Mercurial > repos > iuc > virhunter
changeset 3:302332b914ef draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 58587e05f604590c70550e13fc51b7425e916ed4
| author | iuc |
|---|---|
| date | Sat, 14 Jan 2023 21:08:33 +0000 |
| parents | ea2cccb9f73e |
| children | |
| files | macros.xml predict.py test-data/predicted.csv test-data/predicted.tsv test-data/predicted_fragments.csv test-data/predicted_fragments.tsv virhunter.xml |
| diffstat | 7 files changed, 2015 insertions(+), 2016 deletions(-) [+] |
line wrap: on
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--- a/macros.xml Thu Jan 05 14:27:54 2023 +0000 +++ b/macros.xml Sat Jan 14 21:08:33 2023 +0000 @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">1.0.0</token> - <token name="@VERSION_SUFFIX@">2</token> + <token name="@VERSION_SUFFIX@">3</token> <xml name="requirements"> <requirements> <requirement type="package" version="1.23.3">numpy</requirement>
--- a/predict.py Thu Jan 05 14:27:54 2023 +0000 +++ b/predict.py Sat Jan 14 21:08:33 2023 +0000 @@ -153,7 +153,6 @@ length=l_, use_10=use_10 ) - print(df) df = predict_rf( df=df, rf_weights_path=weights, @@ -168,14 +167,14 @@ df_500 = dfs_fr[0][(dfs_fr[0]['length'] >= limit) & (dfs_fr[0]['length'] < 1500)] df_1000 = dfs_fr[1][(dfs_fr[1]['length'] >= 1500)] df = pd.concat([df_1000, df_500], ignore_index=True) - pred_fr = Path(out_path, 'predicted_fragments.csv') - df.to_csv(pred_fr) + pred_fr = Path(out_path, 'predicted_fragments.tsv') + df.to_csv(pred_fr, sep='\t') df_500 = dfs_cont[0][(dfs_cont[0]['length'] >= limit) & (dfs_cont[0]['length'] < 1500)] df_1000 = dfs_cont[1][(dfs_cont[1]['length'] >= 1500)] df = pd.concat([df_1000, df_500], ignore_index=True) - pred_contigs = Path(out_path, 'predicted.csv') - df.to_csv(pred_contigs) + pred_contigs = Path(out_path, 'predicted.tsv') + df.to_csv(pred_contigs, sep='\t') if return_viral: viral_ids = list(df[df["decision"] == "virus"]["id"])
--- a/test-data/predicted.csv Thu Jan 05 14:27:54 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,274 +0,0 @@ -,length,id,# viral fragments,# plant fragments,# bacterial fragments,decision,# viral / # total,# viral / # total * length -0,19251,KY110737.1,30,2,6,virus,0.789,15189.039 -1,18478,KY707825.2,24,3,9,virus,0.667,12324.826000000001 -2,10427,AM267479.1,20,0,0,virus,1.0,10427.0 -3,9802,MT533611.1,19,0,0,virus,1.0,9802.0 -4,9798,LC537538.1,19,0,0,virus,1.0,9798.0 -5,9736,LC600465.1,19,0,0,virus,1.0,9736.0 -6,9736,LC494681.1,19,0,0,virus,1.0,9736.0 -7,9445,JN936438.1,18,0,0,virus,1.0,9445.0 -8,11892,LC602461.1,18,5,0,virus,0.783,9311.436 -9,9757,MK777994.1,18,1,0,virus,0.947,9239.878999999999 -10,9663,LC038073.1,18,1,0,virus,0.947,9150.860999999999 -11,9429,MK649741.1,17,1,0,virus,0.944,8900.975999999999 -12,9798,LC537503.1,17,0,2,virus,0.895,8769.210000000001 -13,8421,MN059369.1,16,0,0,virus,1.0,8421.0 -14,9798,AB747297.1,16,0,3,virus,0.842,8249.916 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/predicted.tsv Sat Jan 14 21:08:33 2023 +0000 @@ -0,0 +1,274 @@ + length id # viral fragments # plant fragments # bacterial fragments decision # viral / # total # viral / # total * length +0 19251 KY110737.1 30 2 6 virus 0.789 15189.039 +1 18478 KY707825.2 24 3 9 virus 0.667 12324.826000000001 +2 10427 AM267479.1 20 0 0 virus 1.0 10427.0 +3 9802 MT533611.1 19 0 0 virus 1.0 9802.0 +4 9798 LC537538.1 19 0 0 virus 1.0 9798.0 +5 9736 LC600465.1 19 0 0 virus 1.0 9736.0 +6 9736 LC494681.1 19 0 0 virus 1.0 9736.0 +7 9445 JN936438.1 18 0 0 virus 1.0 9445.0 +8 11892 LC602461.1 18 5 0 virus 0.783 9311.436 +9 9757 MK777994.1 18 1 0 virus 0.947 9239.878999999999 +10 9663 LC038073.1 18 1 0 virus 0.947 9150.860999999999 +11 9429 MK649741.1 17 1 0 virus 0.944 8900.975999999999 +12 9798 LC537503.1 17 0 2 virus 0.895 8769.210000000001 +13 8421 MN059369.1 16 0 0 virus 1.0 8421.0 +14 9798 AB747297.1 16 0 3 virus 0.842 8249.916 +15 8745 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/predicted_fragments.tsv Sat Jan 14 21:08:33 2023 +0000 @@ -0,0 +1,1730 @@ + id length fragment pred_plant_5 pred_vir_5 pred_bact_5 pred_plant_7 pred_vir_7 pred_bact_7 RF_decision RF_pred_plant RF_pred_vir RF_pred_bact +0 MT921846.1 2971 0 0.716 0.252 0.032 0.129 0.799 0.072 virus 0.19 0.782 0.028 +1 MT921846.1 2971 1 0.681 0.287 0.033 0.263 0.684 0.053 virus 0.221 0.772 0.007 +2 MT921846.1 2971 2 0.741 0.224 0.036 0.789 0.181 0.029 plant 0.878 0.065 0.057 +3 MT921846.1 2971 3 0.754 0.208 0.038 0.783 0.154 0.063 plant 0.878 0.065 0.057 +4 MT921846.1 2971 4 0.513 0.414 0.073 0.269 0.601 0.13 virus 0.324 0.584 0.091 +5 MF540775.1 3929 0 0.896 0.093 0.011 0.884 0.112 0.004 plant 0.855 0.028 0.117 +6 MF540775.1 3929 1 0.843 0.14 0.016 0.806 0.186 0.009 plant 0.85 0.053 0.098 +7 MF540775.1 3929 2 0.879 0.108 0.013 0.765 0.211 0.024 plant 0.705 0.039 0.256 +8 MF540775.1 3929 3 0.824 0.158 0.017 0.698 0.257 0.045 plant 0.804 0.129 0.066 +9 MF540775.1 3929 4 0.748 0.223 0.029 0.562 0.38 0.058 plant 0.765 0.136 0.099 +10 MF540775.1 3929 5 0.836 0.15 0.015 0.675 0.31 0.015 plant 0.804 0.129 0.066 +11 MF540775.1 3929 6 0.857 0.129 0.015 0.584 0.398 0.018 plant 0.753 0.162 0.085 +12 BK011046.1 7010 0 0.526 0.424 0.05 0.221 0.728 0.051 virus 0.303 0.692 0.004 +13 BK011046.1 7010 1 0.464 0.486 0.05 0.243 0.707 0.05 virus 0.28 0.713 0.007 +14 BK011046.1 7010 2 0.282 0.605 0.112 0.181 0.702 0.117 virus 0.04 0.919 0.041 +15 BK011046.1 7010 3 0.315 0.585 0.1 0.343 0.632 0.025 virus 0.424 0.543 0.032 +16 BK011046.1 7010 4 0.539 0.413 0.048 0.561 0.435 0.004 plant 0.855 0.093 0.052 +17 BK011046.1 7010 5 0.449 0.477 0.075 0.423 0.555 0.022 plant 0.602 0.327 0.071 +18 BK011046.1 7010 6 0.442 0.482 0.076 0.398 0.571 0.031 plant 0.565 0.347 0.088 +19 BK011046.1 7010 7 0.392 0.493 0.115 0.189 0.745 0.065 virus 0.103 0.883 0.013 +20 BK011046.1 7010 8 0.506 0.396 0.098 0.203 0.717 0.08 virus 0.316 0.671 0.013 +21 BK011046.1 7010 9 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787 2 0.073 0.922 0.005 0.232 0.767 0.001 virus 0.026 0.958 0.016 +1578 KF710809.1 1086 0 0.074 0.607 0.319 0.138 0.448 0.414 bacteria 0.241 0.343 0.416 +1579 KF710809.1 1086 1 0.039 0.956 0.005 0.288 0.708 0.004 virus 0.097 0.887 0.016 +1580 KF710809.1 1086 2 0.061 0.933 0.006 0.229 0.767 0.005 virus 0.025 0.959 0.016 +1581 KF710809.1 1086 3 0.149 0.849 0.002 0.18 0.817 0.003 virus 0.018 0.967 0.015 +1582 LC114511.1 1193 0 0.345 0.618 0.037 0.419 0.571 0.01 virus 0.334 0.648 0.018 +1583 LC114511.1 1193 1 0.012 0.966 0.022 0.045 0.947 0.009 virus 0.0 1.0 0.0 +1584 LC114511.1 1193 2 0.013 0.956 0.031 0.036 0.953 0.01 virus 0.0 1.0 0.0 +1585 LC114511.1 1193 3 0.028 0.957 0.015 0.049 0.94 0.012 virus 0.003 0.995 0.002 +1586 KF525380.1 859 0 0.643 0.331 0.026 0.673 0.305 0.022 plant 0.715 0.207 0.077 +1587 KF525380.1 859 1 0.565 0.422 0.012 0.343 0.653 0.004 virus 0.301 0.676 0.023 +1588 KF525380.1 859 2 0.272 0.71 0.018 0.132 0.864 0.005 virus 0.106 0.858 0.035 +1589 HE573849.1 1137 0 0.069 0.921 0.009 0.132 0.861 0.007 virus 0.006 0.99 0.004 +1590 HE573849.1 1137 1 0.021 0.858 0.121 0.03 0.907 0.063 virus 0.005 0.979 0.016 +1591 HE573849.1 1137 2 0.029 0.862 0.109 0.068 0.802 0.13 virus 0.022 0.97 0.008 +1592 HE573849.1 1137 3 0.094 0.88 0.026 0.197 0.792 0.011 virus 0.03 0.939 0.031 +1593 HE573795.1 1137 0 0.166 0.787 0.047 0.169 0.796 0.035 virus 0.024 0.964 0.012 +1594 HE573795.1 1137 1 0.066 0.839 0.095 0.189 0.795 0.017 virus 0.127 0.756 0.117 +1595 HE573795.1 1137 2 0.065 0.905 0.03 0.25 0.736 0.015 virus 0.027 0.951 0.022 +1596 HE573795.1 1137 3 0.098 0.891 0.012 0.276 0.718 0.006 virus 0.093 0.88 0.027 +1597 MK357282.1 1358 0 0.089 0.884 0.027 0.132 0.852 0.016 virus 0.015 0.973 0.012 +1598 MK357282.1 1358 1 0.044 0.948 0.007 0.104 0.892 0.004 virus 0.005 0.991 0.004 +1599 MK357282.1 1358 2 0.285 0.691 0.024 0.56 0.42 0.019 virus 0.474 0.48 0.045 +1600 MK357282.1 1358 3 0.203 0.703 0.094 0.211 0.566 0.223 virus 0.176 0.691 0.132 +1601 MK357282.1 1358 4 0.11 0.747 0.143 0.199 0.535 0.266 virus 0.13 0.67 0.199 +1602 MW519386.1 756 0 0.382 0.588 0.03 0.447 0.522 0.031 virus 0.442 0.54 0.018 +1603 MW519386.1 756 1 0.434 0.561 0.006 0.561 0.437 0.002 plant 0.556 0.416 0.028 +1604 MW519386.1 756 2 0.424 0.571 0.005 0.569 0.428 0.002 plant 0.556 0.416 0.028 +1605 JQ619105.1 810 0 0.035 0.963 0.002 0.078 0.919 0.003 virus 0.005 0.991 0.004 +1606 JQ619105.1 810 1 0.04 0.937 0.023 0.062 0.903 0.035 virus 0.003 0.995 0.002 +1607 JQ619105.1 810 2 0.023 0.969 0.008 0.027 0.966 0.007 virus 0.003 0.987 0.01 +1608 HQ335265.1 890 0 0.486 0.506 0.008 0.517 0.473 0.01 plant 0.52 0.452 0.028 +1609 HQ335265.1 890 1 0.136 0.841 0.023 0.215 0.739 0.047 virus 0.133 0.853 0.015 +1610 HQ335265.1 890 2 0.097 0.88 0.023 0.108 0.877 0.015 virus 0.007 0.985 0.008 +1611 EU384589.1 1370 0 0.056 0.938 0.006 0.106 0.888 0.006 virus 0.005 0.991 0.004 +1612 EU384589.1 1370 1 0.084 0.91 0.007 0.147 0.85 0.003 virus 0.015 0.973 0.012 +1613 EU384589.1 1370 2 0.195 0.785 0.02 0.76 0.221 0.02 plant 0.69 0.26 0.05 +1614 EU384589.1 1370 3 0.087 0.864 0.048 0.141 0.808 0.052 virus 0.015 0.973 0.012 +1615 EU384589.1 1370 4 0.066 0.772 0.162 0.16 0.723 0.117 virus 0.098 0.781 0.12 +1616 DQ364987.1 867 0 0.044 0.937 0.019 0.265 0.679 0.056 virus 0.054 0.915 0.03 +1617 DQ364987.1 867 1 0.045 0.944 0.011 0.175 0.786 0.039 virus 0.026 0.97 0.004 +1618 DQ364987.1 867 2 0.072 0.914 0.014 0.183 0.777 0.04 virus 0.029 0.961 0.01 +1619 KC979054.1 1002 0 0.116 0.881 0.003 0.313 0.686 0.0 virus 0.082 0.889 0.029 +1620 KC979054.1 1002 1 0.046 0.951 0.003 0.116 0.884 0.001 virus 0.005 0.991 0.004 +1621 KC979054.1 1002 2 0.028 0.95 0.022 0.078 0.912 0.01 virus 0.005 0.991 0.004 +1622 KC979054.1 1002 3 0.029 0.945 0.026 0.082 0.903 0.015 virus 0.005 0.991 0.004 +1623 KR076680.1 871 0 0.029 0.908 0.063 0.058 0.892 0.05 virus 0.005 0.987 0.008 +1624 KR076680.1 871 1 0.026 0.961 0.013 0.03 0.965 0.005 virus 0.003 0.987 0.01 +1625 KR076680.1 871 2 0.024 0.967 0.009 0.079 0.919 0.002 virus 0.005 0.991 0.004 +1626 KF010516.1 960 0 0.018 0.189 0.793 0.082 0.166 0.752 bacteria 0.239 0.092 0.669 +1627 KF010516.1 960 1 0.099 0.763 0.137 0.108 0.148 0.744 bacteria 0.218 0.088 0.694 +1628 KF010516.1 960 2 0.097 0.831 0.072 0.239 0.426 0.335 virus 0.152 0.435 0.413 +1629 AF127934.1 1105 0 0.066 0.926 0.008 0.156 0.835 0.009 virus 0.013 0.983 0.004 +1630 AF127934.1 1105 1 0.016 0.911 0.072 0.041 0.953 0.006 virus 0.002 0.992 0.006 +1631 AF127934.1 1105 2 0.047 0.931 0.022 0.069 0.917 0.014 virus 0.003 0.995 0.002 +1632 AF127934.1 1105 3 0.029 0.955 0.015 0.051 0.941 0.008 virus 0.003 0.995 0.002 +1633 AJ875102.1 1074 0 0.112 0.876 0.012 0.308 0.66 0.033 virus 0.082 0.877 0.041 +1634 AJ875102.1 1074 1 0.284 0.694 0.022 0.293 0.683 0.024 virus 0.161 0.784 0.056 +1635 AJ875102.1 1074 2 0.041 0.94 0.019 0.042 0.931 0.027 virus 0.003 0.995 0.002 +1636 AJ875102.1 1074 3 0.02 0.971 0.009 0.021 0.96 0.019 virus 0.003 0.987 0.01 +1637 AY839627.1 1421 0 0.501 0.492 0.007 0.522 0.476 0.002 plant 0.52 0.452 0.028 +1638 AY839627.1 1421 1 0.298 0.625 0.077 0.273 0.7 0.026 virus 0.235 0.678 0.086 +1639 AY839627.1 1421 2 0.192 0.638 0.17 0.239 0.648 0.114 virus 0.268 0.626 0.106 +1640 AY839627.1 1421 3 0.122 0.799 0.079 0.639 0.339 0.022 plant 0.702 0.252 0.046 +1641 AY839627.1 1421 4 0.256 0.702 0.042 0.789 0.202 0.009 plant 0.73 0.216 0.054 +1642 AB697885.1 1216 0 0.534 0.444 0.022 0.559 0.434 0.007 plant 0.546 0.426 0.028 +1643 AB697885.1 1216 1 0.584 0.327 0.089 0.553 0.435 0.011 plant 0.618 0.35 0.032 +1644 AB697885.1 1216 2 0.755 0.179 0.066 0.698 0.295 0.007 plant 0.657 0.229 0.114 +1645 AB697885.1 1216 3 0.803 0.109 0.089 0.752 0.218 0.03 plant 0.674 0.157 0.169 +1646 KY473725.1 1035 0 0.164 0.521 0.315 0.309 0.56 0.131 virus 0.293 0.549 0.158 +1647 KY473725.1 1035 1 0.16 0.795 0.045 0.231 0.728 0.042 virus 0.095 0.892 0.012 +1648 KY473725.1 1035 2 0.533 0.452 0.016 0.505 0.49 0.005 plant 0.557 0.416 0.028 +1649 KY473725.1 1035 3 0.411 0.577 0.011 0.505 0.493 0.003 plant 0.52 0.452 0.028 +1650 JQ954315.1 801 0 0.209 0.785 0.006 0.134 0.86 0.006 virus 0.024 0.964 0.012 +1651 JQ954315.1 801 1 0.053 0.932 0.015 0.08 0.905 0.015 virus 0.005 0.991 0.004 +1652 JQ954315.1 801 2 0.067 0.924 0.009 0.099 0.895 0.005 virus 0.005 0.991 0.004 +1653 MK876224.1 833 0 0.434 0.556 0.009 0.542 0.453 0.005 plant 0.556 0.416 0.028 +1654 MK876224.1 833 1 0.468 0.49 0.042 0.755 0.204 0.04 plant 0.753 0.205 0.041 +1655 MK876224.1 833 2 0.553 0.384 0.063 0.605 0.326 0.069 plant 0.632 0.319 0.048 +1656 KF711177.1 1027 0 0.049 0.892 0.058 0.066 0.891 0.044 virus 0.005 0.987 0.008 +1657 KF711177.1 1027 1 0.059 0.938 0.003 0.102 0.897 0.001 virus 0.005 0.991 0.004 +1658 KF711177.1 1027 2 0.289 0.706 0.005 0.419 0.579 0.003 virus 0.332 0.642 0.026 +1659 KF711177.1 1027 3 0.174 0.821 0.005 0.246 0.752 0.002 virus 0.041 0.94 0.019 +1660 LN880826.1 1361 0 0.228 0.746 0.026 0.504 0.486 0.01 virus 0.401 0.563 0.036 +1661 LN880826.1 1361 1 0.139 0.787 0.074 0.113 0.87 0.017 virus 0.024 0.964 0.012 +1662 LN880826.1 1361 2 0.3 0.682 0.018 0.554 0.44 0.006 virus 0.462 0.52 0.018 +1663 LN880826.1 1361 3 0.418 0.569 0.013 0.653 0.334 0.013 plant 0.662 0.3 0.039 +1664 LN880826.1 1361 4 0.21 0.784 0.006 0.43 0.565 0.004 virus 0.403 0.571 0.026 +1665 MF043148.1 822 0 0.002 0.03 0.968 0.055 0.24 0.705 bacteria 0.13 0.143 0.727 +1666 MF043148.1 822 1 0.014 0.571 0.414 0.027 0.266 0.707 bacteria 0.114 0.136 0.749 +1667 MF043148.1 822 2 0.013 0.525 0.462 0.027 0.239 0.733 bacteria 0.154 0.136 0.709 +1668 MH894504.1 1194 0 0.045 0.927 0.029 0.199 0.704 0.096 virus 0.111 0.873 0.016 +1669 MH894504.1 1194 1 0.042 0.936 0.021 0.23 0.576 0.194 virus 0.065 0.829 0.106 +1670 MH894504.1 1194 2 0.09 0.896 0.014 0.174 0.784 0.042 virus 0.028 0.96 0.012 +1671 MH894504.1 1194 3 0.128 0.864 0.007 0.27 0.728 0.002 virus 0.094 0.892 0.015 +1672 FM883186.1 1298 0 0.082 0.89 0.028 0.477 0.513 0.011 virus 0.222 0.686 0.092 +1673 FM883186.1 1298 1 0.084 0.793 0.123 0.343 0.635 0.022 virus 0.307 0.571 0.122 +1674 FM883186.1 1298 2 0.092 0.887 0.021 0.125 0.868 0.007 virus 0.007 0.982 0.012 +1675 FM883186.1 1298 3 0.117 0.869 0.013 0.184 0.814 0.002 virus 0.018 0.967 0.015 +1676 FM883186.1 1298 4 0.147 0.843 0.01 0.205 0.792 0.003 virus 0.133 0.853 0.015 +1677 KC007531.1 1293 0 0.106 0.826 0.068 0.106 0.87 0.024 virus 0.024 0.964 0.012 +1678 KC007531.1 1293 1 0.115 0.858 0.026 0.461 0.535 0.004 virus 0.472 0.509 0.019 +1679 KC007531.1 1293 2 0.378 0.607 0.015 0.766 0.215 0.019 plant 0.753 0.205 0.041 +1680 KC007531.1 1293 3 0.044 0.906 0.049 0.171 0.818 0.011 virus 0.015 0.975 0.01 +1681 KC007531.1 1293 4 0.056 0.928 0.016 0.147 0.849 0.004 virus 0.013 0.983 0.004 +1682 MK098183.1 1350 0 0.112 0.866 0.021 0.218 0.767 0.015 virus 0.036 0.937 0.027 +1683 MK098183.1 1350 1 0.081 0.914 0.005 0.132 0.866 0.002 virus 0.007 0.982 0.012 +1684 MK098183.1 1350 2 0.29 0.698 0.012 0.676 0.315 0.009 plant 0.637 0.307 0.056 +1685 MK098183.1 1350 3 0.152 0.842 0.006 0.342 0.63 0.028 virus 0.273 0.627 0.1 +1686 MK098183.1 1350 4 0.069 0.924 0.006 0.307 0.67 0.023 virus 0.154 0.815 0.03 +1687 MN814413.1 846 0 0.093 0.864 0.043 0.112 0.839 0.05 virus 0.015 0.973 0.012 +1688 MN814413.1 846 1 0.264 0.72 0.015 0.051 0.938 0.011 virus 0.105 0.862 0.033 +1689 MN814413.1 846 2 0.192 0.802 0.005 0.056 0.939 0.005 virus 0.022 0.968 0.01 +1690 FJ859737.1 1075 0 0.136 0.271 0.593 0.231 0.534 0.235 virus 0.176 0.606 0.217 +1691 FJ859737.1 1075 1 0.34 0.637 0.023 0.261 0.728 0.011 virus 0.28 0.707 0.012 +1692 FJ859737.1 1075 2 0.176 0.812 0.011 0.439 0.553 0.008 plant 0.514 0.478 0.008 +1693 FJ859737.1 1075 3 0.101 0.892 0.007 0.191 0.806 0.003 virus 0.033 0.952 0.015 +1694 KX420987.1 938 0 0.028 0.967 0.005 0.047 0.946 0.007 virus 0.003 0.995 0.002 +1695 KX420987.1 938 1 0.024 0.963 0.013 0.031 0.94 0.029 virus 0.003 0.987 0.01 +1696 KX420987.1 938 2 0.045 0.889 0.065 0.06 0.871 0.069 virus 0.005 0.987 0.008 +1697 KX418448.1 945 0 0.506 0.482 0.012 0.326 0.669 0.005 virus 0.417 0.56 0.023 +1698 KX418448.1 945 1 0.7 0.295 0.005 0.808 0.191 0.001 plant 0.811 0.126 0.063 +1699 KX418448.1 945 2 0.349 0.646 0.005 0.666 0.332 0.002 plant 0.663 0.312 0.026 +1700 KC985038.1 873 0 0.12 0.796 0.084 0.414 0.503 0.083 virus 0.459 0.479 0.062 +1701 KC985038.1 873 1 0.038 0.919 0.043 0.129 0.858 0.012 virus 0.013 0.983 0.004 +1702 KC985038.1 873 2 0.024 0.968 0.008 0.049 0.949 0.002 virus 0.003 0.995 0.002 +1703 MN955028.1 795 0 0.063 0.896 0.041 0.072 0.769 0.159 virus 0.026 0.966 0.008 +1704 MN955028.1 795 1 0.102 0.863 0.035 0.083 0.902 0.016 virus 0.007 0.985 0.008 +1705 MN955028.1 795 2 0.095 0.879 0.027 0.088 0.899 0.013 virus 0.007 0.982 0.012 +1706 KC466374.1 1075 0 0.227 0.745 0.028 0.164 0.742 0.094 virus 0.08 0.88 0.04 +1707 KC466374.1 1075 1 0.182 0.809 0.01 0.176 0.819 0.005 virus 0.027 0.954 0.019 +1708 KC466374.1 1075 2 0.141 0.849 0.01 0.33 0.663 0.007 virus 0.18 0.792 0.028 +1709 KC466374.1 1075 3 0.129 0.867 0.004 0.216 0.782 0.003 virus 0.037 0.949 0.015 +1710 HM035070.1 920 0 0.221 0.767 0.012 0.463 0.531 0.006 virus 0.375 0.606 0.018 +1711 HM035070.1 920 1 0.092 0.866 0.042 0.109 0.872 0.019 virus 0.007 0.982 0.012 +1712 HM035070.1 920 2 0.125 0.846 0.03 0.273 0.707 0.02 virus 0.14 0.845 0.015 +1713 KF711199.1 1028 0 0.06 0.916 0.024 0.063 0.925 0.012 virus 0.005 0.987 0.008 +1714 KF711199.1 1028 1 0.101 0.897 0.003 0.155 0.844 0.001 virus 0.007 0.985 0.008 +1715 KF711199.1 1028 2 0.283 0.713 0.005 0.634 0.363 0.003 plant 0.646 0.29 0.064 +1716 KF711199.1 1028 3 0.179 0.817 0.004 0.454 0.542 0.004 virus 0.478 0.509 0.013 +1717 JF828185.1 1023 0 0.376 0.525 0.099 0.513 0.422 0.065 plant 0.587 0.391 0.022 +1718 JF828185.1 1023 1 0.624 0.212 0.163 0.498 0.337 0.165 plant 0.545 0.306 0.149 +1719 JF828185.1 1023 2 0.21 0.441 0.349 0.274 0.624 0.102 virus 0.193 0.582 0.225 +1720 JF828185.1 1023 3 0.166 0.531 0.303 0.275 0.631 0.094 virus 0.26 0.515 0.225 +1721 MN901875.1 1151 0 0.127 0.676 0.197 0.152 0.698 0.15 virus 0.128 0.815 0.057 +1722 MN901875.1 1151 1 0.202 0.775 0.023 0.082 0.894 0.024 virus 0.024 0.964 0.012 +1723 MN901875.1 1151 2 0.035 0.958 0.007 0.039 0.905 0.056 virus 0.003 0.995 0.002 +1724 MN901875.1 1151 3 0.025 0.966 0.009 0.042 0.936 0.022 virus 0.003 0.995 0.002 +1725 MN167135.1 1139 0 0.046 0.855 0.098 0.279 0.38 0.342 virus 0.172 0.42 0.408 +1726 MN167135.1 1139 1 0.072 0.9 0.028 0.201 0.729 0.07 virus 0.029 0.949 0.022 +1727 MN167135.1 1139 2 0.061 0.916 0.024 0.215 0.779 0.006 virus 0.027 0.951 0.022 +1728 MN167135.1 1139 3 0.117 0.877 0.006 0.314 0.684 0.002 virus 0.082 0.889 0.029
--- a/virhunter.xml Thu Jan 05 14:27:54 2023 +0000 +++ b/virhunter.xml Sat Jan 14 21:08:33 2023 +0000 @@ -18,8 +18,8 @@ --out_path '${predicted_fragments.extra_files_path}' --return_viral True --limit $limit - && cp '${predicted_fragments.extra_files_path}'/predicted_fragments.csv predicted_fragments.csv - && cp '${predicted_fragments.extra_files_path}'/predicted.csv predicted.csv + && cp '${predicted_fragments.extra_files_path}'/predicted_fragments.tsv predicted_fragments.tsv + && cp '${predicted_fragments.extra_files_path}'/predicted.tsv predicted.tsv && cp '${predicted_fragments.extra_files_path}'/viral.fasta viral.fasta ]]></command> @@ -33,16 +33,16 @@ <param argument="--limit" type="integer" min="0" value="750" label="Minimum contig length" help="Do not predict contigs shorter than this value. Default: 750" /> </inputs> <outputs> - <data format="csv" name="predicted_fragments" from_work_dir="predicted_fragments.csv" label="${tool.name} on ${on_string}: predicted fragments"/> - <data format="csv" name="predicted" from_work_dir="predicted.csv" label="${tool.name} on ${on_string}: predicted "/> + <data format="tabular" name="predicted_fragments" from_work_dir="predicted_fragments.tsv" label="${tool.name} on ${on_string}: predicted fragments"/> + <data format="tabular" name="predicted" from_work_dir="predicted.tsv" label="${tool.name} on ${on_string}: predicted "/> <data format="fasta" name="viral" from_work_dir="viral.fasta" label="${tool.name} on ${on_string}: viral FASTA file" /> </outputs> <tests> <test> <param name="fasta_file" value="viruses.fasta"/> <param name="weights" value="test"/> - <output name="predicted_fragments" file="predicted_fragments.csv" ftype="csv" lines_diff="2"/> - <output name="predicted" file="predicted.csv" ftype="csv" lines_diff="2"/> + <output name="predicted_fragments" file="predicted_fragments.tsv" ftype="tabular" lines_diff="2"/> + <output name="predicted" file="predicted.tsv" ftype="tabular" lines_diff="2"/> <output name="viral" file="viral.fasta" ftype="fasta" lines_diff="2"/> </test> </tests>