Updating tools/jasminesv tool to 1.1.5 1.1.5 #3816
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simonbray
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How does the tool know which threshold belongs to which sample?
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I assume the same order as in vcffilelist, anything else would be very strange.
I guess there is the problem that multiple="true" does not allow dataset ordering though.
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Probably the 'nicest' option would be a repeat containing both the VCF file and an optional float param for the threshold, assuming the number of VCF files generally used is not too high.
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A repeat might be nice for interactive tool use, but seems not of much use for automation, eg in workflows.
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What is the best option then? To write a note in the help encouraging users to submit datasets as a collection if they want to use individual thresholds, so that ordering is guaranteed?
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I think so
- collection + tsv using identifiers for automatized use cases
- repeat for interactive use
tools/jasminesv/jasminesv.xml
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| <option value="" selected="true">Don't specify distance thresholds</option> | ||
| </param> | ||
| <when value="sample_dists"> | ||
| <param name="sample_dists_file" type="data" format="txt,tsv" value="" label="A file containing distance thresholds for each sample, one per line"/> |
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Maybe just tsv .. or even better tabular?
planemo-autoupdate
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gxydevbot
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There are new updates, they have been integrated to the PR, check the file diff. |
gxydevbot
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Hello! This is an automated update of the following tool: tools/jasminesv. I created this PR because I think the tool's main dependency is out of date, i.e. there is a newer version available through conda.
Please see https://github.com/planemo-autoupdate/autoupdate for more information.