Mercurial > repos > iuc > vg_convert
changeset 0:e68d9dfa62a2 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
| author | iuc |
|---|---|
| date | Thu, 09 Apr 2020 04:35:27 -0400 |
| parents | |
| children | 7366704232b6 |
| files | convert.xml macros.xml test-data/hla.vg test-data/hla.xg test-data/hla_variants.vcf test-data/snarls.pb test-data/x.gfa test-data/x.json test-data/x.vg |
| diffstat | 9 files changed, 599 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/convert.xml Thu Apr 09 04:35:27 2020 -0400 @@ -0,0 +1,50 @@ +<tool id="vg_convert" name="vg convert" version="@TOOL_VERSION@"> + <description></description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ +ln -s '$infile' ./infile.${infile.ext} && + +vg convert +$output_format +./infile.${infile.ext} +> '$output' + ]]></command> + <inputs> + <param name="infile" type="data" format="vg,xg" label="Input file in vg or xg format" /> + <param name="output_format" type="select" label="Choose your output format"> + <option value="--xg-out">XG format (--xg-out)</option> + <!--option value="- -odgi-out">odgi format (- -odgi-out)</option--> + </param> + </inputs> + <outputs> + <data name="output" format="odgi"> + <change_format> + <when input="output_format" value="--xg-out" format="xg"/> + </change_format> + </data> + </outputs> + <tests> + <test> + <param name="infile" value="hla.vg" ftype="vg" /> + <param name="output_format" value="--xg-out" /> + <output name="output" file="hla.xg" ftype="xg" compare="sim_size" /> + </test> + <!--test> + <param name="infile" value="x.vg" ftype="vg" /> + <param name="output_format" value="- -odgi-out" /> + <output name="output" file="x.odgi" ftype="odgi" compare="sim_size" /> + </test--> + </tests> + <help><![CDATA[ + +variation graph (vg) convert module +----------------------------------- + +This module is converting various variant graphs into each format. + + ]]></help> + <expand macro="citations" /> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu Apr 09 04:35:27 2020 -0400 @@ -0,0 +1,14 @@ +<?xml version="1.0"?> +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">vg</requirement> + </requirements> + </xml> + <token name="@TOOL_VERSION@">1.23.0</token> + <xml name="citations"> + <citations> + <yield /> + </citations> + </xml> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hla_variants.vcf Thu Apr 09 04:35:27 2020 -0400 @@ -0,0 +1,21 @@ +##fileformat=VCFv4.2 +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##contig=<ID=gi|568815592:29791752-29792749,length=998> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT gi|157734152:29563108-29564082 gi|528476637:29761569-29762543 gi|568815454:1057585-1058559 gi|568815529:1275535-1276509 gi|568815551:1054737-1055734 gi|568815561:1054328-1055325 gi|568815564:1054403-1055400 gi|568815567:1054737-1055711 gi|568815569:1097903-1098900 +gi|568815592:29791752-29792749 92 . G A 23 . . GT 1 1 1 1 0 0 0 1 0 +gi|568815592:29791752-29792749 105 . C T 23 . . GT 1 1 1 1 0 0 0 1 0 +gi|568815592:29791752-29792749 151 . CAG C 23 . . GT 1 1 1 1 0 0 0 1 0 +gi|568815592:29791752-29792749 160 . A G 23 . . GT 1 1 1 1 0 0 0 1 0 +gi|568815592:29791752-29792749 222 . G A 23 . . GT 1 1 1 1 0 0 0 1 0 +gi|568815592:29791752-29792749 283 . C G 23 . . GT 1 1 1 1 0 0 0 1 0 +gi|568815592:29791752-29792749 295 . TT CC 23 . . GT 1 1 1 1 0 0 0 1 0 +gi|568815592:29791752-29792749 348 . G A 23 . . GT 1 1 1 1 0 0 0 1 0 +gi|568815592:29791752-29792749 357 . G A 23 . . GT 1 1 1 1 0 0 0 1 0 +gi|568815592:29791752-29792749 395 . T C 23 . . GT 1 1 1 1 0 0 0 1 0 +gi|568815592:29791752-29792749 468 . T C 23 . . GT 1 1 1 1 0 0 0 1 0 +gi|568815592:29791752-29792749 583 . G C 23 . . GT 1 1 1 1 0 0 0 1 0 +gi|568815592:29791752-29792749 621 . G T 23 . . GT 0 1 0 0 0 0 0 1 0 +gi|568815592:29791752-29792749 660 . G A 23 . . GT 1 1 1 1 0 0 0 1 0 +gi|568815592:29791752-29792749 824 . CGCGGGCGCCGTGGATGGAGCA C 23 . . GT 1 1 1 1 0 0 0 1 0 +gi|568815592:29791752-29792749 982 . G A 23 . . GT 1 1 1 1 0 0 0 1 0 +gi|568815592:29791752-29792749 995 . C T 23 . . GT 1 1 1 1 0 0 0 1 0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/x.gfa Thu Apr 09 04:35:27 2020 -0400 @@ -0,0 +1,513 @@ +H VN:Z:1.0 +S 56 ATTAGCCATGTGACTTTGAACAAGTTAGTTAA +S 35 A +S 110 TCATTGTCAAC +S 60 T +S 30 ACGTTTGACAATCTATCAC +S 6 TTG +S 67 T +S 215 A +S 73 A +S 182 CTGCTCTCTT +S 164 G +S 115 ACATTAGGA +S 153 T +S 112 ACAGTCAACGCTCAATACAAGG +S 185 TTGTCAGATC +S 64 A +S 186 G +S 90 GAGGAAAGCCTCTGACAACTGGT +S 139 GGGCAC +S 4 T +S 13 A +S 86 C +S 168 A +S 207 CAAA +S 104 TCCTTG +S 183 A +S 52 A +S 177 T +S 12 ATAT +S 179 TGTCCAGGAATGAACC +S 75 A +S 23 T +S 111 A +S 41 TGGAGCCA +S 43 G +S 11 T +S 68 GGAGAT +S 171 G +S 69 C +S 82 G +S 85 G +S 130 TTGTGT +S 119 G +S 125 T +S 39 C +S 77 A +S 126 G +S 108 C +S 71 AT +S 66 C +S 103 C +S 156 C +S 59 G +S 172 CTGCTCTTTCCCTCAATTGTTCATTTGTCT +S 208 T +S 2 A +S 10 A +S 27 CTTTGATTTATTTGAAGT +S 26 T +S 211 GG +S 124 TAAGACCCAGAGGGCTCACCCAGAGTCGAG +S 144 T +S 127 CTCAAGGACAGCTCTCC +S 116 A +S 100 T +S 79 TTTGCTGTGAAGATTAAATTAGGTGATGCTTG +S 200 C +S 20 TGCTATGTGTAACTAGTAATGGTAATGGATAT +S 81 T +S 195 A +S 141 T +S 187 A +S 213 A +S 135 T +S 9 AAATTTTCTGGAGTTCTAT +S 189 A +S 138 T +S 109 T +S 161 T +S 107 GGCTCTTCTGGCTT +S 46 T +S 57 TCTCTCTGAACTTCAGTT +S 152 GCTCTCCTTGTCCCTCC +S 170 C +S 88 C +S 129 T +S 209 G +S 120 CTCTGCTCACCG +S 78 G +S 133 CAGAGTGTATACGA +S 72 G +S 24 TT +S 8 G +S 184 C +S 37 A +S 1 CAAATAAG +S 137 TAACTCTGTTC +S 22 C +S 83 A +S 154 C +S 190 C +S 201 T +S 99 C +S 121 C +S 206 C +S 14 T +S 33 AGGGGTAATGTGGGGAA +S 40 T +S 113 A +S 174 T +S 165 A +S 142 GGTGAAAGA +S 5 C +S 55 T +S 114 G +S 123 GATCTTCAAGTTTGAAAATTGCATCTCAAATC +S 32 T +S 136 G +S 117 T +S 45 C +S 145 AACAGAGGAAATGCC +S 197 T +S 196 AGGGC +S 210 CTACCCAGGCCATTTTAAGTTTCCTGT +S 151 A +S 54 G +S 63 C +S 191 TTCTCATCCCTCCT +S 91 G +S 62 ATT +S 205 TACTCCACAT +S 158 GATCTCTTCACT +S 150 T +S 176 C +S 122 T +S 58 C +S 199 T +S 28 A +S 173 C +S 148 GGCTTTTTATCAGAACATGTTTCCAAGCTTAT +S 188 G +S 92 A +S 36 TGGAAAGAATAC +S 98 TA +S 204 C +S 118 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