Mercurial > repos > iuc > ivar_consensus
changeset 1:a38934e303b9 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 27fa363aa1289366fd0e888709d022357533e4de"
| author | iuc |
|---|---|
| date | Sat, 04 Apr 2020 12:25:11 -0400 |
| parents | f362150bef41 |
| children | d6e72da3ec35 |
| files | macros.xml test-data/zika/Z52.tsv test-data/zika/Z52_a.tsv test-data/zika/primer_mismatchers_indices.txt |
| diffstat | 4 files changed, 30 insertions(+), 30 deletions(-) [+] |
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--- a/macros.xml Mon Mar 30 06:37:01 2020 -0400 +++ b/macros.xml Sat Apr 04 12:25:11 2020 -0400 @@ -1,5 +1,5 @@ <macros> - <token name="@VERSION@">1.0.1</token> + <token name="@VERSION@">1.2</token> <xml name="requirements"> <requirements> <requirement type="package" version="@VERSION@">ivar</requirement>
--- a/test-data/zika/Z52.tsv Mon Mar 30 06:37:01 2020 -0400 +++ b/test-data/zika/Z52.tsv Sat Apr 04 12:25:11 2020 -0400 @@ -1,11 +1,11 @@ -REGION POS REF ALT REF_DP_Z52_a.tsv REF_RV_Z52_a.tsv REF_QUAL_Z52_a.tsv ALT_DP_Z52_a.tsv ALT_RV_Z52_a.tsv ALT_QUAL_Z52_a.tsv ALT_FREQ_Z52_a.tsv TOTAL_DP_Z52_a.tsv PVAL_Z52_a.tsv PASS_Z52_a.tsv REF_DP_Z52_b.tsv REF_RV_Z52_b.tsv REF_QUAL_Z52_b.tsv ALT_DP_Z52_b.tsv ALT_RV_Z52_b.tsv ALT_QUAL_Z52_b.tsv ALT_FREQ_Z52_b.tsv TOTAL_DP_Z52_b.tsv PVAL_Z52_b.tsv PASS_Z52_b.tsv -PRV 1682 C T 1097 984 37 34 33 37 0.0300088 1133 7.79053e-10 TRUE 1505 1475 37 50 50 37 0.0321543 1555 1.59703e-14 TRUE -PRV 1965 T G 302 113 37 41 3 35 0.119534 343 2.81419e-14 TRUE 469 28 36 71 1 36 0.131481 540 1.31011e-23 TRUE -PRV 2781 T G 353 70 37 48 8 36 0.117936 407 4.05758e-16 TRUE 404 75 37 35 7 36 0.0788288 444 1.12705e-11 TRUE -PRV 2922 C T 263 0 36 11 0 36 0.040146 274 0.000431954 TRUE 277 0 36 19 0 34 0.0641892 296 1.46245e-06 TRUE -PRV 3148 Y C 0 0 0 381 75 36 0.223199 1707 0 TRUE 0 0 0 679 99 37 0.258765 2624 0 TRUE -PRV 3148 Y T 0 0 0 1324 264 36 0.77563 1707 0 TRUE 0 0 0 1943 271 36 0.740473 2624 0 TRUE -PRV 3295 A G 1002 1002 35 38 38 33 0.0365385 1040 4.30837e-11 TRUE 1806 1806 36 69 69 34 0.0368 1875 2.28815e-20 TRUE -PRV 5680 C T 27 5 44 8 2 45 0.228571 35 0.000596701 TRUE 38 5 50 7 1 49 0.155556 45 0.00133612 TRUE -PRV 7916 C T 351 289 36 81 78 37 0.1875 432 5.39655e-27 TRUE 286 227 36 45 38 37 0.135952 331 4.31473e-15 TRUE -PRV 9713 C T 374 0 37 13 0 35 0.0335917 387 0.00010474 TRUE 475 0 37 27 0 36 0.0537849 502 4.66646e-09 TRUE +REGION POS REF ALT GFF_FEATURE REF_CODON REF_AA ALT_CODON ALT_AA REF_DP_./var_0.tsv REF_RV_./var_0.tsv REF_QUAL_./var_0.tsv ALT_DP_./var_0.tsv ALT_RV_./var_0.tsv ALT_QUAL_./var_0.tsv ALT_FREQ_./var_0.tsv TOTAL_DP_./var_0.tsv PVAL_./var_0.tsv PASS_./var_0.tsv REF_DP_./var_1.tsv REF_RV_./var_1.tsv REF_QUAL_./var_1.tsv ALT_DP_./var_1.tsv ALT_RV_./var_1.tsv ALT_QUAL_./var_1.tsv ALT_FREQ_./var_1.tsv TOTAL_DP_./var_1.tsv PVAL_./var_1.tsv PASS_./var_1.tsv +PRV 1682 C T 1505 1475 37 50 50 37 0.0321543 1555 1.59703e-14 TRUE 1097 984 37 34 33 37 0.0300088 1133 7.79053e-10 TRUE +PRV 1965 T G 469 28 36 71 1 36 0.131481 540 1.31011e-23 TRUE 302 113 37 41 3 35 0.119534 343 2.81419e-14 TRUE +PRV 2781 T G 404 75 37 35 7 36 0.0788288 444 1.12705e-11 TRUE 353 70 37 48 8 36 0.117936 407 4.05758e-16 TRUE +PRV 2922 C T 277 0 36 19 0 34 0.0641892 296 1.46245e-06 TRUE 263 0 36 11 0 36 0.040146 274 0.000431954 TRUE +PRV 3148 Y C 0 0 0 679 99 37 0.258765 2624 0 TRUE 0 0 0 381 75 36 0.223199 1707 0 TRUE +PRV 3148 Y T 0 0 0 1943 271 36 0.740473 2624 0 TRUE 0 0 0 1324 264 36 0.77563 1707 0 TRUE +PRV 3295 A G 1806 1806 36 69 69 34 0.0368 1875 2.28815e-20 TRUE 1002 1002 35 38 38 33 0.0365385 1040 4.30837e-11 TRUE +PRV 5680 C T 38 5 50 7 1 49 0.155556 45 0.00133612 TRUE 27 5 44 8 2 45 0.228571 35 0.000596701 TRUE +PRV 7916 C T 286 227 36 45 38 37 0.135952 331 4.31473e-15 TRUE 351 289 36 81 78 37 0.1875 432 5.39655e-27 TRUE +PRV 9713 C T 475 0 37 27 0 36 0.0537849 502 4.66646e-09 TRUE 374 0 37 13 0 35 0.0335917 387 0.00010474 TRUE
--- a/test-data/zika/Z52_a.tsv Mon Mar 30 06:37:01 2020 -0400 +++ b/test-data/zika/Z52_a.tsv Sat Apr 04 12:25:11 2020 -0400 @@ -1,17 +1,17 @@ -REGION POS REF ALT REF_DP REF_RV REF_QUAL ALT_DP ALT_RV ALT_QUAL ALT_FREQ TOTAL_DP PVAL PASS -PRV 350 A T 101 101 36 5 5 35 0.0471698 106 0.0304989 FALSE -PRV 722 C +A 280 234 36 9 0 20 0.0319149 282 0.0349042 FALSE -PRV 1682 C T 1097 984 37 34 33 37 0.0300088 1133 7.79053e-10 TRUE -PRV 1965 T G 302 113 37 41 3 35 0.119534 343 2.81419e-14 TRUE -PRV 2702 A G 31 31 36 1 1 23 0.03125 32 0.507937 FALSE -PRV 2781 T G 353 70 37 48 8 36 0.117936 407 4.05758e-16 TRUE -PRV 2922 C T 263 0 36 11 0 36 0.040146 274 0.000431954 TRUE -PRV 3148 Y T 0 0 0 1324 264 36 0.77563 1707 0 TRUE -PRV 3148 Y C 0 0 0 381 75 36 0.223199 1707 0 TRUE -PRV 3295 A G 1002 1002 35 38 38 33 0.0365385 1040 4.30837e-11 TRUE -PRV 5680 C T 27 5 44 8 2 45 0.228571 35 0.000596701 TRUE -PRV 5723 T G 31 31 35 1 1 21 0.03125 32 0.507937 FALSE -PRV 6201 A G 10 0 35 2 0 25 0.166667 12 0.26087 FALSE -PRV 6211 T C 8 0 36 1 0 35 0.111111 9 0.5 FALSE -PRV 7916 C T 351 289 36 81 78 37 0.1875 432 5.39655e-27 TRUE -PRV 9713 C T 374 0 37 13 0 35 0.0335917 387 0.00010474 TRUE +REGION POS REF ALT REF_DP REF_RV REF_QUAL ALT_DP ALT_RV ALT_QUAL ALT_FREQ TOTAL_DP PVAL PASS GFF_FEATURE REF_CODON REF_AA ALT_CODON ALT_AA +PRV 350 A T 101 101 36 5 5 35 0.0471698 106 0.0304989 FALSE NA NA NA NA NA +PRV 722 C +A 280 234 36 9 0 20 0.0319149 282 0.0349042 FALSE NA NA NA NA NA +PRV 1682 C T 1097 984 37 34 33 37 0.0300088 1133 7.79053e-10 TRUE NA NA NA NA NA +PRV 1965 T G 302 113 37 63 25 37 0.172603 365 4.41891e-21 TRUE NA NA NA NA NA +PRV 2702 A G 31 31 36 1 1 23 0.03125 32 0.507937 FALSE NA NA NA NA NA +PRV 2781 T G 354 70 37 48 8 36 0.117647 408 4.33605e-16 TRUE NA NA NA NA NA +PRV 2922 C T 264 0 36 11 0 36 0.04 275 0.000440953 TRUE NA NA NA NA NA +PRV 3148 Y T 0 0 0 1324 264 36 0.77563 1707 0 TRUE NA NA NA NA NA +PRV 3148 Y C 0 0 0 381 75 36 0.223199 1707 0 TRUE NA NA NA NA NA +PRV 3295 A G 1002 1002 35 38 38 33 0.0365385 1040 4.30837e-11 TRUE NA NA NA NA NA +PRV 5680 C T 27 5 44 8 2 46 0.228571 35 0.000596701 TRUE NA NA NA NA NA +PRV 5723 T G 31 31 35 1 1 21 0.03125 32 0.507937 FALSE NA NA NA NA NA +PRV 6201 A G 10 0 35 2 0 38 0.166667 12 0.26087 FALSE NA NA NA NA NA +PRV 6211 T C 8 0 36 1 0 35 0.111111 9 0.5 FALSE NA NA NA NA NA +PRV 7916 C T 351 289 36 81 78 37 0.1875 432 5.39655e-27 TRUE NA NA NA NA NA +PRV 9713 C T 374 0 37 13 0 35 0.0335917 387 0.00010474 TRUE NA NA NA NA NA
--- a/test-data/zika/primer_mismatchers_indices.txt Mon Mar 30 06:37:01 2020 -0400 +++ b/test-data/zika/primer_mismatchers_indices.txt Sat Apr 04 12:25:11 2020 -0400 @@ -1,1 +1,1 @@ -400_18_out_L** 400_18_out_R** 400_23_out_R 400_23_out_L 400_32_out_L 400_32_out_R \ No newline at end of file +400_18_out_L** 400_23_out_R 400_32_out_L \ No newline at end of file