section.min_PQ} |
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dda05d07d7d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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39 #end if |
dda05d07d7d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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40 |
dda05d07d7d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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41 #set $section = $sec_restrict |
dda05d07d7d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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42 @REGIONS@ |
dda05d07d7d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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43 |
dda05d07d7d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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44 @OUTPUT_TYPE@ |
dda05d07d7d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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45 @THREADS@ |
dda05d07d7d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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46 |
dda05d07d7d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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47 ## Primary Input/Outputs |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
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48 @INPUT_FILES@ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e2075caee2ecdc6aed15a356e5328c5ca09cfb13
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49 #if $sec_default.mode.naive == "yes" and $output_type == 'v': |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
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50 > output.gz && bcftools index output.gz && bcftools view -O v -o '$output_file' output.gz |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e2075caee2ecdc6aed15a356e5328c5ca09cfb13
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51 #else: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
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52 > '$output_file' |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e2075caee2ecdc6aed15a356e5328c5ca09cfb13
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53 #end if |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
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54 ]]></command> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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55 <inputs> |
dda05d07d7d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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56 <expand macro="macro_inputs" /> |
dda05d07d7d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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57 <section name="sec_restrict" expanded="false" title="Restrict to"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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58 <expand macro="macro_restrict" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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59 </section> |
dda05d07d7d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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60 <section name="sec_default" expanded="true" title="Concat Options"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e2075caee2ecdc6aed15a356e5328c5ca09cfb13
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61 <conditional name="mode"> |
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62 <param argument="--naive" type="select" label="Naive concat"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e2075caee2ecdc6aed15a356e5328c5ca09cfb13
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63 <help><![CDATA[ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
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64 --naive concatenates VCF or BCF files without recompression. This can be used used to combine results that were generated separately for each chromosome. This is very fast but requires that all files are of the same type (all VCF or all BCF) and have the same headers. This is because all tags and chromosome names in the BCF body rely on the implicit order of the contig and tag definitions in the header. Currently no sanity checks are in place. Dangerous, use with caution. |
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2d95ed0b720a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e2075caee2ecdc6aed15a356e5328c5ca09cfb13
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65 ]]></help> |
2d95ed0b720a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e2075caee2ecdc6aed15a356e5328c5ca09cfb13
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66 <option value="no">No </option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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67 <option value="yes">Yes </option> |
dda05d07d7d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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68 </param> |
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69 <when value="yes"/> |
2d95ed0b720a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e2075caee2ecdc6aed15a356e5328c5ca09cfb13
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70 <when value="no"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e2075caee2ecdc6aed15a356e5328c5ca09cfb13
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71 <conditional name="overlaps"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
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72 <param name="allow_overlaps" type="select" label="Allow Overlaps"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e2075caee2ecdc6aed15a356e5328c5ca09cfb13
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73 <help> |
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74 First coordinate of the next file can precede last record of the current file. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e2075caee2ecdc6aed15a356e5328c5ca09cfb13
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75 </help> |
2d95ed0b720a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e2075caee2ecdc6aed15a356e5328c5ca09cfb13
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76 <option value="yes">Yes </option> |
2d95ed0b720a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e2075caee2ecdc6aed15a356e5328c5ca09cfb13
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77 <option value="no">No </option> |
2d95ed0b720a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e2075caee2ecdc6aed15a356e5328c5ca09cfb13
iuc
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78 </param> |
2d95ed0b720a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e2075caee2ecdc6aed15a356e5328c5ca09cfb13
iuc
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79 <when value="yes"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
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80 <param name="rm_dups" type="select" label="Remove duplicate" optional="true"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e2075caee2ecdc6aed15a356e5328c5ca09cfb13
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81 <help><![CDATA[ |
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82 Output duplicate records present in multiple files only once: |
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83 rm-dups <snps|indels|both|all|none> |
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84 ]]></help> |
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85 <option value="snps">snps - SNP records</option> |
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86 <option value="indels">indels - indel records</option> |
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87 <option value="both">both - both SNP and indel records</option> |
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88 <option value="all">all - records</option> |
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89 <option value="none">none - output multiple records instead</option> |
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90 </param> |
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91 </when> |
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92 <when value="no"/> |
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93 </conditional> |
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94 <param name="ligate" type="boolean" truevalue="--ligate" falsevalue="" label="Ligate" |
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95 help="Ligate phased VCFs by matching phase at overlapping haplotypes" /> |
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96 <param name="ligate_mode" type="select" optional="true" label="Ligate mode" help="It allows finer control of --ligate behavior"> |
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97 <option value="--ligate-warn">Ligate warn: Drop sites that are present in one chunk but absent in the other (--ligate-warn)</option> |
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98 <option value="--ligate-force">Ligate force: Kepp sites that are present only in one chunk (--ligate-force)</option> |
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99 </param> |
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100 </when> |
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101 </conditional> |
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102 <param name="compact_PS" type="boolean" truevalue="--compact-PS" falsevalue="" label="Compact Ps" |
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103 help="Do not output PS tag at each site, only at the start of a new phase set block." /> |
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104 <param name="min_PQ" type="integer" label="Min Pq" value="30" optional="true" |
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105 help="Break phase set if phasing quality is lower than <int>" /> |
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106 </section> |
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107 <expand macro="macro_select_output_type" /> |
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108 </inputs> |
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109 <outputs> |
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110 <expand macro="macro_vcf_output"/> |
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111 </outputs> |
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112 <tests> |
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113 <test> |
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114 <param name="input_files" ftype="vcf" value="concat.1.b.vcf,concat.1.a.vcf" /> |
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115 <param name="output_type" value="v" /> |
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116 <output name="output_file"> |
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117 <assert_contents> |
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118 <has_text_matching expression="1\t100"/> |
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119 <has_text_matching expression="3\t192"/> |
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120 </assert_contents> |
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121 </output> |
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122 </test> |
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123 <test> |
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124 <param name="input_files" ftype="vcf" value="concat.1.b.vcf,concat.1.a.vcf" /> |
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125 <param name="naive" value="no" /> |
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126 <param name="output_type" value="v" /> |
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127 <output name="output_file"> |
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128 <assert_contents> |
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129 <has_text_matching expression="1\t100"/> |
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130 <has_text_matching expression="3\t192"/> |
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131 </assert_contents> |
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132 </output> |
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133 </test> |
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134 <test> |
0
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135 <param name="input_files" ftype="vcf" value="concat.2.b.vcf,concat.2.a.vcf" /> |
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136 <param name="allow_overlaps" value="yes" /> |
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137 <param name="output_type" value="v" /> |
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138 <output name="output_file"> |
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139 <assert_contents> |
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140 <has_text_matching expression="2\t140\t.\tA\tG"/> |
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141 <has_text_matching expression="2\t140\t.\tGT\tG"/> |
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142 </assert_contents> |
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143 </output> |
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144 </test> |
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145 <test> |
0
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146 <param name="input_files" ftype="vcf" value="concat.2.b.vcf,concat.2.a.vcf" /> |
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147 <param name="allow_overlaps" value="yes" /> |
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148 <param name="rm_dups" value="none" /> |
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149 <param name="output_type" value="v" /> |
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150 <output name="output_file"> |
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151 <assert_contents> |
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152 <has_text_matching expression="2\t160\t.\tTAAAA"/> |
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153 </assert_contents> |
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154 </output> |
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155 </test> |
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156 <!-- Test region overlap--> |
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157 <test> |
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158 <param name="input_files" ftype="vcf" value="concat.1.b.vcf,concat.1.a.vcf" /> |
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159 <param name="output_type" value="v" /> |
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160 <section name="sec_restrict"> |
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161 <param name="regions_overlap" value="1"/> |
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162 </section> |
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163 <output name="output_file"> |
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164 <assert_contents> |
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165 <has_text_matching expression="1\t100"/> |
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166 <has_text_matching expression="3\t192"/> |
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167 </assert_contents> |
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168 </output> |
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169 <assert_command> |
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170 <has_text text="--regions-overlap" /> |
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171 </assert_command> |
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172 </test> |
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173 <!-- Test ligate options --> |
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174 <test> |
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175 <param name="input_files" ftype="vcf" value="concat.1.b.vcf,concat.1.a.vcf" /> |
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176 <param name="output_type" value="v" /> |
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177 <section name="sec_default"> |
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178 <conditional name="mode"> |
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179 <conditional name="overlaps"> |
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180 <param name="allow_overlaps" value="no"/> |
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181 </conditional> |
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182 <param name="ligate" value="true"/> |
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183 <param name="ligate_mode" value="--ligate-warn"/> |
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184 </conditional> |
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185 </section> |
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186 <output name="output_file"> |
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187 <assert_contents> |
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188 <has_text_matching expression="1\t100"/> |
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189 <has_text_matching expression="3\t192"/> |
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190 </assert_contents> |
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191 </output> |
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192 <assert_command> |
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193 <has_text text="--ligate-warn" /> |
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194 </assert_command> |
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195 </test> |
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196 </tests> |
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197 <help><![CDATA[ |
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198 ===================================== |
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199 bcftools @EXECUTABLE@ plugin |
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200 ===================================== |
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201 |
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202 Concatenate or combine VCF/BCF files. All source files must have the same sample columns appearing in the same order. The program can be used, for example, to concatenate chromosome VCFs into one VCF, or combine a SNP VCF and an indel VCF into one. The input files must be sorted by chr and position. The files must be given in the correct order to produce sorted VCF on output unless the -a, --allow-overlaps option is specified. |
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203 |
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204 |
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205 Naive concatenation is useful when using a galaxy workflow that splits a BAM file by chromosome, processes each in parallel, then bcftools concat merges the results into a single VCF file: |
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206 |
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207 BAM -> bamtools split => bcftools mpileup => bcftools call => bcftools concat -> VCF |
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208 |
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209 |
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210 @REGIONS_HELP@ |
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211 |
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212 @BCFTOOLS_MANPAGE@#@EXECUTABLE@ |
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213 |
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214 @BCFTOOLS_WIKI@ |
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215 ]]></help> |
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216 <expand macro="citations" /> |
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217 </tool> |