Mercurial > repos > iuc > bcftools_consensus
annotate bcftools_consensus.xml @ 26:62ed6ee05b6f 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 07:57:56 +0000 |
| parents | 5970245e8525 |
| children |
| rev | line source |
|---|---|
|
19
99550ee60e65
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents:
17
diff
changeset
|
1 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
|
0
05b553a53a7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
2 <description>Create consensus sequence by applying VCF variants to a reference fasta file</description> |
|
05b553a53a7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
3 <macros> |
|
05b553a53a7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
4 <token name="@EXECUTABLE@">consensus</token> |
|
05b553a53a7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
5 <import>macros.xml</import> |
|
05b553a53a7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
6 </macros> |
|
26
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
7 <expand macro="bio_tools"/> |
|
4
a50824596729
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
iuc
parents:
0
diff
changeset
|
8 <expand macro="requirements"> |
|
5
979ba8128e98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
4
diff
changeset
|
9 <expand macro="samtools_requirement"/> |
|
26
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
10 <requirement type="package" version="5.3.0">gawk</requirement> |
|
4
a50824596729
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
iuc
parents:
0
diff
changeset
|
11 </expand> |
|
26
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
12 <expand macro="version_command"/> |
|
0
05b553a53a7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
13 <command detect_errors="aggressive"><![CDATA[ |
|
05b553a53a7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
14 @PREPARE_INPUT_FILE@ |
|
9
130789161fcc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents:
8
diff
changeset
|
15 #set $section = $reference_source |
|
0
05b553a53a7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
16 @PREPARE_FASTA_REF@ |
|
05b553a53a7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
17 |
|
26
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
18 #set $section = $sec_restrict |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
19 #if $section.regions.regions_src != '__none__': |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
20 samtools faidx |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
21 #if $section.regions.regions_src == 'regions': |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
22 #set $intervals = $section.regions.region_specs |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
23 @PARSE_INTERVALS@ |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
24 #set $ref_regions_spec = " ".join("'" + c + "'" for c in $components) |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
25 '$input_fa_ref' $ref_regions_spec | |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
26 #else if $section.regions.regions_src == 'regions_file': |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
27 -r '$section.regions.regions_file' '$input_fa_ref' | |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
28 #end if |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
29 #set $input_fa_ref = "-" |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
30 #end if |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
31 |
|
0
05b553a53a7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
32 bcftools @EXECUTABLE@ |
|
05b553a53a7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
33 |
|
26
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
34 #if $section.regions.regions_src != '__none__': |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
35 --regions-overlap $section.regions_overlap |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
36 #end if |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
37 |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
38 #set $section = $reference_source |
|
9
130789161fcc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents:
8
diff
changeset
|
39 @FASTA_REF@ |
|
130789161fcc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents:
8
diff
changeset
|
40 |
|
26
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
41 $mode.select |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
42 #if not str($mode.select): |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
43 $mode.specify_samples.how |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
44 #if str($mode.specify_samples.how) in ["-s", "-S"]: |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
45 '${mode.specify_samples.invert_samples}${mode.specify_samples.samples_spec}' |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
46 #end if |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
47 #else if str($mode.select) == "-H": |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
48 #if str(mode.haplotype.rule) in ["", "pIu"]: |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
49 #set haplotype_option = str(mode.haplotype.allele_n) + str(mode.haplotype.rule) |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
50 #else: |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
51 #set haplotype_option = str(mode.haplotype.rule) |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
52 #end if |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
53 $haplotype_option |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
54 #if $mode.sample: |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
55 --sample '$mode.sample' |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
56 #end if |
|
0
05b553a53a7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
57 #end if |
|
05b553a53a7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
58 |
|
26
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
59 #set $masks = [] |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
60 #for $m in $masking_options.mask: |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
61 #if $m: |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
62 #silent $masks.append($m) |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
63 #end if |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
64 #end for |
|
19
99550ee60e65
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents:
17
diff
changeset
|
65 |
|
26
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
66 #if $masks: |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
67 #if $masking_options.mask_with: |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
68 #set $masking_instructions = [] |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
69 #for $i in str($masking_options.mask_with).split(",", maxsplit=len($masks)-1): |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
70 #silent $masking_instructions.append("--mask-with '" + $i + "'") |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
71 #end for |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
72 #else: |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
73 #set $masking_instructions = [""] |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
74 #end if |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
75 #if len($masking_instructions) == 1: |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
76 ## use same masking instruction for all masks |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
77 #set $masking_instructions = [""] * (len($masks) - 1) + $masking_instructions |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
78 #else if len($masking_instructions) < len($masks): |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
79 ## fill in empty masking instructions for missing ones, which will make bcftools complain about them |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
80 #silent $masking_instructions.extend(["--mask-with ''"] * (len($masks) - len($masking_instructions))) |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
81 #end if |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
82 |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
83 #for $m, $i in zip($masks, $masking_instructions): |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
84 --mask '$m' $i |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
85 #end for |
|
19
99550ee60e65
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents:
17
diff
changeset
|
86 #end if |
|
99550ee60e65
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents:
17
diff
changeset
|
87 |
|
26
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
88 #if $masking_options.absent: |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
89 --absent '$masking_options.absent' |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
90 #end if |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
91 |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
92 #if $masking_options.mark_del: |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
93 --mark-del '$masking_options.mark_del' |
|
19
99550ee60e65
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents:
17
diff
changeset
|
94 #end if |
|
99550ee60e65
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents:
17
diff
changeset
|
95 |
|
26
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
96 $masking_options.insertions.mark_ins |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
97 #if str($masking_options.insertions.mark_ins) == "--mark-ins": |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
98 '$masking_options.insertions.ins_custom' |
|
0
05b553a53a7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
99 #end if |
|
26
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
100 |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
101 $masking_options.snvs.mark_snv |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
102 #if str($masking_options.snvs.mark_snv) == "--mark-snv": |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
103 '$masking_options.snvs.snv_custom' |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
104 #end if |
|
0
05b553a53a7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
105 |
|
14
b0911dc4ad74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
iuc
parents:
13
diff
changeset
|
106 #set $section = $sec_restrict |
|
b0911dc4ad74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
iuc
parents:
13
diff
changeset
|
107 @INCLUDE@ |
|
b0911dc4ad74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
iuc
parents:
13
diff
changeset
|
108 @EXCLUDE@ |
|
b0911dc4ad74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
iuc
parents:
13
diff
changeset
|
109 |
|
0
05b553a53a7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
110 #if $chain: |
|
26
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
111 --chain '$chain_file' |
|
0
05b553a53a7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
112 #end if |
|
05b553a53a7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
113 |
|
05b553a53a7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
114 ## Primary Input/Outputs |
|
12
91c3ed51093d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3c56c04b42c70a072429e4534a136dc28c98b642"
iuc
parents:
9
diff
changeset
|
115 #if str($rename) == "no" |
|
26
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
116 --output '$output_file' |
|
12
91c3ed51093d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3c56c04b42c70a072429e4534a136dc28c98b642"
iuc
parents:
9
diff
changeset
|
117 #end if |
|
0
05b553a53a7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
118 @INPUT_FILE@ |
|
12
91c3ed51093d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3c56c04b42c70a072429e4534a136dc28c98b642"
iuc
parents:
9
diff
changeset
|
119 #if str($rename) == "yes": |
|
26
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
120 #set basename=$input_file.element_identifier |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
121 | awk 'BEGIN {i=1} {if (match($0, /^>/)) {if (i==1) {name="${basename}"} else {name=sprintf("%s-%d","${basename}",i);} print(gensub(/>[^ ]+( ?.*)/, ">" name "\\1", 1)); i=i+1;} else {print}}' > '$output_file' |
|
12
91c3ed51093d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3c56c04b42c70a072429e4534a136dc28c98b642"
iuc
parents:
9
diff
changeset
|
122 #end if |
|
0
05b553a53a7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
123 ]]> |
|
05b553a53a7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
124 </command> |
|
05b553a53a7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
125 <inputs> |
|
26
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
126 <expand macro="macro_input"/> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
127 <expand macro="macro_fasta_ref"/> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
128 <conditional name="mode"> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
129 <param name="select" type="select" label="Consensus building mode; at each variant site ..."> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
130 <option value="-s -">ignore any sample genotypes; incorporate first allele from ALT column (-s -)</option> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
131 <option value="-I -s -">ignore any sample genotypes; incorporate IUPAC code representing all alleles from REF/ALT coulmns (-I -s -)</option> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
132 <option value="" selected="true">incorporate IUPAC code representing the genotypes of all selected samples (default)</option> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
133 <option value="-H">incorporate specific haplotype allele of one selected sample</option> |
|
19
99550ee60e65
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents:
17
diff
changeset
|
134 </param> |
|
26
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
135 <when value="-s -" /> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
136 <when value="-I -s -" /> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
137 <when value=""> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
138 <expand macro="macro_samples_enhanced" /> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
139 </when> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
140 <when value="-H"> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
141 <expand macro="macro_sample" help="The name of the single sample alleles of which should get used for the consensus sequence. This field is optional only if your input VCF dataset specifies exactly one sample."/> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
142 <conditional name="haplotype"> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
143 <param name="rule" type="select" label="From the selected sample's genotype use ...'"> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
144 <option value="">the Nth allele (for both phased and unphased genotypes) (-H N)</option> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
145 <option value="pIu">the Nth allele if the genotype is phased, the IUPAC code representing the genotype if it's unphased (-H NpIu)</option> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
146 <option value="R">the ALT allele where the sample is homozygous, the REF allele otherwise (-H R)</option> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
147 <option value="A">the ALT allele where the sample is homozygous or heterozygous (-H A)</option> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
148 <option value="LR">the ALT allele where the sample is homozygous, the REF allele where it's heterozygous unless the ALT allele is longer (-H LR)</option> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
149 <option value="LA">the ALT allele where the sample is homozygous, the ALT allele where it's heterozygous unless the REF allele is longer (-H LA)</option> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
150 <option value="SR">the ALT allele where the sample is homozygous, the REF allele where it's heterozygous unless the ALT allele is shorter (-H SR</option> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
151 <option value="SA">the ALT allele where the sample is homozygous, the ALT allele where it's heterozygous unless the REF allele is shorter (-H SA)</option> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
152 </param> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
153 <when value=""> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
154 <param name="allele_n" type="integer" min="1" value="1" label="where N is" /> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
155 </when> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
156 <when value="pIu"> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
157 <param name="allele_n" type="integer" min="1" value="1" label="where N is" /> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
158 </when> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
159 <when value="R" /> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
160 <when value="A" /> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
161 <when value="LR" /> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
162 <when value="LA" /> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
163 <when value="SR" /> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
164 <when value="SA" /> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
165 </conditional> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
166 </when> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
167 </conditional> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
168 <section name="masking_options" expanded="false" title="Masking and marking options" help="The various options in this section are applied in the order they appear, i.e. 1) masking, 2) marking of absent sites, 3) SNV/indel marking."> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
169 <param argument="--mask" type="data" format="tabular" multiple="true" optional="true" label="Mask" help="Replace regions according to the next --mask-with option"/> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
170 <param argument="--mask-with" type="text" value="" optional="true" label="Mask with" help="Replace with CHAR (skips overlapping variants; default: N); use "uc" or "lc" to change to uppercase or lowercase, respectively. If you have provided more than one Mask dataset and you would like to apply a unique mask for the regions in each of them, then you can specify a comma-separated list of masking instructions (as many as mask datasets)." /> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
171 <param argument="--absent" type="text" value="" optional="true" label="Mark absent" help="Replace reference bases at positions absent from the VCF input with a custom character."> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
172 <validator type="regex">^.$</validator> |
|
19
99550ee60e65
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents:
17
diff
changeset
|
173 </param> |
|
26
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
174 <param argument="--mark-del" type="text" value="" optional="true" label="Mark deletions" help="Instead of removing the reference base at deleted positions, replace the base with a custom character."> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
175 <validator type="regex">^.$</validator> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
176 </param> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
177 <conditional name="insertions"> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
178 <param argument="--mark-ins" type="select" label="Mark insertions" help="Highlight insertions in uppercase or lowercase, or by using a fixed character instead of inserted bases, leaving the rest as is"> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
179 <option value="">Do not mark insertions</option> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
180 <option value="--mark-ins uc">Uppercase (uc)</option> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
181 <option value="--mark-ins lc">Lowercase (lc)</option> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
182 <option value="--mark-ins">Custom character</option> |
|
19
99550ee60e65
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents:
17
diff
changeset
|
183 </param> |
|
26
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
184 <when value="" /> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
185 <when value="--mark-ins uc" /> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
186 <when value="--mark-ins lc" /> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
187 <when value="--mark-ins"> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
188 <param name="ins_cutom" type="text" optional="false" label="Character to use instead of an inserted base"> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
189 <validator type="empty_field"/> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
190 </param> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
191 </when> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
192 </conditional> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
193 <conditional name="snvs"> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
194 <param argument="--mark-snv" type="select" label="Mark substitutions" help="Highlight substitutions in uppercase or lowercase, or by using a fixed character instead of substituted bases, leaving the rest as is"> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
195 <option value="">Do not mark substitutions</option> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
196 <option value="--mark-snv uc">Uppercase (uc)</option> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
197 <option value="--mark-snv lc">Lowercase (lc)</option> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
198 <option value="--mark-snv">Custom character</option> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
199 </param> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
200 <when value="" /> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
201 <when value="--mark-snv uc" /> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
202 <when value="--mark-snv lc" /> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
203 <when value="--mark-snv"> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
204 <param name="snv_custom" type="text" optional="false" label="Character to use instead of a subtituted base"> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
205 <validator type="empty_field"/> |
|
19
99550ee60e65
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents:
17
diff
changeset
|
206 </param> |
|
99550ee60e65
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents:
17
diff
changeset
|
207 </when> |
|
99550ee60e65
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents:
17
diff
changeset
|
208 </conditional> |
|
0
05b553a53a7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
209 </section> |
|
26
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
210 <section name="sec_restrict" expanded="false" title="Restrict to"> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
211 <expand macro="macro_include"/> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
212 <expand macro="macro_exclude"/> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
213 <expand macro="macro_region_restrict" label_select="Restrict consensus building to only specified regions of reference?"/> |
|
14
b0911dc4ad74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
iuc
parents:
13
diff
changeset
|
214 </section> |
|
26
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
215 <param name="chain" type="boolean" truevalue="yes" falsevalue="no" label="Write a chain file for liftover"/> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
216 <param name="rename" type="boolean" truevalue="yes" falsevalue="no" label="Set output FASTA ID from name of VCF"/> |
|
0
05b553a53a7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
217 </inputs> |
|
05b553a53a7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
218 <outputs> |
|
05b553a53a7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
219 <data name="output_file" format="fasta" label="${tool.name} on ${on_string}: consensus fasta"/> |
|
05b553a53a7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
220 <data name="chain_file" format="txt" label="${tool.name} on ${on_string}: chain"> |
|
05b553a53a7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
221 <filter>chain</filter> |
|
05b553a53a7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
222 </data> |
|
05b553a53a7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
223 </outputs> |
|
05b553a53a7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
224 <tests> |
|
23
5970245e8525
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bfc4ff4956b94885638ae07a2560bac5f84fcca8
iuc
parents:
19
diff
changeset
|
225 <test expect_num_outputs="2"> |
|
26
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
226 <expand macro="test_using_reference" ref="consensus.fa"/> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
227 <param name="input_file" ftype="vcf" value="consensus.vcf"/> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
228 <section name="masking_options"> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
229 <param name="mask" ftype="tabular" value="consensus.tab"/> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
230 </section> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
231 <param name="chain" value="true"/> |
|
0
05b553a53a7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
232 <output name="output_file"> |
|
05b553a53a7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
233 <assert_contents> |
|
26
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
234 <has_text text="NNNNNNNNNNNNNNNNNNNNNNNNNN"/> |
|
0
05b553a53a7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
235 </assert_contents> |
|
05b553a53a7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
236 </output> |
|
05b553a53a7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
237 <output name="chain_file"> |
|
05b553a53a7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
238 <assert_contents> |
|
26
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
239 <has_text text="chain 497 1 501 + 1 501 1 502 + 1 502 1"/> |
|
0
05b553a53a7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
240 </assert_contents> |
|
05b553a53a7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
241 </output> |
|
05b553a53a7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
242 </test> |
|
23
5970245e8525
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bfc4ff4956b94885638ae07a2560bac5f84fcca8
iuc
parents:
19
diff
changeset
|
243 <test expect_num_outputs="2"> |
|
26
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
244 <expand macro="test_using_reference" select_from="cached" ref="consensus"/> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
245 <param name="input_file" ftype="vcf" dbkey="?" value="consensus.vcf"/> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
246 <section name="masking_options"> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
247 <param name="mask" ftype="tabular" value="consensus.tab"/> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
248 </section> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
249 <param name="chain" value="true"/> |
|
9
130789161fcc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents:
8
diff
changeset
|
250 <output name="output_file"> |
|
130789161fcc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents:
8
diff
changeset
|
251 <assert_contents> |
|
26
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
252 <has_text text="NNNNNNNNNNNNNNNNNNNNNNNNNN"/> |
|
9
130789161fcc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents:
8
diff
changeset
|
253 </assert_contents> |
|
130789161fcc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents:
8
diff
changeset
|
254 </output> |
|
130789161fcc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents:
8
diff
changeset
|
255 <output name="chain_file"> |
|
130789161fcc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents:
8
diff
changeset
|
256 <assert_contents> |
|
26
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
257 <has_text text="chain 497 1 501 + 1 501 1 502 + 1 502 1"/> |
|
9
130789161fcc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents:
8
diff
changeset
|
258 </assert_contents> |
|
130789161fcc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents:
8
diff
changeset
|
259 </output> |
|
130789161fcc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents:
8
diff
changeset
|
260 </test> |
|
23
5970245e8525
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bfc4ff4956b94885638ae07a2560bac5f84fcca8
iuc
parents:
19
diff
changeset
|
261 <test expect_num_outputs="1"> |
|
26
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
262 <expand macro="test_using_reference" ref="consensus.fa"/> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
263 <param name="input_file" ftype="vcf" value="consensus.vcf"/> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
264 <section name="masking_options"> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
265 <param name="mask" ftype="tabular" value="consensus.tab"/> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
266 </section> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
267 <param name="chain" value="false"/> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
268 <param name="rename" value="true"/> |
|
12
91c3ed51093d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3c56c04b42c70a072429e4534a136dc28c98b642"
iuc
parents:
9
diff
changeset
|
269 <output name="output_file"> |
|
91c3ed51093d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3c56c04b42c70a072429e4534a136dc28c98b642"
iuc
parents:
9
diff
changeset
|
270 <assert_contents> |
|
26
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
271 <has_text text=">consensus.vcf"/> |
|
12
91c3ed51093d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3c56c04b42c70a072429e4534a136dc28c98b642"
iuc
parents:
9
diff
changeset
|
272 </assert_contents> |
|
91c3ed51093d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3c56c04b42c70a072429e4534a136dc28c98b642"
iuc
parents:
9
diff
changeset
|
273 <assert_contents> |
|
26
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
274 <has_text text=">consensus.vcf-2"/> |
|
12
91c3ed51093d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3c56c04b42c70a072429e4534a136dc28c98b642"
iuc
parents:
9
diff
changeset
|
275 </assert_contents> |
|
91c3ed51093d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3c56c04b42c70a072429e4534a136dc28c98b642"
iuc
parents:
9
diff
changeset
|
276 </output> |
|
91c3ed51093d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3c56c04b42c70a072429e4534a136dc28c98b642"
iuc
parents:
9
diff
changeset
|
277 </test> |
|
23
5970245e8525
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bfc4ff4956b94885638ae07a2560bac5f84fcca8
iuc
parents:
19
diff
changeset
|
278 <test expect_num_outputs="1"> |
|
26
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
279 <expand macro="test_using_reference" ref="consensus.fa"/> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
280 <param name="input_file" ftype="vcf" value="consensus.vcf"/> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
281 <conditional name="mode"> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
282 <param name="select" value="-s -"/> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
283 </conditional> |
|
14
b0911dc4ad74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
iuc
parents:
13
diff
changeset
|
284 <section name="sec_restrict"> |
|
26
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
285 <param name="include" value="TYPE="snp""/> |
|
14
b0911dc4ad74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
iuc
parents:
13
diff
changeset
|
286 </section> |
|
b0911dc4ad74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
iuc
parents:
13
diff
changeset
|
287 <output name="output_file"> |
|
b0911dc4ad74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
iuc
parents:
13
diff
changeset
|
288 <assert_contents> |
|
26
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
289 <has_text text="TACAAAATATGACATATCAAAAAGAACATAACCTACGTATCAACTAAAGTGGTTGTTTGA"/> |
|
14
b0911dc4ad74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
iuc
parents:
13
diff
changeset
|
290 </assert_contents> |
|
b0911dc4ad74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
iuc
parents:
13
diff
changeset
|
291 </output> |
|
b0911dc4ad74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
iuc
parents:
13
diff
changeset
|
292 </test> |
|
19
99550ee60e65
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents:
17
diff
changeset
|
293 <!--Test absent option--> |
|
23
5970245e8525
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bfc4ff4956b94885638ae07a2560bac5f84fcca8
iuc
parents:
19
diff
changeset
|
294 <test expect_num_outputs="1"> |
|
26
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
295 <expand macro="test_using_reference" ref="consensus.fa"/> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
296 <param name="input_file" ftype="vcf" value="consensus.vcf"/> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
297 <conditional name="mode"> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
298 <param name="select" value="-s -"/> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
299 </conditional> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
300 <section name="masking_options"> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
301 <param name="absent" value="W"/> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
302 </section> |
|
19
99550ee60e65
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents:
17
diff
changeset
|
303 <section name="sec_restrict"> |
|
26
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
304 <param name="include" value="TYPE="snp""/> |
|
19
99550ee60e65
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents:
17
diff
changeset
|
305 </section> |
|
99550ee60e65
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents:
17
diff
changeset
|
306 <output name="output_file"> |
|
99550ee60e65
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents:
17
diff
changeset
|
307 <assert_contents> |
|
26
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
308 <has_text text="WWWAWAWWAWWWWWWWWCWWWWWWWW"/> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
309 </assert_contents> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
310 </output> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
311 <assert_command> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
312 <has_text text="--absent"/> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
313 </assert_command> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
314 </test> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
315 <test expect_num_outputs="1"> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
316 <expand macro="test_using_reference" ref="consensus.fa"/> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
317 <param name="input_file" ftype="vcf" value="consensus.vcf"/> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
318 <conditional name="mode"> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
319 <param name="select" value="-s -"/> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
320 </conditional> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
321 <section name="masking_options"> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
322 <param name="mark_del" value="-"/> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
323 <conditional name="insertions"> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
324 <param name="mark_ins" value="--mark-ins uc"/> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
325 </conditional> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
326 <conditional name="snvs"> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
327 <param name="mark_snv" value="--mark-snv uc"/> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
328 </conditional> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
329 </section> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
330 <section name="sec_restrict"> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
331 <param name="include" value="TYPE="snp""/> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
332 </section> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
333 <output name="output_file"> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
334 <assert_contents> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
335 <has_text text="TACAAAATATGACATATCAAAAAGAACATAACCTACGTATCAACTAAAGTGGTTGTTTGA"/> |
|
19
99550ee60e65
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents:
17
diff
changeset
|
336 </assert_contents> |
|
99550ee60e65
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents:
17
diff
changeset
|
337 </output> |
|
99550ee60e65
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents:
17
diff
changeset
|
338 <assert_command> |
|
26
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
339 <has_text text="--mark-del"/> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
340 <has_text text="--mark-ins"/> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
341 <has_text text="--mark-snv"/> |
|
19
99550ee60e65
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents:
17
diff
changeset
|
342 </assert_command> |
|
99550ee60e65
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents:
17
diff
changeset
|
343 </test> |
|
23
5970245e8525
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bfc4ff4956b94885638ae07a2560bac5f84fcca8
iuc
parents:
19
diff
changeset
|
344 <test expect_num_outputs="1"> |
|
26
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
345 <expand macro="test_using_reference" ref="csq.fa"/> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
346 <param name="input_file" ftype="vcf" value="csq.vcf"/> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
347 <section name="masking_options"> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
348 <param name="absent" value="."/> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
349 <param name="mark_del" value="-"/> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
350 </section> |
|
19
99550ee60e65
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents:
17
diff
changeset
|
351 <section name="sec_restrict"> |
|
26
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
352 <conditional name="regions"> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
353 <param name="regions_src" value="regions"/> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
354 <repeat name="region_specs"> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
355 <param name="chrom" value="1"/> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
356 <param name="start" value="161"/> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
357 <param name="stop" value="190"/> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
358 </repeat> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
359 </conditional> |
|
19
99550ee60e65
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents:
17
diff
changeset
|
360 </section> |
|
99550ee60e65
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents:
17
diff
changeset
|
361 <output name="output_file"> |
|
99550ee60e65
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents:
17
diff
changeset
|
362 <assert_contents> |
|
26
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
363 <has_line line=">1:161-190"/> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
364 <has_line line="-............................Y"/> |
|
19
99550ee60e65
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents:
17
diff
changeset
|
365 </assert_contents> |
|
99550ee60e65
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents:
17
diff
changeset
|
366 </output> |
|
26
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
367 </test> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
368 <test expect_num_outputs="1"> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
369 <expand macro="test_using_reference" ref="csq.fa"/> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
370 <param name="input_file" ftype="vcf" value="csq.vcf"/> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
371 <section name="masking_options"> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
372 <param name="absent" value="."/> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
373 <param name="mark_del" value="-"/> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
374 </section> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
375 <section name="sec_restrict"> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
376 <conditional name="regions"> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
377 <param name="regions_src" value="regions"/> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
378 <repeat name="region_specs"> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
379 <param name="chrom" value="1"/> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
380 <param name="start" value="161"/> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
381 <param name="stop" value="190"/> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
382 </repeat> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
383 <param name="regions_overlap" value="0"/> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
384 </conditional> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
385 </section> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
386 <output name="output_file"> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
387 <assert_contents> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
388 <has_line line=">1:161-190"/> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
389 <has_line line=".............................Y"/> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
390 </assert_contents> |
|
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
391 </output> |
|
19
99550ee60e65
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents:
17
diff
changeset
|
392 </test> |
|
0
05b553a53a7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
393 </tests> |
|
05b553a53a7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
394 <help><![CDATA[ |
|
05b553a53a7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
395 ===================================== |
|
05b553a53a7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
396 bcftools @EXECUTABLE@ plugin |
|
05b553a53a7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
397 ===================================== |
|
05b553a53a7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
398 |
|
05b553a53a7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
399 |
|
05b553a53a7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
400 Create consensus sequence by applying VCF variants to a reference fasta file. |
|
05b553a53a7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
401 |
|
05b553a53a7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
402 @BCFTOOLS_MANPAGE@#@EXECUTABLE@ |
|
05b553a53a7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
403 |
|
26
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
404 @BCFTOOLS_HOWTOS@ |
|
12
91c3ed51093d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3c56c04b42c70a072429e4534a136dc28c98b642"
iuc
parents:
9
diff
changeset
|
405 |
|
91c3ed51093d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3c56c04b42c70a072429e4534a136dc28c98b642"
iuc
parents:
9
diff
changeset
|
406 The option to set the new consensus' FASTA ID from the name of the VCF is provided by post-processing |
|
91c3ed51093d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3c56c04b42c70a072429e4534a136dc28c98b642"
iuc
parents:
9
diff
changeset
|
407 the bcftools consensus output. It is primarily intended for use when the VCF is coming from a list |
|
91c3ed51093d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3c56c04b42c70a072429e4534a136dc28c98b642"
iuc
parents:
9
diff
changeset
|
408 collection where the elements of the list are named meaningfully (e.g. named after sample names). This |
|
91c3ed51093d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3c56c04b42c70a072429e4534a136dc28c98b642"
iuc
parents:
9
diff
changeset
|
409 is useful when consensus sequences are being prepared for, for example, feeding a multiple sequence |
|
91c3ed51093d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3c56c04b42c70a072429e4534a136dc28c98b642"
iuc
parents:
9
diff
changeset
|
410 alignment to a phylogeny program. |
|
0
05b553a53a7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
411 ]]> |
|
05b553a53a7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
412 </help> |
|
26
62ed6ee05b6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents:
23
diff
changeset
|
413 <expand macro="citations"/> |
|
0
05b553a53a7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
414 </tool> |