| Previous changeset 9:6595517c2dd8 (2022-07-28) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 06a92568f3409b035fd8a08725db20933d8d15e6 |
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modified:
column_maker.py column_maker.xml |
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added:
test-data/column_maker_out5.interval |
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| diff -r 6595517c2dd8 -r aff5135563c6 column_maker.py --- a/column_maker.py Thu Jul 28 15:28:30 2022 +0000 +++ b/column_maker.py Thu Aug 22 08:25:44 2024 +0000 |
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| @@ -13,12 +13,61 @@ import sys # Functions that may be used in the compute expression from math import ( # noqa: F401 + acos, + acosh, + asin, + asinh, + atan, + atan2, + atanh, + cbrt, ceil, + comb, + copysign, + cos, + cosh, + degrees, + dist, + erf, + erfc, exp, + exp2, + expm1, + fabs, + factorial, floor, + fmod, + frexp, + fsum, + gamma, + gcd, + hypot, + inf, + isclose, + isfinite, + isinf, + isnan, + isqrt, + ldexp, + lgamma, log, log10, + log1p, + log2, + modf, + nextafter, + perm, + pi, + pow, + prod, + remainder, + sin, sqrt, + tan, + tanh, + tau, + trunc, + ulp, ) from numpy import format_float_positional @@ -121,10 +170,10 @@ 'lambda fields: [from_str(s, t) for s, t in zip(fields, [%s])]' % args.column_types ) -except Exception as e: +except Exception as err: sys.exit( 'While parsing column types, the following problem occured: "%s"' - % e + % err ) # Get and parse actions @@ -150,11 +199,19 @@ # COL_NAME is required with the --header option and specifies the name of the # new column; without --header, any COL_NAME gets ignored. operators = 'is|not|or|and' -builtin_and_math_functions = ( +builtin_functions = ( 'abs|all|any|ascii|bin|bool|chr|complex|divmod|float|format|hex|int|len|' - 'list|map|max|min|oct|ord|pow|range|reversed|round|set|sorted|str|sum|type|' - 'log|log10|exp|sqrt|ceil|floor' + 'list|map|max|min|oct|ord|pow|range|reversed|round|set|sorted|str|sum|type' ) + +math_functions = ( + 'acos|acosh|asin|asinh|atan|atan2|atanh|cbrt|ceil|comb|copysign|cos|cosh|degrees|' + 'dist|erf|erfc|exp|exp2|expm1|fabs|factorial|floor|fmod|frexp|fsum|gamma|gcd|' + 'hypot|inf|isclose|isfinite|isinf|isnan|isqrt|ldexp|lgamma|log|log10|log1p|' + 'log2|modf|nextafter|perm|pi|pow|prod|remainder|sin|' + 'sqrt|tan|tanh|tau|trunc|ulp' +) +builtin_and_math_functions = builtin_functions + '|' + math_functions imported_numpy_function = 'format_float_positional' string_and_list_methods = [ name for name in dir('') + dir([]) if not name.startswith('_') @@ -171,6 +228,7 @@ for ac in actions: try: expr_string, col_add_spec, new_col_name = ac.split(';') + print(expr_string) except ValueError: sys.exit( 'Invalid Action: "%s". ' |
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| diff -r 6595517c2dd8 -r aff5135563c6 column_maker.xml --- a/column_maker.xml Thu Jul 28 15:28:30 2022 +0000 +++ b/column_maker.xml Thu Aug 22 08:25:44 2024 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="Add_a_column1" name="Compute" version="2.0"> +<tool id="Add_a_column1" name="Compute" version="2.1" profile="23.0"> <description>on rows</description> <macros> <xml name="compute_repeat"> @@ -34,8 +34,8 @@ </xml> </macros> <requirements> - <requirement type="package" version="3.8">python</requirement> - <requirement type="package" version="1.23.1">numpy</requirement> + <requirement type="package" version="3.12">python</requirement> + <requirement type="package" version="2.1.0">numpy</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ python '$__tool_directory__/column_maker.py' @@ -193,6 +193,11 @@ </repeat> <output name="out_file1" file="column_maker_out4.tab" /> </test> + <test> + <param name="cond" value="cos(pi)+sin(tau)*c2"/> + <param name="input" value="1.bed" ftype="bed" /> + <output name="out_file1" file="column_maker_out5.interval"/> + </test> <!-- Test list column type in input --> <test> <param name="input" value="bed12.bed" ftype="bed12" /> @@ -311,13 +316,13 @@ - The following built-in Python functions are available for use in expressions:: - abs | all | any | ascii | bin | bool | chr | ceil | complex | divmod - - exp | float | floor | format | hex | int | len | list | log | log10 + abs | all | any | ascii | bin | bool | chr | complex | divmod | float | format | hex | int | len | list + map | max | min | oct | ord | pow | range | reversed | round | set | sorted | str | sum | type - list | map | max | min | oct | ord | pow | range | reversed - - round | set | sorted | sqrt | str | sum | type + acos | acosh | asin | asinh | atan | atan2 | atanh | cbrt | ceil | comb | copysign | cos | cosh | degrees + dist | erf | erfc | exp | exp2 | expm1 | fabs | factorial | floor | fmod | frexp | fsum | gamma | gcd + hypot | inf | isclose | isfinite | isinf | isnan | isqrt | ldexp | lgamma | log | log10 | log1p | log2 + modf | nextafter | perm | pow | prod | remainder | sin | sqrt | tan | tanh | tau | trunc | ulp - In addition the numpy function ``format_float_positional`` is available to control the formatting of floating point numbers. @@ -434,5 +439,7 @@ **Replacement value**: `.` ]]></help> - <citations /> + <citations> + <citation type="doi">10.1093/nar/gkae410</citation> + </citations> </tool> |
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| diff -r 6595517c2dd8 -r aff5135563c6 test-data/column_maker_out5.interval --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/column_maker_out5.interval Thu Aug 22 08:25:44 2024 +0000 |
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