Code

Improved CTD to galaxy conversion#54

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jpfeuffer merged 123 commits intoWorkflowConversion:masterWorkflowConversion/CTDConverter:masterfrom bernt-matthias:topic/cdatabernt-matthias/CTDConverter:topic/cdataCopy head branch name to clipboardFeb 10, 2021

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Commits on Jul 6, 2019

• test data: initial commit

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Commits on Jan 27, 2020

• add unit tests

  

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• switch CTDopts branch

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• fixed CTDopts branch name

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• improved indentation of float.ctd

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• update test results

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• added test files for bool, in/out files

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• - added filetypes to test call

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• added filetypes.txt

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• advanced repeats were not advanced

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• add missing tests

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• make help and command CDATA

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• render all bools are rendered as booleans

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• improved handling of selects & always render optional

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• fix specification of select default value

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• fix indentation of advanced parameters in command block

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• use argument attribute, remove size attribute

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• int and float wo default need empty value attribute

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• simplify code for advanced node generation

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• Itemlist (wo restrictions) as comma separated list

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• remove duplicate format entries in inputs

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• remove sanitizer from input files

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• infile input needs no help info that a comma separated list is needed

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• bool input for optional outputs

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• further simplify cli generation

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• link input files to identifier.ext

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• added code to autogenerate a simple test for unit tests

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• test w expect_num_outputs and some bug fixes in cli generation

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• add bool as in ctd 1.7

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• allow for list outputs

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• multiple outputs:

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• make default data type txt

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• cont.

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• fixed category in test ctd files

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• add argument attribute

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• - add option to integrate automatically generated tests

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• - improve parsing of hardcoded values file

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• cont

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• switch to exit_code (instead of aggressive)

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• switched to yml hased hardcoder

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• switch to json hardcoder

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• add special case for booleans

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• big update

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• remove . from element identifiers

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• fixed output handling

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• updates: no if for optional strings

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• improvements test macros, type conversion, command line

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• single quotes for itemlist strings

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• fixes for listitems

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• fixed ofile command line handling

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• outfile handling improvements

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• add missing attributes to output boolean

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• update test data

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• add script to create Galaxy tool xml files for tests

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• revert to double quotes .. for now

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• hardcoding CTD restrictions, format selector

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• fix optional restricted itemlists

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• remove value attrribute from selects

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• use a available server but unavailable URL in tests

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• add test for param, label and help generation

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• simplify and improve label/help generation

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• add Galaxy section analoguous to CTD nodes

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• sections: description -> title

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• sections: title and help

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• prototype for CTD based input

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• also parse params + test only generation

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• update test

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• python3 and pep8

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• f

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• make formats sorted

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• fix

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• update test data for filetype sorting

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• no lint but test

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• testing improvements and fixes

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• also rename select in the tests

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• add debug msgwq

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Commits on Jan 28, 2020

• try to use planemo with deactivated conda env

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• try to switch to pip

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• fix test data

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Commits on Feb 4, 2020

• fill_ctd: galaxyfy json reading

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• remove codecov from travis test

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• remove unnecessary prints from test script

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• test generation fixes and more

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• simplify code for cli mapping generation

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Commits on Feb 10, 2020

• add nodes to tests

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Commits on Mar 2, 2020

• fixes fixes fixes

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• fix for outputs in sections

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Commits on Mar 4, 2020

• adds ftype to all test outputs

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Commits on Mar 25, 2020

• use CTDopts from env

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Commits on Apr 7, 2020

• remove optional from bool params

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Commits on Apr 9, 2020

• add optional output for generated ctd file

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• fix

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Commits on Apr 23, 2020

• improved handling of hardcoded parameters

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Commits on Apr 25, 2020

• hardcoded parameters:

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• fix bug in fill_ctd

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• add parameter to specify tool profile

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Commits on Apr 29, 2020

• only overwrite type parameter if not set

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• fix creation of hardcoder json for multi level keys

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Commits on Aug 4, 2020

• output prefix parameters etc.

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• remove input type parameters, optional output select

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Commits on Aug 5, 2020

• fix output filters

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Commits on Aug 6, 2020

• improvements to formats handling in tests

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Commits on Sep 21, 2020

• don't produce empty sections in Galaxy xml

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Commits on Oct 5, 2020

• make optional outputs optional

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• make optional outputs optional

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Commits on Oct 6, 2020

• Merge branch 'topic/cdata' of https://github.com/bernt-matthias/CTDConverter into topic/cdata

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Commits on Oct 9, 2020

• use correct variable

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Commits on Oct 12, 2020

• use full parameter name for hardcoder

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Commits on Dec 2, 2020

• add tool category to help text

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• Merge branch 'topic/cdata' of https://github.com/bernt-matthias/CTDConverter into topic/cdata

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Commits on Dec 3, 2020

• Revert "add tool category to help text"

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Commits on Dec 4, 2020

• allow to specify wrapper version with bump file

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Commits on Feb 7, 2021

• allow for inputs with the same identifier

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Commits on Feb 8, 2021

• use latest CTDOpts for testing

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• fix test case

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• update test data

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• few testing fixes

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Commits on Feb 10, 2021

• change format only for non defaults

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• exclude some unsupported/nonsense test cases

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• import os

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• update docs

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• flake8 fixes

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• use continuous integers instead of dataset id

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