hicBuildMatrix SAM inputs changed from repeat to plain params #6670
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@joachimwolff does this look good to you? |
| @@ -32,7 +29,7 @@ | |||
| #if $dbKey: | |||
| --genomeAssembly '$dbKey' | |||
| #else | |||
| --genomeAssembly '$samFiles[0].samFile.metadata.dbkey' | |||
| --genomeAssembly '$samFile1.metadata.dbkey' | |||
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We should add a unspecified_build validator to both inputs.
tools/hicexplorer/macros.xml
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| @@ -47,6 +47,11 @@ | |||
| <param argument='--dpi' type='integer' optional='true' min="10" max="1000" label='DPI for image' help='Change the default resolution of the plot.' /> | |||
| </xml> | |||
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| <xml name="samFiles"> | |||
| <param name="samFile1" type="data" format="sam,qname_input_sorted.bam" label="Forward SAM/BAM file to process" help="Please use the special BAM datatype: qname_input_sorted.bam and use for 'bowtie2' the '--reorder' option to create a BAM file."/> | |||
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Probably you want unsorted.bam instead of qname_input_sorted.bam. unsorted.bam will allow any bam file.
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Please do not change this behavior at all. You would need to change the behavior of the according mappers, and test if the unsorted type hicBuildMatrix still works under all unsorted scenarios.
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OK. Was just wondering, because sam has to be assumed unsorted. But I guess this is treated in the command block (if so analogous changes could be done for the other bam types).
Ok for me. May I ask, what is the intention of making this cosmetic change? |
@bgruening was going through some very old issues and we thought the old labeling which is "forward/reverse" was causing confusion to the users. Anyways, it should not change the tool behavior and the tool form will be a bit cleaner without unused repeats. |
FOR CONTRIBUTOR:
A repeat with exactly 2 params can be replaced with two params. With two params, at least the labels are better.
version bump only for the affected tools.