| Previous changeset 0:74093fb62bdf (2016-08-17) Next changeset 2:bdb752f3c6bb (2019-02-07) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit e0cd7ae10ce97bed51594e7cc0b969a803d698b7 |
|
modified:
macros.xml progressivemauve.xml test-data/1.gff3 test-data/1.xmfa xmfa2gff3.py xmfa2gff3.xml |
|
added:
test-data/2.xmfa |
|
removed:
tool_dependencies.xml |
| b |
| diff -r 74093fb62bdf -r bca52822843e macros.xml --- a/macros.xml Wed Aug 17 14:46:55 2016 -0400 +++ b/macros.xml Fri Sep 07 11:30:11 2018 -0400 |
| b |
| @@ -2,14 +2,11 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="2.4.0">progressivemauve</requirement> - <requirement type="package" version="2.7">python</requirement> - <requirement type="package" version="1.65">biopython</requirement> - <requirement type="package" version="0.6.2">bcbiogff</requirement> + <requirement type="package" version="snapshot_2015_02_13">progressivemauve</requirement> <yield/> </requirements> </xml> - <token name="@WRAPPER_VERSION@">2.4.0</token> + <token name="@WRAPPER_VERSION@">2015_02_13</token> <xml name="stdio"> <stdio> <!-- Anything other than zero is an error --> |
| b |
| diff -r 74093fb62bdf -r bca52822843e progressivemauve.xml --- a/progressivemauve.xml Wed Aug 17 14:46:55 2016 -0400 +++ b/progressivemauve.xml Fri Sep 07 11:30:11 2018 -0400 |
| [ |
| @@ -191,10 +191,10 @@ </change_format> </data> <data format="nhx" name="output_guide_tree_file" label="${tool.name} alignment of ${on_string}: Guide tree"> - <when>output_guide_tree</when> + <filter>output_guide_tree</filter> </data> <data format="tabular" name="output_backbone_file" label="${tool.name} alignment of ${on_string}: Backbone"> - <when>output_backbone</when> + <filter>output_guide_tree</filter> </data> </outputs> <tests> @@ -204,12 +204,12 @@ </test> <test> <param name="sequences" value="merged.fa" /> - <output name="output" file="1.xmfa" lines_diff="20"/> + <output name="output" file="2.xmfa" lines_diff="20"/> </test> <test> <param name="sequences" value="merged.fa" /> <param name="output_guide_tree" value="True" /> - <output name="output" file="1.xmfa" lines_diff="20"/> + <output name="output" file="2.xmfa" lines_diff="20"/> <output name="output_guide_tree_file" file="1.nhx" /> </test> <test> @@ -220,7 +220,7 @@ <test> <param name="sequences" value="merged.fa" /> <param name="match_input" value="1.mums" /> - <output name="output" file="1.xmfa" lines_diff="24"/> + <output name="output" file="2.xmfa" lines_diff="24"/> </test> </tests> <help><![CDATA[ |
| b |
| diff -r 74093fb62bdf -r bca52822843e test-data/1.gff3 --- a/test-data/1.gff3 Wed Aug 17 14:46:55 2016 -0400 +++ b/test-data/1.gff3 Fri Sep 07 11:30:11 2018 -0400 |
| b |
| @@ -1,25 +1,82 @@ ##gff-version 3 ##sequence-region karma 1 1 -karma progressiveMauve match 83032 140930 . - . ID=phagey;target=phagey -karma progressiveMauve match_part 83032 83041 50.0 + . Parent=phagey -karma progressiveMauve match_part 83042 83051 60.0 + . Parent=phagey -karma progressiveMauve match_part 83060 83069 60.0 + . Parent=phagey -karma progressiveMauve match_part 83070 83079 40.0 + . Parent=phagey -karma progressiveMauve match_part 83080 83089 40.0 + . Parent=phagey -karma progressiveMauve match_part 83108 83117 40.0 + . Parent=phagey -karma progressiveMauve match_part 83125 83134 70.0 + . Parent=phagey -karma progressiveMauve match_part 83144 83153 60.0 + . Parent=phagey -karma progressiveMauve match_part 83154 83163 40.0 + . Parent=phagey -karma progressiveMauve match_part 83164 83173 70.0 + . Parent=phagey -karma progressiveMauve match_part 83196 83205 40.0 + . Parent=phagey -karma progressiveMauve match_part 83206 83215 30.0 + . Parent=phagey -karma progressiveMauve match_part 140791 140800 40.0 + . Parent=phagey -karma progressiveMauve match_part 140801 140810 20.0 + . Parent=phagey -karma progressiveMauve match_part 140811 140820 60.0 + . Parent=phagey -karma progressiveMauve match_part 140821 140830 50.0 + . Parent=phagey -karma progressiveMauve match_part 140831 140840 50.0 + . Parent=phagey -karma progressiveMauve match_part 140841 140850 60.0 + . Parent=phagey -karma progressiveMauve match_part 140851 140860 20.0 + . Parent=phagey -karma progressiveMauve match_part 140861 140870 50.0 + . Parent=phagey -karma progressiveMauve match_part 140871 140880 40.0 + . Parent=phagey -karma progressiveMauve match_part 140906 140915 80.0 + . Parent=phagey +karma progressiveMauve match 83044 149558 . - . ID=phagey;target=phagey +karma progressiveMauve match_part 83044 83053 30.0 + . Parent=phagey +karma progressiveMauve match_part 83054 83063 70.0 + . Parent=phagey +karma progressiveMauve match_part 83064 83073 30.0 + . Parent=phagey +karma progressiveMauve match_part 83074 83083 40.0 + . Parent=phagey +karma progressiveMauve match_part 83084 83093 50.0 + . Parent=phagey +karma progressiveMauve match_part 83094 83103 30.0 + . Parent=phagey +karma progressiveMauve match_part 83104 83113 10.0 + . Parent=phagey +karma progressiveMauve match_part 83114 83123 60.0 + . Parent=phagey +karma progressiveMauve match_part 83124 83133 60.0 + . Parent=phagey +karma progressiveMauve match_part 83134 83143 40.0 + . Parent=phagey +karma progressiveMauve match_part 83144 83153 40.0 + . Parent=phagey +karma progressiveMauve match_part 83154 83163 50.0 + . Parent=phagey +karma progressiveMauve match_part 83164 83173 30.0 + . Parent=phagey +karma progressiveMauve match_part 83174 83183 50.0 + . Parent=phagey +karma progressiveMauve match_part 83184 83193 30.0 + . Parent=phagey +karma progressiveMauve match_part 83203 83212 70.0 + . Parent=phagey +karma progressiveMauve match_part 83213 83222 60.0 + . Parent=phagey +karma progressiveMauve match_part 83223 83232 60.0 + . Parent=phagey +karma progressiveMauve match_part 83233 83242 20.0 + . Parent=phagey +karma progressiveMauve match_part 85518 85527 20.0 + . Parent=phagey +karma progressiveMauve match_part 85528 85537 70.0 + . Parent=phagey +karma progressiveMauve match_part 85538 85547 20.0 + . Parent=phagey +karma progressiveMauve match_part 85554 85563 30.0 + . Parent=phagey +karma progressiveMauve match_part 85564 85573 30.0 + . Parent=phagey +karma progressiveMauve match_part 85574 85583 50.0 + . Parent=phagey +karma progressiveMauve match_part 85602 85611 60.0 + . Parent=phagey +karma progressiveMauve match_part 85612 85621 10.0 + . Parent=phagey +karma progressiveMauve match_part 85622 85631 50.0 + . Parent=phagey +karma progressiveMauve match_part 85632 85641 30.0 + . Parent=phagey +karma progressiveMauve match_part 85642 85651 50.0 + . Parent=phagey +karma progressiveMauve match_part 85660 85669 50.0 + . Parent=phagey +karma progressiveMauve match_part 86170 86179 50.0 + . Parent=phagey +karma progressiveMauve match_part 86180 86189 40.0 + . Parent=phagey +karma progressiveMauve match_part 86190 86199 60.0 + . Parent=phagey +karma progressiveMauve match_part 86200 86209 20.0 + . Parent=phagey +karma progressiveMauve match_part 86210 86219 30.0 + . Parent=phagey +karma progressiveMauve match_part 86220 86229 30.0 + . Parent=phagey +karma progressiveMauve match_part 86230 86239 40.0 + . Parent=phagey +karma progressiveMauve match_part 86240 86249 20.0 + . Parent=phagey +karma progressiveMauve match_part 86250 86259 60.0 + . Parent=phagey +karma progressiveMauve match_part 86260 86269 50.0 + . Parent=phagey +karma progressiveMauve match_part 86270 86279 30.0 + . Parent=phagey +karma progressiveMauve match_part 86280 86289 30.0 + . Parent=phagey +karma progressiveMauve match_part 86298 86307 60.0 + . Parent=phagey +karma progressiveMauve match_part 86308 86317 30.0 + . Parent=phagey +karma progressiveMauve match_part 86318 86327 40.0 + . Parent=phagey +karma progressiveMauve match_part 86328 86337 60.0 + . Parent=phagey +karma progressiveMauve match_part 86338 86347 50.0 + . Parent=phagey +karma progressiveMauve match_part 86348 86357 30.0 + . Parent=phagey +karma progressiveMauve match_part 86358 86367 30.0 + . Parent=phagey +karma progressiveMauve match_part 86368 86377 70.0 + . Parent=phagey +karma progressiveMauve match_part 86378 86387 30.0 + . Parent=phagey +karma progressiveMauve match_part 86405 86414 40.0 + . Parent=phagey +karma progressiveMauve match_part 91694 91703 80.0 + . Parent=phagey +karma progressiveMauve match_part 91704 91713 30.0 + . Parent=phagey +karma progressiveMauve match_part 91714 91723 40.0 + . Parent=phagey +karma progressiveMauve match_part 91724 91733 30.0 + . Parent=phagey +karma progressiveMauve match_part 91742 91751 60.0 + . Parent=phagey +karma progressiveMauve match_part 91759 91768 50.0 + . Parent=phagey +karma progressiveMauve match_part 91778 91787 40.0 + . Parent=phagey +karma progressiveMauve match_part 91788 91797 70.0 + . Parent=phagey +karma progressiveMauve match_part 91798 91807 40.0 + . Parent=phagey +karma progressiveMauve match_part 91816 91825 50.0 + . Parent=phagey +karma progressiveMauve match_part 91830 91839 60.0 + . Parent=phagey +karma progressiveMauve match_part 91840 91849 30.0 + . Parent=phagey +karma progressiveMauve match_part 91850 91859 20.0 + . Parent=phagey +karma progressiveMauve match_part 91860 91869 50.0 + . Parent=phagey +karma progressiveMauve match_part 91870 91879 30.0 + . Parent=phagey +karma progressiveMauve match_part 91880 91889 60.0 + . Parent=phagey +karma progressiveMauve match_part 91890 91899 30.0 + . Parent=phagey +karma progressiveMauve match_part 149454 149463 60.0 + . Parent=phagey +karma progressiveMauve match_part 149464 149473 50.0 + . Parent=phagey +karma progressiveMauve match_part 149474 149483 50.0 + . Parent=phagey +karma progressiveMauve match_part 149484 149493 50.0 + . Parent=phagey +karma progressiveMauve match_part 149494 149503 20.0 + . Parent=phagey +karma progressiveMauve match_part 149504 149513 60.0 + . Parent=phagey +karma progressiveMauve match_part 149514 149523 40.0 + . Parent=phagey +karma progressiveMauve match_part 149531 149540 60.0 + . Parent=phagey +karma progressiveMauve match_part 149549 149558 70.0 + . Parent=phagey |
| b |
| diff -r 74093fb62bdf -r bca52822843e test-data/1.xmfa --- a/test-data/1.xmfa Wed Aug 17 14:46:55 2016 -0400 +++ b/test-data/1.xmfa Fri Sep 07 11:30:11 2018 -0400 |
| b |
| b'@@ -1,2385 +1,4539 @@\n #FormatVersion Mauve1\n-#Sequence1File\ttest-data/phagey.fa\n+#Sequence1File\tdataset_1.dat\n #Sequence1Format\tFastA\n-#Sequence2File\ttest-data/karma.fa\n+#Sequence2File\tdataset_2.dat\n #Sequence2Format\tFastA\n-#BackboneFile\ttest-data/1.xmfa.bbcols\n-> 1:83031-140929 - test-data/phagey.fa\n-ttttctcctcttttttcttagt--gaccgagggctttttaccctcggatggtttactttcactgagtct--agatgttaa\n-atatttatgta---gtttaccagtgaatga-ccccattatacatcaccgccttagtgtaagacaagcctt--atttactt\n-ttagtca------cggaaaacgaagtagccaataccaagaccgatcattacgtggtaaaaatcattccaatatgcagctg\n-ctctagggaagtttaactcacctaaaatcgcccagatcatcgaaccaacaaatgaagatacaactaaccagattattagt\n-ttaccataactcatgcgtgttcccctcctcagtcaataataacgtatattttctttaactctttttctagttctacttcc\n-caggatcgtaactcacttctaagtgcgtataatgccacggttgggaggttatttcgttcttcgactaaacgtaccccctc\n-ctttaggcctgctatgccctgtcgtatggaacttatggagctacacacctgaatacctgttgttagcctcttttcgaaat\n-ttgcaagagacaagtcaccttcccagtgaattactcgggaagcacatacagcctggtaattttcctctgcttccttctct\n-gctttcgcatcatttccttggtagttgcctcgcatactacgccaaaactctatacgatcgtgtagctggtgccctgtaat\n-ttgctcaagattcactcacttacacctccttaaaggtaactttagcaaaattgtctaattcttctactgcagaaacgtga\n-gccccttttataagctcgtaggctaggctatcaaaacctagtttggattctgcctccaccgatgctttctccgttatatg\n-cactctgttctctaattcctcatatgttttaactatctgccctacagtcattgtacgttgcctcatattaactctcctcc\n-atttcttcttcttcttgtaaaataattcggtacttttcacgagtaagacgctcaatatatgcttcgacatcggatatata\n-agcctctagtagcggtggcgttttattttcgatgcaaccaccatacctgtacttatgctcaacctctcgtaacgtagcca\n-aatcgtcttgagccatttcgagtgccttctctatacccttcttgcctagcgcttgtatagcttctctgcttgccttagta\n-tcatatttacggataatagcctcaagcacaccaatatggtgctgtaatgttgctatctgcttcttcaactcgtatattgt\n-ttgtgaagcgcttttctctttttctgctttcgcatcatttccttggtagttgcctcgcatactacgccaaaactctatac\n-gatcgtgtagctggtgccctgtaatttgctcaaaattcattcgtctaccccccgaaacaataacatattttttccgcttc\n-tctttttctgctttgttatctctactattgaacataattaattctcctcctttgtcggtgtaaacctcactaacgcataa\n-tccgcagcacatagtccatttaactcttgttctagtcgagatagctccctgtttaacgtttgtgtagctgcattgatttg\n-aggtagtctagtattagctatagcatctttaccctctaatagttgttctttcttcttataggctgagtaaatgctaaagt\n-agatgtcataagcgtttcggtcaggtacacctagaactaagctacctcctggtttatcagctaaatgatacacatgtgcc\n-tctgctgcctccttaactttcattagcttatctcgttcctctaggagcacctgcgatccttttgataatcctcctcgttt\n-ctctactacatacattcttgccacttcaatttccttaatatcctccatcgtatgacgtagtgcctgataaatttcaatac\n-ctgttgtcagtttttcgaatttcatattatttgtcctcctctaatttagctattcttttttcaaggctcgctatacactt\n-agcttgctcgctcattaaagccataacatcgtcaaatgtatctgttaatttatcaagtatgatagtcatttttaacatgt\n-taaactctgttgtcggttccatattagttatcctcctaggggactacttagtttaagcatcccgtatagtgtaaatattc\n-ctgttaaaggtagtaaagggtcgagggccggagccttaaaagggttatgttcctcgactggttgggttgttacactcggc\n-tcctggactttcttttgtacaacgggttctttatatgtaggttgttgctctaaggtggcgatccgctgctctaactcgat\n-ggtgttggtatggtaagctttcctggtagcatccatttggagtgctagtctattgatctggtaatcttggtacttttgat\n-gttgcataagataagcgtacttccctgcaatcatatttgctgtaacaaagagtaacaatattagtaagagtatgagaaga\n-cgcttaaaccattttcgcttagttggtttgcgtttcttctgcataaggtttacttctcctttctgcggtgactggccatg\n-taacctagtgtataagcgcctagaaaagtaatcataagctgtgtaataactgacgtatgttggtcggccactaagccatc\n-tgtgacccctactgcagcagccgtcaataaaataataccagcgtcgattaaaaagtttttcatttaattttcctccttct\n-ctgaatctatctttattgtacaagcttatatactaaaagtcaatacttatttaaaaaaaaatctgagggagtttttagct\n-ccctacattgatccggaaattaactgcatcgatgtcgatatgtgatagtacagtctttaactcgtctaacttcgcaataa\n-cctcctccttagaaaccatttgaccagacacgttaaaattaaagttatactctactttagctttactctctttaactaat\n-tctggttcgtcccattgctctctatttaggctattggctagtgcagccatctcttcttttgaaaacttatttttctcgtc\n-cattttgttcacgtagttcatcatcccttctgcttgtactcttatcatatgtgtagctaactgtttaccttgctcctcca\n-ttcgttgcatagccggagacaactcagcgttacctaacacgtatatatcttttggtggagtcggtgttgcaataggctgt\n-aacggtaccttcttagctaccggaacactaataggtggcgtagcctgtacaggagtagcttgagtaggtgctggtttctt\n-tttcatcgtctccttatttttaggcttcttattacctttacgaggtgcattattcgctctatttttattcttaactgctt\n-tagaacgatacttactagctaagtaacctatagtactcaatggaacctctgtacgagttgcaatctccttgtacgttagc\n-tctgtagactccaataaacgaatcgcttcctcacggtttccttttggatttttattataacccacagtatccatctcctc\n-ttctttttgttttttaactttacccacagcaacaaccatctttttaactttaggttctggtttaactactacctgttcct\n-cttcg'..b'cggtatcatcgcctcctttgagcgcgagacgggcgaatatcgcgtgaccctgcgctttggcccgctccccatggggcg\n+cggcgcccaagagtggatgcgcgcgcgccgcgaagccgtcgccagctacagcgacgacaaggccgacgccctggccaccg\n+cccgcgacatgtccgcccgctgggaggcgatgagcgccgaagagcgttcgcgcctctatcacaaccccgcctaagacccc\n+gcgcgccgccctggccttcgccggggcggctccctcaacccctcgcaaggatcgcaccccatgaccgcccgtaagcccct\n+gaccaaggaacaaaaggcccgccgccgcgcgacccgccgcgccgcccgcctcaactggtcggatgagcgccgcgctcgcg\n+aattcgagcgtcaagcccgcttcttcctgatgatcgccacccgcgcccaaggcgccggccaaggccaggaagccgcccgc\n+ctcgccacggtcgcacaacgcaaggtgactaactggcgcatggcgcaggcctgcgcccggattaacgccctggccgcgca\n+tccgttcgcggccgtggtcgcctaaggaggcccgcccgatgacgcaccctcacgccctggcgctgatcgccctcgccgaa\n+aaggtgttaccgcttacccggctgcacccgctcgaccaacgcgccgccgccgtcgatctaatcggcgacctctaccgcct\n+cgccgacgatatcgacgcgaccccgcaagcccccgccctgacgcaaccgaaggccgcctaagccatgaacccgaaccgct\n+accgcctcgcgccccgcgaccgcttcagccgtgagcttgccgaaacgctctatcaggcggccgaagccgtcgcccgcgtg\n+attccgctcatgccggagtccgcccccgatgagcgccgcgcgctgggcaaggtccgcgccgaccttctaacccatagcgc\n+cggcgcccttgttcccaagccgccggccgccgtgctcgaaaccctcgtttgggttgtcgagatggcgcaagatcgcgcga\n+ctaacgccgatttcaacaccgcccaagaaggactcgacgagcacgagtccctagcctttgtcgccgactggctggaagcc\n+gaaggccaggacgtgacgccgattcgcaacgcgcaaccgtccgccgacgccctggccgaactcgccgcccgccgcgacgc\n+cgaacaagcggcgctagacgccttggaggccgaagccctggccgaagcgccgggcgacgtgatcaccgacgccttgcgcc\n+cctatctgggcgccgccctggccgaaaaccacgccgacgacgtgctagacgccctcacgcgcgccggcttccaaatcacc\n+cgcaaggaggcctaaagcccatgaccgactccgccaagatcaccggcgcgctcgcgctactcgccatcgcggccgataat\n+ctccgccaaggcccggccatgtccaaggccgccgacaacgtcaccaacgtctgtaactacgccctgacgcgcgcgaccat\n+gctcaaggccgccgaccaaatcggcgaggcgctggaggcgctgggcgccctgcaagcgggcggctatgtgatcgcccgcc\n+gccgcgacgttttcaccgatgcgggcgagaagctgggcgacctgttggcggcgctttatgacgccgtcccgaactacgcc\n+gtaagatcgcagcgcctcgccgacgccctgagtcccgcgcgaaattacgtctatcagccccggttccgggtcaagctgga\n+cgccgcgcccggcgcgcttttgaccgactgcgacacgggcgcaacggtctatttccagccgggcgacgacgccgacgcct\n+tccgggccgaattcgccccgtgggttcacgccgccaacgtgacggccgaaggcgcggccctggcctcgatgatgaacccg\n+accgccgaagagtatttcagccccgccacgggggtctaacgcccgtggccctgaccttcgccccgcaatcgacgcgctac\n+gccgtggaagtccccgaacgcgactttctggccctgacccgcgccgaggaaattctagcccctggcccctatctggagcc\n+gtcgcttagcgagcgtttggaggcgcaagccggcgtttgggatgtcgagtataacggccatttcggcgcggccgtttact\n+tgacgctcgacgttgacgccgactccccggccgcccgcgacgccctggcctcgatcatcgccgaccaactggccaaggcc\n+aaggcgtggaagcgccagcccgcctaagtcatcattcctatcgtctatgacttgtcaccggccgaactcttgcccggtga\n+cagtctgggcaagtaaagctcactctggattttatgacttagcgcaaaggattgaaattgctcgaaaaattcctcgaagc\n+tcacaaagttgttttctggctgcttttgctggcctgtttgtggcgcttttaacggtttgttaacccctggccctctaggg\n+tcgaattcccggcgcggcaatcccgccgcccggccttccttcggagcttctgatcatgttcgcttccgtgacccttcccg\n+cccatgacgcccaaggcctgagcctcgaaaccgtccacatggttttcgcccgcgaactggcgcaacatttcgaccacgtg\n+atttccgcccccgtggtcgaaagctggcgcgacgaggacaccggcgccgaccacgcgcaagccgccgtttgcttcaccgt\n+ctcggcgacccccgccgcgtgggaagccaagggcgggcgcctcgcgcgccggctggaaaacctcgccgcgcgctatgccg\n+ccgactgcgacgccccggccctgactgtcacccactgcgacggccaaacggtctatgtcggcgctctggaagccctggcg\n+cgccccgccccggtgcaaggcccgacccgtgaggcggacccggctttcctcccccgccagcgtgaggacaaggccgcccg\n+cttcgatcgcctgaccgcctagcccctggcctccccctagcgcaccgcccctagaaaggcggtgcgcttttctgtgtctg\n+tttacttgttgttaaggaatagcctgctagtgtccccttgttggcggacgcatcccgcgcccgcccctttctggatcgct\n+ccccatggctcgcccctctgacctgctcaacgtcaacgccgcccgcgtcctggcttgccttgagcctatcgccgccgccg\n+ctaagaccgccccggccgccgaccgcgccgccctttcctacctgctcgacgctggcgagtatgtcgccgcgtggcgccgc\n+aacctcacggaaaccgaccgccgcaaggcctatggcgcggcctgcgccgccgaagccctggcgctcgctaacgcctatca\n+gcccgccaccctgcaaggcggcgccgtccgccgcgctctgggcgcctatgccgccgccctaaaggtcctgctagacgggg\n+agccggtcaaggcggtgcgcgccgccgaaggcgcggcgctttcggtccgcgctcgctacgccaacacccgcctttaacct\n+cttgttaacacctcccggctatggtcgggaggtcgcaaggagacacccgacatgacccgccccggccccgcctcgctcct\n+gaccccgcaagcccgcttctcgtcgccgcgcgtcctgatccttccgggcgcggctcccatgccgattcgccagccgcgcg\n+gcctttgcgccgtcgagtgcgtcgcccttggcgtgacgctgggcgcggcgctctacctcgccgcccgcgtgttcggtctg\n+gtctgaccagacccccgccccgcccccggtcggaccggtcgggggtgtgtcccataatgacacacccccgccacctagta\n+tcttttttgattcggagggacccaaaggccccctacgttaaccatttttggcggcgccccc\n =\n' |
| b |
| diff -r 74093fb62bdf -r bca52822843e test-data/2.xmfa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/2.xmfa Fri Sep 07 11:30:11 2018 -0400 |
| b |
| b'@@ -0,0 +1,6309 @@\n+#FormatVersion Mauve1\n+#Sequence1File\tdataset_9.dat\n+#Sequence1Entry\t1\n+#Sequence1Format\tFastA\n+#Sequence2File\tdataset_9.dat\n+#Sequence2Entry\t2\n+#Sequence2Format\tFastA\n+#BackboneFile\t/tmp/tmprlpq7n/files/000/dataset_10.dat.bbcols\n+> 1:83043-149557 - dataset_9.dat\n+acagtagtacctaacccgactccgaatatagttgtgtaatccttattcttgttcagtctaaaactaatcgcagtaggtaa\n+gttggccttaatccgcccgcttacaatatctgcactaggatactgggtagccaccactaaatgtatacctgttttc-ctt\n+gccttctgccctaaccgagcaatataatcttctacccctttgtcaacagcacgtaaatctgcatattcatctacaataca\n+cactagatagggtaacggctcctccgctacttcattatacaaagataacaacttcgtacctttttccttcataagagcat\n+atcgcttatccatctccattgtcagccctgctaatacttggcaagcttctttagcatctgtcactacgtctagtacgtgt\n+ggactatcctcatacttacttagctctaccatagccgggtcaatcataataaactgtagcttttcaggtggatacattaa\n+catcatgcttacaataatcacatttacgaagaccgacttaccgctacctgttgtccctgccaccaataaatgtacacatt\n+cagtcaaagatagatagatcggctcccctagtgtatctacaccagccacgaacattaattctttttcttctaccatactg\n+ataaactcctcggtttcaaccagttcacggagactaataaccggtgaagcagctaaaggaaccgtaaacttaaccgtgtc\n+ggcaatatccccattctcaacacctaacccgctaatacctgttgcagctcgtaagtcattaatggacttttcaatcttag\n+aaaaggttacatctttaggtatacttacctggacaacccctaaccgcaccccacagtcaatccgttcattgtataaccta\n+gccgtatcaatcaattttacccgcttcataccttccgctagcttactaactattccttcatctagagtaccttgctctcg\n+cttatacataggtaacagatcaaatgggtacgccttacgctccactacctcttctaatactttttccgttttctctactg\n+taccacctaataaggagaatacttcgtttaagctaagtagttgatcttttgtgtaagctgctaatacacagtcagtatag\n+ttagtaataaattgtttatctgacgacttaaccagtttcaactcgtttaaagccgtataagaccctagagcgtattgaat\n+atactggatgatatcgtttaccctctcggacttaactgctattctgagctgaaattggaagcactcactctttatcttct\n+cttctgctaacggttcgtaaggcttgtaatcctctggctgtattttgtttaacactcgaacagctttatcctgcagttta\n+cgactccatctagaccaagaaggtttttcgttcccttgaatatagctatcgtacatatcaattgcgcgatcttgccaacc\n+ataccgcctgcgtaataaccattgcgcatgtacctcttcatcaggatgtaaagccaagtccagtaaatcagtaaggaaga\n+ggccgttcttatcctgtctgagagggagaaagaacgcttccgataaatacccctcgaagaaattaaaaccctctgtaggc\n+gcttctcgatgtcttagaacaagttctgccccggtttcgatatgagagggtgcaatgacaaaagtattagccccctcacc\n+ggttaaatgggtctctactccgaataccgaatcgttaatctgttcaaggatatcgacaaagtgaccttctatatcttcta\n+caggcataaacaagttagctaggttatggtaatttgcagaaagctttttcatcttctctcccccttaatatgcttcataa\n+ccattaaactgtttgcgatctgcatcccgctgctgaaaacaagcgaggtaagattaatgataattaatactgatactgta\n+ctcatgttattcactccttattttctttttggtttaggcgtagacttacctggttttggtactggcgggtggaaacgttg\n+catacgagtcttacctacccgctcaggagtttgtaatcgctcgtgtaccttctttacaacagtagtaggtttacggataa\n+tgtccactgtatctcggaagttacgaactgttttagagactgtatctttagctggtgtatatactgagtcaaaccctgat\n+ccattatctaagtgtttacttacaaattttggaggagagcttaactttgagaacccgccaatggtgaccagtagctttaa\n+gataaatccagtgaagctcgcaggggtcggtgtgccgaacaatacccaaccgatcactagaagaaaaatagaatagtata\n+cttgaacaagagacaagtgtttaacatttcccaaccatgtgttaaaataatttctatagctgtcaaatatccagcaggtg\n+caggcgagaggacttactagcccgagcactaacaaatcaaagaaccggcgaccgtttttccacagc--------------\n+--------------------------------------------------------------------------------\n+--------------------------------------------------------------------------------\n+--------------------------------------------------------------------------------\n+--------------------------------------------------------------------------------\n+--------------------------------------------------------------------------------\n+--------------------------------------------------------------------------------\n+--------------------------------------------------------------------------------\n+--------------------------------------------------------------------------------\n+--------------------------------------------------------------------------------\n+--------------------------------------------------------------------------------\n+--------------------------------------------------------------------------------\n+--------------------------------------------------------------------------------\n+--------------------------------------------------------------------------------\n+--------------------------------------------------------------------------------\n+------------------------'..b'cggtatcatcgcctcctttgagcgcgagacgggcgaatatcgcgtgaccctgcgctttggc\n+ccgctccccatggggcgcggcgcccaagagtggatgcgcgcgcgccgcgaagccgtcgccagctacagcgacgacaaggc\n+cgacgccctggccaccgcccgcgacatgtccgcccgctgggaggcgatgagcgccgaagagcgttcgcgcctctatcaca\n+accccgcctaagaccccgcgcgccgccctggccttcgccggggcggctccctcaacccctcgcaaggatcgcaccccatg\n+accgcccgtaagcccctgaccaaggaacaaaaggcccgccgccgcgcgacccgccgcgccgcccgcctcaactggtcgga\n+tgagcgccgcgctcgcgaattcgagcgtcaagcccgcttcttcctgatgatcgccacccgcgcccaaggcgccggccaag\n+gccaggaagccgcccgcctcgccacggtcgcacaacgcaaggtgactaactggcgcatggcgcaggcctgcgcccggatt\n+aacgccctggccgcgcatccgttcgcggccgtggtcgcctaaggaggcccgcccgatgacgcaccctcacgccctggcgc\n+tgatcgccctcgccgaaaaggtgttaccgcttacccggctgcacccgctcgaccaacgcgccgccgccgtcgatctaatc\n+ggcgacctctaccgcctcgccgacgatatcgacgcgaccccgcaagcccccgccctgacgcaaccgaaggccgcctaagc\n+catgaacccgaaccgctaccgcctcgcgccccgcgaccgcttcagccgtgagcttgccgaaacgctctatcaggcggccg\n+aagccgtcgcccgcgtgattccgctcatgccggagtccgcccccgatgagcgccgcgcgctgggcaaggtccgcgccgac\n+cttctaacccatagcgccggcgcccttgttcccaagccgccggccgccgtgctcgaaaccctcgtttgggttgtcgagat\n+ggcgcaagatcgcgcgactaacgccgatttcaacaccgcccaagaaggactcgacgagcacgagtccctagcctttgtcg\n+ccgactggctggaagccgaaggccaggacgtgacgccgattcgcaacgcgcaaccgtccgccgacgccctggccgaactc\n+gccgcccgccgcgacgccgaacaagcggcgctagacgccttggaggccgaagccctggccgaagcgccgggcgacgtgat\n+caccgacgccttgcgcccctatctgggcgccgccctggccgaaaaccacgccgacgacgtgctagacgccctcacgcgcg\n+ccggcttccaaatcacccgcaaggaggcctaaagcccatgaccgactccgccaagatcaccggcgcgctcgcgctactcg\n+ccatcgcggccgataatctccgccaaggcccggccatgtccaaggccgccgacaacgtcaccaacgtctgtaactacgcc\n+ctgacgcgcgcgaccatgctcaaggccgccgaccaaatcggcgaggcgctggaggcgctgggcgccctgcaagcgggcgg\n+ctatgtgatcgcccgccgccgcgacgttttcaccgatgcgggcgagaagctgggcgacctgttggcggcgctttatgacg\n+ccgtcccgaactacgccgtaagatcgcagcgcctcgccgacgccctgagtcccgcgcgaaattacgtctatcagccccgg\n+ttccgggtcaagctggacgccgcgcccggcgcgcttttgaccgactgcgacacgggcgcaacggtctatttccagccggg\n+cgacgacgccgacgccttccgggccgaattcgccccgtgggttcacgccgccaacgtgacggccgaaggcgcggccctgg\n+cctcgatgatgaacccgaccgccgaagagtatttcagccccgccacgggggtctaacgcccgtggccctgaccttcgccc\n+cgcaatcgacgcgctacgccgtggaagtccccgaacgcgactttctggccctgacccgcgccgaggaaattctagcccct\n+ggcccctatctggagccgtcgcttagcgagcgtttggaggcgcaagccggcgtttgggatgtcgagtataacggccattt\n+cggcgcggccgtttacttgacgctcgacgttgacgccgactccccggccgcccgcgacgccctggcctcgatcatcgccg\n+accaactggccaaggccaaggcgtggaagcgccagcccgcctaagtcatcattcctatcgtctatgacttgtcaccggcc\n+gaactcttgcccggtgacagtctgggcaagtaaagctcactctggattttatgacttagcgcaaaggattgaaattgctc\n+gaaaaattcctcgaagctcacaaagttgttttctggctgcttttgctggcctgtttgtggcgcttttaacggtttgttaa\n+cccctggccctctagggtcgaattcccggcgcggcaatcccgccgcccggccttccttcggagcttctgatcatgttcgc\n+ttccgtgacccttcccgcccatgacgcccaaggcctgagcctcgaaaccgtccacatggttttcgcccgcgaactggcgc\n+aacatttcgaccacgtgatttccgcccccgtggtcgaaagctggcgcgacgaggacaccggcgccgaccacgcgcaagcc\n+gccgtttgcttcaccgtctcggcgacccccgccgcgtgggaagccaagggcgggcgcctcgcgcgccggctggaaaacct\n+cgccgcgcgctatgccgccgactgcgacgccccggccctgactgtcacccactgcgacggccaaacggtctatgtcggcg\n+ctctggaagccctggcgcgccccgccccggtgcaaggcccgacccgtgaggcggacccggctttcctcccccgccagcgt\n+gaggacaaggccgcccgcttcgatcgcctgaccgcctagcccctggcctccccctagcgcaccgcccctagaaaggcggt\n+gcgcttttctgtgtctgtttacttgttgttaaggaatagcctgctagtgtccccttgttggcggacgcatcccgcgcccg\n+cccctttctggatcgctccccatggctcgcccctctgacctgctcaacgtcaacgccgcccgcgtcctggcttgccttga\n+gcctatcgccgccgccgctaagaccgccccggccgccgaccgcgccgccctttcctacctgctcgacgctggcgagtatg\n+tcgccgcgtggcgccgcaacctcacggaaaccgaccgccgcaaggcctatggcgcggcctgcgccgccgaagccctggcg\n+ctcgctaacgcctatcagcccgccaccctgcaaggcggcgccgtccgccgcgctctgggcgcctatgccgccgccctaaa\n+ggtcctgctagacggggagccggtcaaggcggtgcgcgccgccgaaggcgcggcgctttcggtccgcgctcgctacgcca\n+acacccgcctttaacctcttgttaacacctcccggctatggtcgggaggtcgcaaggagacacccgacatgacccgcccc\n+ggccccgcctcgctcctgaccccgcaagcccgcttctcgtcgccgcgcgtcctgatccttccgggcgcggctcccatgcc\n+gattcgccagccgcgcggcctttgcgccgtcgagtgcgtcgcccttggcgtgacgctgggcgcggcgctctacctcgccg\n+cccgcgtgttcggtctggtctgaccagacccccgccccgcccccggtcggaccggtcgggggtgtgtcccataatgacac\n+acccccgccacctagtatcttttttgattcggagggacccaaaggccccctacgttaaccatttttggcggcgccccc\n+=\n' |
| b |
| diff -r 74093fb62bdf -r bca52822843e tool_dependencies.xml --- a/tool_dependencies.xml Wed Aug 17 14:46:55 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,15 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="progressivemauve" version="2.4.0"> - <repository changeset_revision="0aeb3a1b5106" name="package_progressivemauve_2_4_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="python" version="2.7"> - <repository changeset_revision="8b09fe018cac" name="package_python_2_7" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="biopython" version="1.65"> - <repository changeset_revision="030f1a505d40" name="package_biopython_1_65" owner="biopython" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="bcbiogff" version="0.6.2"> - <repository changeset_revision="8ee2210f6074" name="package_python_2_7_bcbiogff_0_6_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency> |
| b |
| diff -r 74093fb62bdf -r bca52822843e xmfa2gff3.py --- a/xmfa2gff3.py Wed Aug 17 14:46:55 2016 -0400 +++ b/xmfa2gff3.py Fri Sep 07 11:30:11 2018 -0400 |
| [ |
| @@ -1,12 +1,17 @@ #!/usr/bin/env python +import argparse +import logging import sys + +from BCBio import GFF from Bio import SeqIO from Bio.Seq import Seq +from Bio.SeqFeature import ( + FeatureLocation, + SeqFeature +) from Bio.SeqRecord import SeqRecord -from Bio.SeqFeature import SeqFeature, FeatureLocation -import argparse -from BCBio import GFF -import logging + logging.basicConfig(level=logging.INFO) log = logging.getLogger(__name__) @@ -131,6 +136,10 @@ # Ignore 0% identity sequences if pid == 0: continue + + # Support for Biopython 1.68 and above, which removed sub_features + if not hasattr(other['feature'], "sub_features"): + other['feature'].sub_features = [] other['feature'].sub_features.append( SeqFeature( FeatureLocation(real_start, real_end), |
| b |
| diff -r 74093fb62bdf -r bca52822843e xmfa2gff3.xml --- a/xmfa2gff3.xml Wed Aug 17 14:46:55 2016 -0400 +++ b/xmfa2gff3.xml Fri Sep 07 11:30:11 2018 -0400 |
| [ |
| @@ -4,19 +4,23 @@ <macros> <import>macros.xml</import> </macros> - <expand macro="requirements"/> + <requirements> + <requirement type="package" version="2.7">python</requirement> + <requirement type="package" version="1.72">biopython</requirement> + <requirement type="package" version="0.6.4">bcbiogff</requirement> + </requirements> <expand macro="stdio"/> <version_command>python xmfa2gff3.py --version</version_command> - <command interpreter="python"><![CDATA[ -xmfa2gff3.py + <command><![CDATA[ +python '${__tool_directory__}/xmfa2gff3.py' $xmfa --window_size $window_size --relative_to $relative_to --sequences #for file in $sequences: - "${file}" + '${file}' #end for -> $output +> '$output' ]]></command> <inputs> @@ -39,7 +43,7 @@ </outputs> <tests> <test> - <param name="xmfa" value="1.xmfa"/> + <param name="xmfa" value="2.xmfa"/> <param name="sequences" value="karma.fa,phagey.fa" /> <param name="window_size" value="10" /> <param name="relative_to" value="1" /> |