| Previous changeset 19:6bbd30d58cf4 (2025-02-20) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit ed98c907217fd95aa455f4f74de74e9b3893c1d3 |
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modified:
iqtree.xml iqtree_macros.xml |
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added:
test-data/ufboot_out.txt |
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| diff -r 6bbd30d58cf4 -r 18a61a9c1601 iqtree.xml --- a/iqtree.xml Thu Feb 20 20:11:40 2025 +0000 +++ b/iqtree.xml Mon May 05 16:50:56 2025 +0000 |
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| @@ -715,9 +715,13 @@ <data name="lsd_report" format="txt" from_work_dir="PREF.timetree.lsd" label="${tool.name} on ${on_string}: LSD Report"> <filter>time_tree['date_source']['select_source'] != 'none'</filter> </data> + <data name="ufboot_out" format="nhx" from_work_dir="*.ufboot" label="${tool.name} on ${on_string}: UFBoot Bootstrap trees"> + <filter>bootstrap_parameters['ultrafast_bootstrap']['boot_trees'] </filter> + </data> + </outputs> <tests> - <test expect_num_outputs="5"> + <test expect_num_outputs="6"> <param name="seed" value="1257" /> <param name="seqtype" value="DNA" /> <param name="s" value="example.phy" /> @@ -726,6 +730,7 @@ <param name="madd" value="LG4M,LG4X" /> <param name="merit" value="AICc" /> <param name="ufboot" value="1000" /> + <param name="boot_trees" value="--boot-trees"/> <output name="bionj"> <assert_contents> <has_text_matching expression=".*Whale.*" /> @@ -761,6 +766,12 @@ <has_line line="END; [Splits]" /> </assert_contents> </output> + <output name="ufboot_out" > + <assert_contents> + <has_text text="(LngfishAu" /> + <has_text text="(Platypus,Opossum)" /> + </assert_contents> + </output> </test> <test expect_num_outputs="5"> <!-- bootstrap sans model --> |
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| diff -r 6bbd30d58cf4 -r 18a61a9c1601 iqtree_macros.xml --- a/iqtree_macros.xml Thu Feb 20 20:11:40 2025 +0000 +++ b/iqtree_macros.xml Mon May 05 16:50:56 2025 +0000 |
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| @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">2.4.0</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">iqtree</requirement> |
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| diff -r 6bbd30d58cf4 -r 18a61a9c1601 test-data/ufboot_out.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ufboot_out.txt Mon May 05 16:50:56 2025 +0000 |
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| b'@@ -0,0 +1,1000 @@\n+(LngfishAu,(LngfishSA,LngfishAf),(Frog,((((Turtle,(Crocodile,Bird)),Lizard),Sphenodon),(((Human,(Seal,(Cow,Whale))),(Mouse,Rat)),(Platypus,Opossum)))));\n+(LngfishAu,(LngfishSA,LngfishAf),(Frog,((((Turtle,(Crocodile,Bird)),Lizard),Sphenodon),(((Human,(Seal,(Cow,Whale))),(Mouse,Rat)),(Platypus,Opossum)))));\n+(LngfishAu,(LngfishSA,LngfishAf),(Frog,((((Turtle,(Crocodile,Bird)),Sphenodon),Lizard),((((Human,Seal),(Cow,Whale)),(Mouse,Rat)),(Platypus,Opossum)))));\n+(LngfishAu,(LngfishSA,LngfishAf),(Frog,((((Turtle,(Crocodile,Bird)),Sphenodon),Lizard),((((Human,Seal),(Cow,Whale)),(Mouse,Rat)),(Platypus,Opossum)))));\n+(LngfishAu,(LngfishSA,LngfishAf),(Frog,((Turtle,((Sphenodon,Lizard),(Crocodile,Bird))),((((Human,Seal),(Cow,Whale)),(Mouse,Rat)),(Platypus,Opossum)))));\n+(LngfishAu,(LngfishSA,LngfishAf),(Frog,((Turtle,((Sphenodon,(Crocodile,Bird)),Lizard)),(((Human,(Seal,(Cow,Whale))),(Mouse,Rat)),(Platypus,Opossum)))));\n+(LngfishAu,(LngfishSA,LngfishAf),(Frog,((((Turtle,(Crocodile,Bird)),Lizard),Sphenodon),(((Human,(Seal,(Cow,Whale))),(Mouse,Rat)),(Platypus,Opossum)))));\n+(LngfishAu,(LngfishSA,LngfishAf),(Frog,((((Turtle,(Crocodile,Bird)),Sphenodon),Lizard),(((Human,(Seal,(Cow,Whale))),(Mouse,Rat)),(Platypus,Opossum)))));\n+(LngfishAu,(LngfishSA,LngfishAf),(Frog,((((Turtle,(Crocodile,Bird)),Sphenodon),Lizard),(((Human,(Seal,(Cow,Whale))),(Mouse,Rat)),(Platypus,Opossum)))));\n+(LngfishAu,(LngfishSA,LngfishAf),(Frog,((((Turtle,(Crocodile,Bird)),Lizard),Sphenodon),(((Human,(Seal,(Cow,Whale))),(Mouse,Rat)),(Platypus,Opossum)))));\n+(LngfishAu,(LngfishSA,LngfishAf),(Frog,((((Turtle,(Crocodile,Bird)),Sphenodon),Lizard),(((Human,(Seal,(Cow,Whale))),(Mouse,Rat)),(Platypus,Opossum)))));\n+(LngfishAu,(LngfishSA,LngfishAf),(Frog,(((Turtle,(Crocodile,Bird)),(Sphenodon,Lizard)),(((Human,(Seal,(Cow,Whale))),(Mouse,Rat)),(Platypus,Opossum)))));\n+(LngfishAu,(LngfishSA,LngfishAf),(Frog,((((Turtle,(Crocodile,Bird)),Lizard),Sphenodon),(((Human,(Seal,(Cow,Whale))),(Mouse,Rat)),(Platypus,Opossum)))));\n+(LngfishAu,(LngfishSA,LngfishAf),(Frog,((Turtle,((Sphenodon,(Crocodile,Bird)),Lizard)),(((Human,(Seal,(Cow,Whale))),(Mouse,Rat)),(Platypus,Opossum)))));\n+(LngfishAu,(LngfishSA,LngfishAf),(Frog,((((Turtle,(Crocodile,Bird)),Sphenodon),Lizard),(((Human,(Seal,(Cow,Whale))),(Mouse,Rat)),(Platypus,Opossum)))));\n+(LngfishAu,(LngfishSA,LngfishAf),(Frog,((Turtle,((Sphenodon,Lizard),(Crocodile,Bird))),(((Human,(Seal,(Cow,Whale))),(Mouse,Rat)),(Platypus,Opossum)))));\n+(LngfishAu,(LngfishSA,LngfishAf),(Frog,(((Turtle,(Sphenodon,(Crocodile,Bird))),Lizard),((((Human,Seal),(Cow,Whale)),(Mouse,Rat)),(Platypus,Opossum)))));\n+(LngfishAu,(LngfishSA,LngfishAf),(Frog,(((Turtle,(Sphenodon,(Crocodile,Bird))),Lizard),((((Human,(Seal,(Cow,Whale))),(Mouse,Rat)),Opossum),Platypus))));\n+(LngfishAu,(LngfishSA,LngfishAf),(Frog,((((Turtle,(Crocodile,Bird)),Sphenodon),Lizard),(((Human,(Seal,(Cow,Whale))),(Mouse,Rat)),(Platypus,Opossum)))));\n+(LngfishAu,(LngfishSA,LngfishAf),(Frog,((((Turtle,(Crocodile,Bird)),Lizard),Sphenodon),(((Human,(Seal,(Mouse,Rat))),(Cow,Whale)),(Platypus,Opossum)))));\n+(LngfishAu,(LngfishSA,LngfishAf),(Frog,((((Turtle,(Crocodile,Bird)),Sphenodon),Lizard),(((Human,(Seal,(Cow,Whale))),(Mouse,Rat)),(Platypus,Opossum)))));\n+(LngfishAu,(LngfishSA,LngfishAf),(Frog,((((Turtle,(Crocodile,Bird)),Sphenodon),Lizard),(((Human,(Seal,(Cow,Whale))),(Mouse,Rat)),(Platypus,Opossum)))));\n+(LngfishAu,(LngfishSA,LngfishAf),(Frog,((((Turtle,(Crocodile,Bird)),Sphenodon),Lizard),(((Human,(Seal,(Cow,Whale))),(Mouse,Rat)),(Platypus,Opossum)))));\n+(LngfishAu,(LngfishSA,LngfishAf),(Frog,((Turtle,((Sphenodon,Lizard),(Crocodile,Bird))),(((Human,(Seal,(Cow,Whale))),(Mouse,Rat)),(Platypus,Opossum)))));\n+(LngfishAu,(LngfishSA,LngfishAf),(Frog,((Turtle,((Sphenodon,(Crocodile,Bird)),Lizard)),((((Human,Seal),(Cow,Whale)),(Mouse,Rat)),(Platypus,Opossum)))));\n+(LngfishAu,(LngfishSA,LngfishAf),(Frog,((Turtle,((Sphenodon,(Crocodile,Bird)),Lizard)),(((Human,(Seal,(Cow,Whale))),(Mouse,Rat)),'..b'fishAu,(LngfishSA,LngfishAf),(Frog,((Turtle,((Sphenodon,(Crocodile,Bird)),Lizard)),((((Human,Seal),(Cow,Whale)),(Mouse,Rat)),(Platypus,Opossum)))));\n+(LngfishAu,(LngfishSA,LngfishAf),(Frog,((((Turtle,(Crocodile,Bird)),Lizard),Sphenodon),(((Human,(Seal,(Cow,Whale))),(Mouse,Rat)),(Platypus,Opossum)))));\n+(LngfishAu,(LngfishSA,LngfishAf),(Frog,((Turtle,(((Sphenodon,Crocodile),Bird),Lizard)),(((Human,(Seal,(Cow,Whale))),(Mouse,Rat)),(Platypus,Opossum)))));\n+(LngfishAu,(LngfishSA,LngfishAf),(Frog,((((Turtle,(Crocodile,Bird)),Lizard),Sphenodon),(((Human,(Seal,(Cow,Whale))),(Mouse,Rat)),(Platypus,Opossum)))));\n+(LngfishAu,(LngfishSA,LngfishAf),(Frog,((Turtle,((Sphenodon,(Crocodile,Bird)),Lizard)),((((Human,Seal),(Cow,Whale)),(Mouse,Rat)),(Platypus,Opossum)))));\n+(LngfishAu,(LngfishSA,LngfishAf),(Frog,((Turtle,((Sphenodon,(Crocodile,Bird)),Lizard)),(((Human,(Seal,(Cow,Whale))),(Mouse,Rat)),(Platypus,Opossum)))));\n+(LngfishAu,(LngfishSA,LngfishAf),(Frog,((Turtle,((Sphenodon,Lizard),(Crocodile,Bird))),((((Human,(Seal,(Cow,Whale))),(Mouse,Rat)),Platypus),Opossum))));\n+(LngfishAu,(LngfishSA,LngfishAf),(Frog,((((Turtle,(Crocodile,Bird)),Sphenodon),Lizard),((((Human,Seal),(Cow,Whale)),(Mouse,Rat)),(Platypus,Opossum)))));\n+(LngfishAu,(LngfishSA,LngfishAf),(Frog,((((Turtle,(Crocodile,Bird)),Sphenodon),Lizard),((((Human,Seal),(Cow,Whale)),(Mouse,Rat)),(Platypus,Opossum)))));\n+(LngfishAu,(LngfishSA,LngfishAf),(Frog,(((Turtle,(Sphenodon,(Crocodile,Bird))),Lizard),(((Human,(Seal,(Cow,Whale))),(Mouse,Rat)),(Platypus,Opossum)))));\n+(LngfishAu,(LngfishSA,LngfishAf),(Frog,((((Turtle,(Crocodile,Bird)),Lizard),Sphenodon),(((Human,(Seal,(Cow,Whale))),(Mouse,Rat)),(Platypus,Opossum)))));\n+(LngfishAu,(LngfishSA,LngfishAf),(Frog,((((Turtle,(Crocodile,Bird)),Lizard),Sphenodon),(((Human,(Seal,(Cow,Whale))),(Mouse,Rat)),(Platypus,Opossum)))));\n+(LngfishAu,(LngfishSA,LngfishAf),(Frog,((((Turtle,(Crocodile,Bird)),Sphenodon),Lizard),(((Human,(Seal,(Cow,Whale))),(Mouse,Rat)),(Platypus,Opossum)))));\n+(LngfishAu,(LngfishSA,LngfishAf),(Frog,((((Turtle,(Crocodile,Bird)),Sphenodon),Lizard),(((Human,(Mouse,Rat)),(Seal,(Cow,Whale))),(Platypus,Opossum)))));\n+(LngfishAu,(LngfishSA,LngfishAf),(Frog,((((Turtle,(Crocodile,Bird)),Sphenodon),Lizard),(((Human,(Mouse,Rat)),(Seal,(Cow,Whale))),(Platypus,Opossum)))));\n+(LngfishAu,(LngfishSA,LngfishAf),(Frog,((((Turtle,(Crocodile,Bird)),Sphenodon),Lizard),((((Human,(Cow,Whale)),Seal),(Mouse,Rat)),(Platypus,Opossum)))));\n+(LngfishAu,(LngfishSA,LngfishAf),(Frog,((((Turtle,(Crocodile,Bird)),Lizard),Sphenodon),(((Human,(Seal,(Cow,Whale))),(Mouse,Rat)),(Platypus,Opossum)))));\n+(LngfishAu,(LngfishSA,LngfishAf),(Frog,((((Turtle,(Crocodile,Bird)),Sphenodon),Lizard),(((Human,(Seal,(Cow,Whale))),(Mouse,Rat)),(Platypus,Opossum)))));\n+(LngfishAu,(LngfishSA,LngfishAf),(Frog,((Turtle,((Sphenodon,(Crocodile,Bird)),Lizard)),(((Human,(Seal,(Cow,Whale))),(Mouse,Rat)),(Platypus,Opossum)))));\n+(LngfishAu,(LngfishSA,LngfishAf),(Frog,((((Turtle,(Crocodile,Bird)),Lizard),Sphenodon),(((Human,(Seal,(Cow,Whale))),(Mouse,Rat)),(Platypus,Opossum)))));\n+(LngfishAu,(LngfishSA,LngfishAf),(Frog,((Turtle,((Sphenodon,(Crocodile,Bird)),Lizard)),(((Human,(Mouse,Rat)),(Seal,(Cow,Whale))),(Platypus,Opossum)))));\n+(LngfishAu,(LngfishSA,LngfishAf),(Frog,((((Turtle,(Crocodile,Bird)),Sphenodon),Lizard),((Human,((Seal,(Cow,Whale)),(Mouse,Rat))),(Platypus,Opossum)))));\n+(LngfishAu,(LngfishSA,LngfishAf),(Frog,((((Turtle,(Crocodile,Bird)),Sphenodon),Lizard),(((Human,(Seal,(Cow,Whale))),(Mouse,Rat)),(Platypus,Opossum)))));\n+(LngfishAu,(LngfishSA,LngfishAf),(Frog,((((Turtle,(Crocodile,Bird)),Sphenodon),Lizard),(((Human,(Mouse,Rat)),(Seal,(Cow,Whale))),(Platypus,Opossum)))));\n+(LngfishAu,(LngfishSA,LngfishAf),(Frog,(((Turtle,(Sphenodon,(Crocodile,Bird))),Lizard),(((Human,(Seal,(Cow,Whale))),(Mouse,Rat)),(Platypus,Opossum)))));\n+(LngfishAu,(LngfishSA,LngfishAf),(Frog,(((Turtle,(Sphenodon,(Crocodile,Bird))),Lizard),((((Human,(Seal,(Cow,Whale))),(Mouse,Rat)),Opossum),Platypus))));\n' 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