| Previous changeset 6:224c75ad0518 (2021-08-12) Next changeset 8:c1d53e95327f (2021-08-18) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 255253945d747156f59c7834998725afdc7499af" |
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modified:
iqtree.xml |
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added:
test-data/dates.fa test-data/dates.tabular |
| b |
| diff -r 224c75ad0518 -r 524d31add34a iqtree.xml --- a/iqtree.xml Thu Aug 12 07:52:10 2021 +0000 +++ b/iqtree.xml Fri Aug 13 21:35:49 2021 +0000 |
| [ |
| @@ -20,6 +20,10 @@ -s '$general_options.s' #end if +#if $general_options.o + -o '$general_options.o' +#end if + ## file #if $general_options.t -t '$general_options.t' @@ -363,7 +367,11 @@ <inputs> <section name="general_options" expanded="true" title="General options"> <param argument="-s" type="data" format="txt" optional="true" label="Specify input alignment file in PHYLIP, FASTA, NEXUS, CLUSTAL or MSF format."/> - <param type="boolean" name="short_alignments" truevalue="true" falsevalue="false" label="Short alignments" help="IQ-TREE will fail if given too many threads on input data that consists of short alignments, this option will force the use of a single thread." /> + <param argument="-o" type="text" optional="true" label="Comma-separated list of taxons to output"> + <expand macro="sanitize_query" /> + </param> + + <param type="boolean" name="short_alignments" label="Short alignments" help="IQ-TREE will fail if given too many threads on input data that consists of short alignments, this option will force the use of a single thread." /> <param argument="--seqtype" type="select" label="Specify sequence type as either of DNA, AA, BIN, MORPH, CODON or NT2AA for DNA, amino-acid, binary, morphological, codon or DNA-to-AA-translated sequences"> <help><![CDATA[ Note that --seqtype CODON is always necessary when using codon models and you also need to specify a genetic code like this if differed from the standard genetic code. @@ -682,9 +690,12 @@ <data name="mldist" format="mldist" from_work_dir="*.mldist" label="${tool.name} on ${on_string}: MaxLikelihood Distance Matrix"/> <data name="splits" format="nex" from_work_dir="*.splits.nex" label="${tool.name} on ${on_string}: Occurence Frequencies in Bootstrap Trees" /> <data name="iqtree" format="iqtree" from_work_dir="*.iqtree" label="${tool.name} on ${on_string}: Report and Final Tree" /> - <data name="mlrate" format="data" from_work_dir="*.mlrate" label=""> + <data name="mlrate" format="data" from_work_dir="*.mlrate" label="${tool.name} on ${on_string}: ML Rates"> <filter>modelling_parameters['rate_heterogeneity']['mlrate']</filter> </data> + <data name="timetree" format="nex" from_work_dir="PREF.timetree.nex" label="${tool.name} on ${on_string}: Tree labeled with dates"> + <filter>time_tree['date_source']['select_source'] != 'none'</filter> + </data> </outputs> <tests> <test expect_num_outputs="6"> @@ -837,6 +848,18 @@ </assert_contents> </output> </test> + <test expect_num_outputs="7"> + <param name="s" value="dates.fa" /> + <param name="n" value="100" /> + <param name="seed" value="122125" /> + <param name="select_source" value="dataset" /> + <param name="date" value="dates.tabular" /> + <output name="timetree"> + <assert_contents> + <has_line_matching expression=".+222-3pu_03-28-01_985737600.+" /> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[ IQ-TREE |
| b |
| diff -r 224c75ad0518 -r 524d31add34a test-data/dates.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dates.fa Fri Aug 13 21:35:49 2021 +0000 |
| b |
| b'@@ -0,0 +1,5400 @@\n+>222-4im_12-02-08_1228176000\n+cctcagatcactctttggcaacgaccccttgtcacagtaaaadtaggagggcagctaaag\n+gargctctattagatacaggagcagatgatacagtattagaagaaa------tgartmtr\n+ycaggaaratggaaaccaaaaatgatagggggaattggaggctttatcaaagtaagacag\n+tatgatcagrtaccagtagaaatctgtggacataaagctataggtacagtattaatagga\n+cctacacctgtcaacataattggaagaaayctgttgactcarattggttgcactttaaat\n+tttcccattagtcctattgaaactgtaccagtaaaattgaagccaggaatggatggccca\n+aaagttaaacaatggccattgacagaagaaaaaataaaagcattaatggaaatttgttca\n+gaaatggaaaargaaggaaaaatttcaaaaattgggcctgaaaatccatacaatactcca\n+atatttgcaataaagaaaaaaga------cagyactamatggagaaaattagtagatttc\n+agagaacttaataagagaacacaagacttctgggaagttcaactaggaatmccacatccc\n+gcagggctaaaacagaaaaagtcagtaacagtactggatgtgggtgatgcatatttctca\n+gttcccttggacaaagatttcaggaagtatactgcatttaccatacctagtacaaacaat\n+gagacaccagggattagatatcagtacaatgtrctyccacagggatggaarggatcacca\n+gcaatattycaaagtagcatgacaaaaatcttagagccttttagaaarcaaaatccagam\n+atrrttatctatcartacatggatgatttgtatgtaggatctgacttagaratagagmwg\n+catagaacaaaaatagargaactgagacagcatctgttgmrktggggatttaccacccca\n+gacaagaagcatcagaaagaacctccattcctctggatggggtatgaactccatcctgat\n+aaatggacagtacagcctatagtgctgccagaaaargacagctggactgtcaatgacmta\n+cagaagttagtgggaaaattgaattgggcaagtcagatttatccagggattaaagtgarr\n+caattatgtaaactcctkagaggaaccaaakcrctaacagaggtartaccactaacaraa\n+gaagcagaactagaactggcagaa------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+---------\n+>222-3sw_03-06-09_1236297600\n+cctcagatcactctttggcaacgaccccttgtcacaataaagataggagggcarctaaag\n+gaagctctattagatacaggagcagaygatacagtattagaagaaa------traatttg\n+ccaggaagatggaaaccaaaaatgatagggggaattggaggatttatcaaagtaagacag\n+tatgatcaggtatcygtagacatctgtggacataaagctgtaggtacagtattagtagga\n+cctacacctgtcaacataattggcagaaatctgttgactcagattggatgcactttaaat\n+ttycccattagtcctattgaaactgtaccagtraaattraaaccaggaatggaygggcca\n+agagttaaacartggccattgacagaagaaaaaataaaagcattagtagaaatttgtaca\n+gaaatggaaaaggagggaaaaatttcaaaaattgggcctgaaaatccatayaatactcca\n+atatttgcaataaagaaaaagga------tagtactaaatggagaaaattagtagatttc\n+agagaacttaataagagaactcaagacttctgggaagttcaattaggaataccacatcct\n+gcagggctaaaaaagaagaaatcagtaacagtactggatgtgggtgatgcatatttytca\n+gttcccttagataaagacttcaggaagtatacagcattcaccatacctagtacaaacaat\n+gagacaccagggattagatatcagtacaatgtactyccacagggatggaaaggatcacca\n+gcaatattccaacatagcatgacaaaaatcttagagccttwtagaaarcaaaatccagac\n+atagttatctatcagtacatggatgatttgtatgtaggatctgacttagaaatagggcag\n+catagagcaaaaatagaggaactgagagaacatytgttgaagtggggatttaccacacca\n+gacaaaaaacatcagaaagaacctccattcctttggatgggttatgaactccatcctgay\n+aaatggacagtacagcctatagtgctgccagagaaagayagctggactgtcaatgacata\n+caaaagttagtgggaaaaytaaattgggcaagtcagatttacccaggrattaaaataaag\n+cagttatgtaaactccttaggggagccaaagcactaacagaagtaatacaactaacaaaa\n+gaagcagagctagaactggcagaa------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+---------\n+>222-whj_07-15-09_1247616000\n+cctcagatcactctttggcaacgacccctcgtcacaataaggataggggggcaactaaag\n+gaagctctattagatacaggagcagatgatacagtaytagaagaaa------tgaayttg\n+ccagggaaatggaagccaaaaatgatagggggaattggaggttttatcaaagtaagacag\n+tatgatcagatacccatagaaatttgtggrcataaagctataggtacagtattagtagga\n+cctacacctgtcaacataattggaagaaayctgttgactcagcttggttgcactttaaat\n+tttcccattagtcctattgaaactgtaccagtraaattaaagccaggaatggatggccca\n+aaagttaaacaatggccattgacagaagaaaaaataaaagcattagtagaaatttgtaca\n+gaaatggaaaaggaagggaaaatttcaagaattggrcctgaaaatccrtacaatactcca\n+atatttgcyataaagaaaaaaga------cagtactmagtggagaaaattagtagatttc\n+agagaacttaataagaaaactcaagayttctgggaagttcaattaggaataccacatccc\n+gcaggattaaaaaagaaaaattcagtaacagtactggaygtgggtgatgcatatttytca\n+gtycccttagatccagacttcaggaagtatactgcattcaccatacctagcacaaacaat\n+gagacaccagggattagatatca'..b'aatgtgcttccacaaggatggaaaggatcacca\n+gcaatattccaaagtagcatgacaaaaatcttagaaccttttagaaaacaaaatccagac\n+atagttatctatcagtacatggatgatttgtatgtaggatctgacttagaaataggacag\n+catagaacaaaaatagaggaactgagacaacatttattgaggtggggacttaccacccca\n+gacaaaaaacatcagaaagaacctccattcctttggatgggttatgaactccatcctgat\n+aaatggacagtacagcctatagtgctaccagaaaaggacagctggactgtcaatgacata\n+cagaagttagtgggaaaattgaattgggcaagtcagatttatgcagggattaaagtaagg\n+caattatgtaaactccttagaggacccaaagcactaacagaagtagtaccattaacaaaa\n+gaagcagagctagaactggcagaaaacagggagattctaagagaaccagtacatggagta\n+tattatgacccatcaaaaggcttaatagcagagatacagaagcaggggcaaggc------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+---------\n+>222-3wc_05-22-03_1053561600\n+cctcagatcactctttggcaacgaccccttgtcacaataaaggtaggggggcaactaaag\n+gaagctctattagatacaggagcagatgatacagtattagaagaaa------tgagttta\n+ccaggaagatggaaaccaaaaatgatagggggaattggaggttttatcaaagtaagacag\n+tatgatcagatactsgtagaaatytgtggacayaaagctataggtacagtattagtggga\n+cctacacctgtcaacataattggaagaaatctgttgactcagattggttgcactttaaat\n+tttcctattagtcctattgaaactgtaccagtaaarttaaagccaggaatggatggccca\n+aaagttaaacaatggccattgacagaggaaaaaataaaagcattaatagaaatttgtaca\n+gaaatggaaaaggaaggaaaaatttcaaaaatwgggcctgaaaatccatacaatactcca\n+gtatttgccataaaaaagaaaga------cagtactaaatggagaaaattagtagatttc\n+agagaacttaataagagaactcaagacttctgggaagttcaactaggaataccacatcct\n+gcagggttaaaaaagaaaaaatcagtaacagtactggatgtgggtgatgcatayttttca\n+gttcctttagataaagacttcaggaagtatactgcatttaccatacctagtttaaacaat\n+gagacaccaggrattagatatcagtacaatgtgcttccacagggatggaaaggatcacca\n+gcaatattccaatgtagcatgacaaaaatcttagagccttttagaaaacaaaayccagac\n+atagttatctatcaatacatggatgatttgtatgtaggatcwgacttagaaatagggcag\n+catagagcaaaaatagaggaactragacaacatctgttgaggtggggatttaccacacca\n+gacaagaagcatcagaaagaacctccattcctytggatggggtatgaactccatcctgat\n+aartggacagtacagcctatacagctgccagaaaaggacagctggactgtcaatgacata\n+cagaagttagtgggaaaaytraattgggcaagtcagatttatgcagggattaaagtaagg\n+caattatgtaaactccttaggggagccaaakcactaacagaaatagtaccactaacagaa\n+gaagcagagttagaactggcagaaaacagggagattttaaaagaaccagtacatggagtg\n+tattatgacccatcaaaagacttaatagcagagatacagaaacaggagcaaggc------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+---------\n+>222-3wd_11-27-02_1038355200\n+cctcaaatcactctttggcaacgacccgtcgtcgcaataaaggtaggggggcaactaaag\n+gaagctctattagatacaggagcagatgatacagtattagaagaaa------tgactttg\n+ccaggaaaatggaaaccaaaaatgatagggggaattggaggttttatcaaagtaagacag\n+tatgatcaagtactcatagaaatctgtggacataaagctataggtacggtattagtagga\n+cccacacctgtcaacataattggaagaaatctgttgactcagcttggttgcactttaaat\n+tttcccattagtcctattgaaactgtaccagtaaaattgaagccaggaatggatggccca\n+aaagttaaacaatggccattgacagaagaaaaaataaaagcattaatagaaatttgtaca\n+gaaatggaaaaggaaggaaaaatttcaaaaattgggcctgaaaatccatacaatactcca\n+gtatttgccataaagaaaaaaga------cagtactaaatggagaaaattagtagatttc\n+agagaactcaataagaagactcaagacttctgggaaattcaattaggaataccacatccc\n+gcagggttaaaaaagaacaagtcagtaacagtactggatgtgggtgatgcatatttttca\n+gttcccttagataaggacttcaggaagtatactgcatttaccatacctagtataaacaat\n+gagacaccagggattagatatcagtacaatgtgcttccacagggatggaaaggatcacca\n+gcaatattccaaggtagcatgacaaaaatcttagagccttttagaaaacaaaatccagac\n+atagttatctatcaatacatggatgatttgtatgtaggatctgacttagaaatagggcag\n+catagaacaaaaatagaggaactgagacaacatctgttgaggtgggggtttaccacacca\n+gacaaaaaacatcagaaagaacccccattcctttggatgggttatgaactccatcctgat\n+aaatggacagtacaacctatagagctaccagaaaaagacagctggactgtcaatgacata\n+cagaagttagtgggaaaattaaattgggcaagtcagatttacgcagggattaaagtaaag\n+caattatgtaaactccttaggggagccaaagcactaacagaaatagtaccactaacaaaa\n+gaagcagagctagaactggcagaa------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+---------\n\\ No newline at end of file\n' |
| b |
| diff -r 224c75ad0518 -r 524d31add34a test-data/dates.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dates.tabular Fri Aug 13 21:35:49 2021 +0000 |
| b |
| @@ -0,0 +1,200 @@ +222-4im_12-02-08_1228176000 2008-12-02 +222-3sw_03-06-09_1236297600 2009-03-06 +222-whj_07-15-09_1247616000 2009-07-15 +222-4cy_08-28-09_1251417600 2009-08-28 +222-46q_10-08-09_1254960000 2009-10-08 +222-4zb_11-17-09_1258416000 2009-11-17 +222-52b_04-01-10_1270080000 2010-04-01 +222-47b_08-05-10_1280966400 2010-08-05 +222-5dz_02-25-11_1298592000 2011-02-25 +222-22j_03-15-11_1300147200 2011-03-15 +222-gn3_03-22-11_1300752000 2011-03-22 +222-47w_09-28-11_1317168000 2011-09-28 +222-3x9_02-10-12_1328832000 2012-02-10 +222-3wi_02-15-12_1329264000 2012-02-15 +222-43w_07-16-12_1342396800 2012-07-16 +222-fht_08-06-12_1344211200 2012-08-06 +222-gjx_10-30-12_1351555200 2012-10-30 +222-3h5_06-19-97_866678400 1997-06-19 +222-3h6_07-20-96_837820800 1996-07-20 +222-3h7_08-16-96_840153600 1996-08-16 +222-3h8_10-02-96_844214400 1996-10-02 +222-3hb_10-17-96_845510400 1996-10-17 +222-3hc_10-14-96_845251200 1996-10-14 +222-3he_10-25-96_846201600 1996-10-25 +222-3hf_10-25-96_846201600 1996-10-25 +222-3hg_10-29-96_846547200 1996-10-29 +222-5ht_04-10-97_860630400 1997-04-10 +222-3hm_12-17-96_850780800 1996-12-17 +222-3hn_12-18-96_850867200 1996-12-18 +222-3hq_01-14-97_853200000 1997-01-14 +222-3hr_01-07-97_852595200 1997-01-07 +222-3ht_01-28-97_854409600 1997-01-28 +222-3hv_01-30-97_854582400 1997-01-30 +222-3hx_03-05-97_857520000 1997-03-05 +222-3hy_04-01-97_859852800 1997-04-01 +222-3hz_02-24-97_856742400 1997-02-24 +222-5hu_02-27-97_857001600 1997-02-27 +222-3i3_04-08-97_860457600 1997-04-08 +222-3i4_04-03-97_860025600 1997-04-03 +222-3i6_03-18-97_858643200 1997-03-18 +222-3i7_04-28-97_862185600 1997-04-28 +222-3i8_04-28-97_862185600 1997-04-28 +222-3ia_06-02-97_865209600 1997-06-02 +222-3ib_02-11-00_950227200 2000-02-11 +222-3ic_07-11-97_868579200 1997-07-11 +222-3id_07-23-97_869616000 1997-07-23 +222-3ie_07-29-97_870134400 1997-07-29 +222-3ig_08-25-97_872467200 1997-08-25 +222-3ih_09-16-97_874368000 1997-09-16 +222-3im_10-07-97_876182400 1997-10-07 +222-3in_07-24-03_1059004800 2003-07-24 +222-3iq_12-03-97_881107200 1997-12-03 +222-3ir_07-22-99_932601600 1999-07-22 +222-3is_12-23-97_882835200 1997-12-23 +222-3it_01-13-98_884649600 1998-01-13 +222-3iv_03-05-02_1015286400 2002-03-05 +222-3ix_03-19-98_890265600 1998-03-19 +222-3iy_03-20-98_890352000 1998-03-20 +222-3j2_04-13-98_892425600 1998-04-13 +222-3j3_04-13-98_892425600 1998-04-13 +222-3j4_04-06-98_891820800 1998-04-06 +222-3j5_04-13-98_892425600 1998-04-13 +222-3j8_04-07-99_923443200 1999-04-07 +222-3jf_08-13-98_902966400 1998-08-13 +222-3jg_08-12-98_902880000 1998-08-12 +222-3jj_03-18-05_1111104000 2005-03-18 +222-3jk_09-29-98_907027200 1998-09-29 +222-3jq_11-18-98_911347200 1998-11-18 +222-3jr_11-30-98_912384000 1998-11-30 +222-3jx_02-21-06_1140480000 2006-02-21 +222-3k8_04-20-99_924566400 1999-04-20 +222-3kb_05-20-99_927158400 1999-05-20 +222-3kc_06-07-99_928713600 1999-06-07 +222-3kd_02-29-00_951782400 2000-02-29 +222-3ke_06-07-00_960336000 2000-06-07 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