Allow single file processing spades#7802
Allow single file processing spades#7802paulzierep wants to merge 2 commits intogalaxyproject:mainfrom
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bernt-matthias
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bernt-matthias
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Why not use Galaxy's possibilities to achieve the same?
I wish we could :) I guess you are referring to the nest collection tool to force mapping over. |
bernt-matthias
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I won't object the change. Still, my (weak) preference would be implement this with nested collections, but @mvdbeek had some good reasons to have this implemented on the tool side. Guess we can/should discuss this also in the next tool dev meeting.
We definitely need test coverage for individual + coassembly of the main read set (input_files_paired) and the additional reads (input_additional_files_paired) + the possible combinations.
| <option value="single">Single-end</option> | ||
| <option value="paired_interlaced">Paired-end: interlaced reads</option> | ||
| <option value="paired_collection" selected="true">Paired-end: list of dataset pairs</option> | ||
| <param name="sPaired" type="select" label="Input format for reads" help="@HELP@"> |
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This macro could reuse input_files_paired
| <param name="sPaired" type="select" label="Input format for reads" help="@HELP@"> | ||
| <option value="single">Single-end (individual assembly)</option> | ||
| <option value="paired">Paired-end: forward + reverse (individual assembly)</option> | ||
| <option value="interlaced">Paired-end: interlaced reads (individual assembly)</option> |
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Could we drop interlaced? I have never seen an interlaced dataset in my life.
| #set ext = $fix_ext($input_file.ext) | ||
| #set fname = re.sub('[^\w\-_.]', '_', $input_file.element_identifier) + '.' + $ext | ||
| #set file_path = 'reads1/' + $fname |
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Could imagine that having this implemented as a function would be beneficial.
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FOR CONTRIBUTOR:
There are two labels that allow to ignore specific (false positive) tool linter errors:
skip-version-check: Use it if only a subset of the tools has been updated in a suite.skip-url-check: Use it if github CI sees 403 errors, but the URLs work.