Mercurial > repos > iuc > bcftools_stats
annotate bcftools_stats.xml @ 20:bf8325a07ce7 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bfc4ff4956b94885638ae07a2560bac5f84fcca8
author | iuc |
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date | Tue, 16 Jul 2024 17:04:38 +0000 |
parents | a2f8dc22d7c0 |
children | 591cc8518033 |
rev | line source |
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0
92e47ae9a121
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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92e47ae9a121
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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3 <description>Parses VCF or BCF and produces stats which can be plotted using plot-vcfstats</description> |
92e47ae9a121
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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4 <macros> |
92e47ae9a121
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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5 <token name="@EXECUTABLE@">stats</token> |
92e47ae9a121
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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6 <import>macros.xml</import> |
92e47ae9a121
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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7 </macros> |
14
80844da35ed5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit af43d9cf6824f88726900857116f333ff4cdd336"
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8 <expand macro="bio_tools" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
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9 <expand macro="requirements"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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10 <expand macro="samtools_requirement"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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11 <expand macro="matplotlib_requirement" /> |
19
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 96c0663be587b73bdf09ddf060cb559f28f9eba7
iuc
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12 <requirement type="package" version="0.12.0">tectonic</requirement> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
iuc
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13 </expand> |
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92e47ae9a121
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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14 <expand macro="version_command" /> |
92e47ae9a121
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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15 <command detect_errors="aggressive"><![CDATA[ |
92e47ae9a121
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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16 @PREPARE_ENV@ |
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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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17 #set $input_files = [$input_file] |
baa8823f8073
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
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18 #if $inputB_file: |
baa8823f8073
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents:
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19 #silent $input_files.append($inputB_file) |
baa8823f8073
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
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20 #end if |
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92e47ae9a121
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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21 @PREPARE_INPUT_FILES@ |
92e47ae9a121
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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22 #set $section = $sec_restrict |
92e47ae9a121
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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23 @PREPARE_TARGETS_FILE@ |
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3afcc6474c79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
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24 @PREPARE_REGIONS_FILE@ |
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92e47ae9a121
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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25 ## Stats section |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
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26 #set $section = $sec_default.reference_source |
e3c64225cbe6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
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27 @PREPARE_FASTA_REF@ |
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92e47ae9a121
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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28 #set $section = $sec_default |
92e47ae9a121
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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29 @PREPARE_EXONS_FILE@ |
92e47ae9a121
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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30 |
92e47ae9a121
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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31 bcftools @EXECUTABLE@ |
92e47ae9a121
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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32 |
92e47ae9a121
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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33 ## Stats section |
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e3c64225cbe6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
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34 #set $section = $sec_default.reference_source |
e3c64225cbe6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
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35 @FASTA_REF@ |
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92e47ae9a121
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
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36 #set $section = $sec_default |
92e47ae9a121
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
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37 @EXONS_FILE@ |
92e47ae9a121
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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38 ${section.first_allele_only} |
92e47ae9a121
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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39 #if $section.depth.set_depth == '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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40 --depth ${section.depth.depth_min},${section.depth.depth_max},${section.depth.depth_bin_size} |
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92e47ae9a121
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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41 #end if |
92e47ae9a121
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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42 #if $section.user_tstv: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
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43 --user-tstv '${section.user_tstv}' |
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92e47ae9a121
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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44 #end if |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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45 #if $section.afbins.afbins_select == 'af_bins_list': |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
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46 --af-bins '$section.afbins.af_bins_list' |
5
3afcc6474c79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
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47 #elif $section.afbins.afbins_select == 'af_bins_file': |
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baa8823f8073
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
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48 --af-bins '$section.afbins.af_bins_file' |
5
3afcc6474c79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
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49 #end if |
3afcc6474c79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
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50 #if $section.af_tag: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
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51 --af-tag '${section.af_tag}' |
5
3afcc6474c79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
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52 #end if |
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92e47ae9a121
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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53 #if len($input_vcfs) == 1: |
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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 ${section.split_by_ID} |
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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 #end if |
92e47ae9a121
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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56 ${section.verbose} |
92e47ae9a121
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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57 |
92e47ae9a121
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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58 ## Stats section |
92e47ae9a121
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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59 #set $section = $sec_restrict |
92e47ae9a121
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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60 @APPLY_FILTERS@ |
92e47ae9a121
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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61 @COLLAPSE@ |
92e47ae9a121
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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62 @REGIONS@ |
92e47ae9a121
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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63 @SAMPLES@ |
92e47ae9a121
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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64 @TARGETS@ |
92e47ae9a121
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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65 @INCLUDE@ |
92e47ae9a121
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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66 @EXCLUDE@ |
92e47ae9a121
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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67 |
92e47ae9a121
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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68 ## Primary Input/Outputs |
92e47ae9a121
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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69 @INPUT_FILES@ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
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70 > '$output_file' |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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71 #if $plot_title: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
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72 && plot-vcfstats |
baa8823f8073
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
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73 -p 'plot_tmp/' |
baa8823f8073
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
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74 -T '$plot_title' |
baa8823f8073
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
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75 -s |
baa8823f8073
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
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76 '$output_file' |
baa8823f8073
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
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77 || (printf "The content of plot_tmp/plot-vcfstats.log is:\n" >&2 && cat plot_tmp/plot-vcfstats.log >&2 && exit 1) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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78 #end if |
7
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
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79 ]]></command> |
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92e47ae9a121
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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80 <inputs> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
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81 <expand macro="macro_input" /> |
baa8823f8073
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
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82 <param name="inputB_file" type="data" format="vcf,vcf_bgzip,bcf" optional="true" label="Optional VCF/BCF Data to compare against" help="When this second dataset is also specified, separate stats for intersection and the complements are generated" /> |
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83 <section name="sec_restrict" expanded="false" title="Restrict to"> |
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84 <expand macro="macro_samples" /> |
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85 <expand macro="macro_apply_filters" /> |
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86 <expand macro="macro_collapse" /> |
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87 <expand macro="macro_restrict" /> |
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88 <expand macro="macro_restrict" type="target" label_type="Target" /> |
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89 <expand macro="macro_include" /> |
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90 <expand macro="macro_exclude" /> |
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91 </section> |
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92 <section name="sec_default" expanded="true" title="Stats options"> |
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93 <param name="first_allele_only" type="boolean" truevalue="--1st-allele-only" falsevalue="" label="First allele only" |
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94 help="Include only first allele at multiallelic sites" /> |
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95 <conditional name="depth"> |
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96 <param name="set_depth" type="select" label="Depth distribution"> |
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97 <option value="no">Use depth defaults</option> |
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98 <option value="yes">Set depth values</option> |
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99 </param> |
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100 <when value="no"/> |
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101 <when value="yes"> |
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102 <param name="depth_min" type="integer" value="0" min="0" label="Depth min"/> |
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103 <param name="depth_max" type="integer" value="500" min="1" label="Depth max" /> |
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104 <param name="depth_bin_size" type="integer" value="1" min="1" label="Depth bin size" /> |
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105 </when> |
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106 </conditional> |
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107 <conditional name="reference_source"> |
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108 <param name="reference_source_selector" type="select" label="Choose a reference genome"> |
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109 <option value="">Run without a reference genome</option> |
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110 <option value="cached">Use a built-in genome</option> |
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111 <option value="history">Use a genome from the history</option> |
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112 </param> |
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113 <when value="" /> |
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114 <when value="cached"> |
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115 <param name="fasta_ref" type="select" label="Reference genome"> |
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116 <options from_data_table="fasta_indexes"> |
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117 <filter type="data_meta" column="dbkey" key="dbkey" ref="input_file" /> |
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118 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file" /> |
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119 </options> |
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120 </param> |
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121 </when> |
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122 <when value="history"> |
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123 <param name="fasta_ref" type="data" format="fasta" label="Reference genome" /> |
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124 </when> |
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125 </conditional> |
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126 <expand macro="macro_exons_file" /> |
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127 <param name="split_by_ID" type="boolean" truevalue="--split-by-ID" falsevalue="" label="Split by ID (ignored on multiple inputs)" |
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128 help="Collect stats for sites with ID separately (known vs novel)" /> |
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129 <param name="user_tstv" type="text" value="" optional="true" label="User Tstv" |
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130 help="Collect Ts/Tv stats for any tag using the given binning: TAG[:min:max:binsize]" > |
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131 <validator type="regex" message="TAG optionally followed by :min:max:binsize">^([^ \t\n\r\f\v:,](:\d+:\d+:\d+)?)?$</validator> |
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132 </param> |
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133 <conditional name="afbins"> |
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134 <param name="afbins_select" type="select" label="Set af-bins"> |
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135 <option value="default">Use default</option> |
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136 <option value="af_bins_list">Enter bins</option> |
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137 <option value="af_bins_file">Read bins from file</option> |
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138 </param> |
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139 <when value="default"/> |
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140 <when value="af_bins_list"> |
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141 <param name="af_bins_list" type="text" value="0.1,0.5,1" label="List of allele frequency bins" help="e.g. 0.1,0.5,1"> |
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142 <validator type="regex" message="Comma-separated list of floats of increasing value">^[-+]?(\d+(\.\d*)?|\.\d+)([eE][-+]?\d+)?(,[-+]?(\d+(\.\d*)?|\.\d+)([eE][-+]?\d+)?)*$</validator> |
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143 </param> |
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144 </when> |
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145 <when value="af_bins_file"> |
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146 <param name="af_bins_file" type="data" format="tabular" label="File listing the allele frequency bins one per line"/> |
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147 </when> |
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148 </conditional> |
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149 <param name="af_tag" type="text" value="" optional="true" label="Allele frequency tag to use, by default estimated from AN,AC or GT"> |
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150 <validator type="regex" message="TAG">^\w*$</validator> |
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151 </param> |
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152 <param name="verbose" type="boolean" truevalue="--verbose" falsevalue="" label="Verbose" |
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153 help="Produce verbose per-site and per-sample output" /> |
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154 </section> |
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155 <param name="plot_title" type="text" value="" optional="true" label="Create a plots pdf with this title"> |
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156 <validator type="regex" message="">^\w.*\w$</validator> |
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157 </param> |
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158 </inputs> |
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159 <outputs> |
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160 <data name="output_file" format="txt" label="${tool.name} on ${on_string}: txt" /> |
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161 <data name="output_pdf" format="pdf" label="${tool.name} on ${on_string}: PDF" from_work_dir="plot_tmp/summary.pdf"> |
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162 <filter>plot_title</filter> |
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163 </data> |
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164 </outputs> |
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165 <tests> |
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166 <test expect_num_outputs="1"> |
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167 <param name="input_file" ftype="vcf" value="stats.b.vcf" /> |
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168 <param name="inputB_file" ftype="vcf" value="stats.a.vcf" /> |
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169 <output name="output_file"> |
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170 <assert_contents> |
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171 <has_text_matching expression="SN\t0\tnumber of samples:\t3"/> |
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172 <has_text_matching expression="SN\t1\tnumber of samples:\t3"/> |
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173 </assert_contents> |
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174 </output> |
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175 </test> |
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176 <test expect_num_outputs="1"> |
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177 <param name="input_file" ftype="vcf" value="mpileup.vcf" /> |
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178 <section name="sec_default"> |
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179 <expand macro="test_using_reference" select_from="cached" ref="mpileup" /> |
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180 </section> |
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181 <output name="output_file"> |
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182 <assert_contents> |
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183 <has_text_matching expression="SN\t0\tnumber of samples:\t3"/> |
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184 <has_text_matching expression="SN\t0\tnumber of records:\t4103"/> |
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185 <has_text_matching expression="ST\t0\tA>C\t16"/> |
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186 </assert_contents> |
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187 </output> |
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188 </test> |
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189 <test expect_num_outputs="2"> |
8
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190 <param name="input_file" ftype="vcf" value="mpileup.vcf" /> |
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191 <param name="plot_title" value="Plot for mpileup.vcf" /> |
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192 <output name="output_file"> |
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193 <assert_contents> |
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194 <has_text_matching expression="SN\t0\tnumber of samples:\t3"/> |
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195 <has_text_matching expression="SN\t0\tnumber of records:\t4103"/> |
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196 <has_text_matching expression="ST\t0\tA>C\t16"/> |
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197 </assert_contents> |
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198 </output> |
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199 <output name="output_pdf" file="summary.pdf" compare="sim_size" delta="25000" /> |
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200 </test> |
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201 <!-- Test region overlap option--> |
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202 <test expect_num_outputs="1"> |
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203 <param name="input_file" ftype="vcf" value="stats.b.vcf" /> |
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204 <param name="inputB_file" ftype="vcf" value="stats.a.vcf" /> |
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205 <section name="sec_restrict"> |
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206 <param name="regions_overlap" value="1"/> |
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207 </section> |
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208 <output name="output_file"> |
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209 <assert_contents> |
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210 <has_text_matching expression="SN\t0\tnumber of samples:\t3"/> |
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211 <has_text_matching expression="SN\t1\tnumber of samples:\t3"/> |
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212 </assert_contents> |
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213 </output> |
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214 <assert_command> |
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215 <has_text text="--regions-overlap" /> |
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216 </assert_command> |
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217 </test> |
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218 <!-- Test VCF.gz input file -> REQUIRES https://github.com/galaxyproject/galaxy/pull/14605 |
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219 <test expect_num_outputs="1"> |
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220 <param name="input_file" value="mpileup.vcf.gz" /> |
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221 <output name="output_file"> |
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222 <assert_contents> |
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223 <has_text_matching expression="bcftools stats input0.vcf.gz"/> |
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224 <has_text_matching expression="SN\t0\tnumber of samples:\t3"/> |
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225 <has_text_matching expression="SN\t0\tnumber of records:\t4103"/> |
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226 </assert_contents> |
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227 </output> |
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228 </test> |
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229 --> |
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230 <!-- Test modification in samples option --> |
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231 <test expect_num_outputs="1"> |
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232 <param name="input_file" ftype="vcf" value="mpileup.vcf" /> |
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233 <section name="sec_restrict"> |
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234 <param name="samples" value="-" /> |
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235 </section> |
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236 <output name="output_file"> |
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237 <assert_contents> |
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238 <has_text_matching expression="bcftools stats --samples - "/> |
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239 <has_text_matching expression="PSC\t0\tHG00101\t0\t0\t0\t0\t0\t0\t4.8"/> |
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240 <has_text_matching expression="PSI\t0\tHG00102\t0"/> |
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241 </assert_contents> |
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242 </output> |
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243 </test> |
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244 </tests> |
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245 <help><![CDATA[ |
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246 ===================================== |
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247 bcftools @EXECUTABLE@ |
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248 ===================================== |
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249 |
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250 Parses VCF or BCF and produces stats which can be plotted using plot-vcfstats. |
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251 |
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252 When two files are given, the program generates separate stats for intersection and the complements. |
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253 By default only sites are compared, -s/-S must given to include also sample columns. |
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254 |
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255 When one VCF file is specified, then stats by non-reference allele frequency, depth distribution, stats by quality and per-sample counts, singleton stats, etc. are printed. When two VCF files are given, then stats such as concordance (Genotype concordance by non-reference allele frequency, Genotype concordance by sample, Non-Reference Discordance) and correlation are also printed. Per-site discordance (PSD) is also printed in --verbose mode. |
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256 |
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257 @COLLAPSE_HELP@ |
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258 @REGIONS_HELP@ |
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259 @TARGETS_HELP@ |
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260 @EXPRESSIONS_HELP@ |
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261 |
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262 @BCFTOOLS_MANPAGE@#@EXECUTABLE@ |
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263 |
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264 @BCFTOOLS_WIKI@ |
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265 ]]> |
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266 </help> |
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267 <expand macro="citations" /> |
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268 </tool> |