Mercurial > repos > iuc > vg_view
changeset 0:95ec8f978762 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
author | iuc |
---|---|
date | Thu, 09 Apr 2020 04:38:19 -0400 (2020-04-09) |
parents | |
children | ee62774bb5bd |
files | 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 view.xml |
diffstat | 9 files changed, 638 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu Apr 09 04:38:19 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 04:38:19 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 04:38:19 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 TGGCAGTAGCTCAGAGATCT +S 162 C +S 84 AAGCT +S 7 A +S 25 C +S 203 G +S 95 TTACTG +S 76 G +S 34 G +S 50 TCCTCACTTTGCC +S 93 A +S 18 TCCTGG +S 194 G +S 147 T +S 42 T +S 87 AGGGAATAGTGCCTGGCAT +S 132 C +S 140 C +S 157 A +S 167 G +S 169 GAA +S 202 TAA +S 16 G +S 180 G +S 160 GCCT +S 19 T +S 49 A +S 44 ACAAATCTGGGT +S 31 C +S 146 G +S 74 CTACTGACAGCAGA +S 106 A +S 61 A +S 29 G +S 94 G +S 212 ACTAAGGACAAAGGTGCGGGGAGAT +S 102 GAAACATTTGGCTATTGACCTCTTTC +S 128 C +S 159 G +S 70 G +S 21 GTTGGGCTT +S 193 C +S 38 AAGAT +S 163 TTATCTTTACTGTTACC +S 131 T +S 192 T +S 101 TTACTATGAATCCTCACCTTCCTTGACTTCTT +S 105 G +S 17 T +S 53 CA +S 47 CAA +S 175 A +S 166 AATCTTTCC +S 89 A +S 214 G +S 198 C +S 3 G +S 80 TGA +S 96 C +S 51 G +S 178 A +S 149 CCCTTTTCCC +S 155 A +S 181 A +S 143 A +S 48 G +S 15 CCAACTCTCTGG +S 65 TCTCTAATA +S 97 T +S 134 A +P x 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/view.xml Thu Apr 09 04:38:19 2020 -0400 @@ -0,0 +1,89 @@ +<tool id="vg_view" name="vg view" version="@TOOL_VERSION@"> + <description></description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ +vg view +$input_format.input_format_selector +'$input_format.infile' +$output_format +--threads=\${GALAXY_SLOTS:-1} +> '$output' + ]]></command> + <inputs> + <conditional name="input_format"> + <param name="input_format_selector" type="select" label="Your input is in format"> + <option value="--vg-in" selected="true">variant graph (vg)</option> + <option value="--json-in">JSON</option> + <option value="--gfa-in">GFA</option> + <option value="--bam">BAM</option> + </param> + <when value="--vg-in"> + <param name="infile" type="data" format="vg" label="Input file in variant graph format (vg)" /> + </when> + <when value="--gfa-in"> + <param name="infile" type="data" format="gfa1" label="Input file in Graphical Fragment Assembly (gfa)" /> + </when> + <when value="--json-in"> + <param name="infile" type="data" format="json" label="Input file in JSON" /> + </when> + <when value="--bam"> + <param name="infile" type="data" format="bam" label="Input file in BAM" /> + </when> + </conditional> + + <param name="output_format" type="select" label="Choose your output format"> + <option value="--vg">VG</option> + <option value="--json">JSON</option> + <option value="--gfa">GFA</option> + <option value="--dot">dot</option> + </param> + + </inputs> + <outputs> + <data name="output" format="vg"> + <change_format> + <when input="output_format" value="--dot" format="graph_dot"/> + <when input="output_format" value="--json" format="json"/> + <when input="output_format" value="--gfa" format="gfa1"/> + </change_format> + </data> + </outputs> + <tests> + <test> + <conditional name="input_format"> + <param name="input_format_selector" value="--gfa-in" /> + <param name="infile" value="x.gfa" ftype="gfa1" /> + </conditional> + <param name="output_format" value="--vg" /> + <output name="output" file="x.vg" ftype="vg" /> + </test> + <test> + <conditional name="input_format"> + <param name="input_format_selector" value="--vg-in" /> + <param name="infile" value="x.vg" /> + </conditional> + <param name="output_format" value="--json" /> + <output name="output" file="x.json" ftype="json" /> + </test> + <test> + <conditional name="input_format"> + <param name="input_format_selector" value="--json-in" /> + <param name="infile" value="x.json" ftype="json" /> + </conditional> + <param name="output_format" value="--vg" /> + <output name="output" file="x.vg" ftype="vg" /> + </test> + </tests> + <help><![CDATA[ + +variation graph (vg) view module +----------------------------------- + +Inspect and convert variant graphs in different file formats. + + ]]></help> + <expand macro="citations" /> +</tool>