Fix Tiara wrapper when outputs are missing#1846
Fix Tiara wrapper when outputs are missing#1846Minamehr wants to merge 3 commits intobgruening:masterfrom
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| @@ -1,16 +1,18 @@ | |||
| <tool id="tiara" name="tiara" version="@TOOL_VERSION@+galaxy1" profile="21.05"> | |||
| <tool id="tiara" name="tiara" version="@TOOL_VERSION@+galaxy2" profile="21.05"> | |||
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| <tool id="tiara" name="tiara" version="@TOOL_VERSION@+galaxy2" profile="21.05"> | |
| <tool id="tiara" name="tiara" version="@TOOL_VERSION@+galaxy@VERSION_SUFFiX@" profile="@PROFILE@"> |
Can we introduce a VERSION_SUFFIX token in macros and bump the PROFILE to more recent version 25.1?
| <collection name="output" type="list" label="${tool.name} on ${on_string}: classified sequences in txt and Fasta Output"> | ||
| <discover_datasets pattern="__name_and_ext__" ext="fasta,txt" directory="results" /> | ||
| <collection name="output_fasta" type="list" label="${tool.name} on ${on_string}: Fasta Output"> | ||
| <discover_datasets pattern="__name_and_ext__" ext="fasta" directory="fasta" /> |
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Is the find business in the command section really necessary?
Would sth like:
| <discover_datasets pattern="__name_and_ext__" ext="fasta" directory="fasta" /> | |
| <discover_datasets pattern="(?P<designation>.+)\.dat$" directory="txt" format="fasta"/> |
not work directly?
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I tested this, but it failed. It works in principle, but due to how tiara names the outputs, it breaks the expected identifiers, so I kept the current approach for now.
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Can you be a bit more specific on this?
What are the names of the outputs, what would you like the identifiers to be and what are you getting instead. I feel this really should be solvable with the framework instead of via the command section.
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You’re right, my bad. The issue was Tiara’s output naming. Fixed now and updated tests.
wm75
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Much better already, thanks!
| <collection name="output_txt" type="list" label="${tool.name} on ${on_string}: Classified sequences in txt"> | ||
| <discover_datasets pattern="(?P<designation>.+)\.txt$" format="txt" directory="txt" /> | ||
| </collection> |
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Are there ever more txt files than the:
- main results and the
- log output
?
If not, then I don't think this is a good use of a collection and both outputs should just be added as individual datatsets. You can also discover them with from_work_dir and their known names.
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Also a more specific output format for the main results is tabular.
| <xml name="requirements"> | ||
| <requirements> | ||
| <requirement type="package" version="@TOOL_VERSION@">tiara</requirement> | ||
| <requirement type="package" version="3.8">python</requirement> |
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Why is there a Python requirement here? When I'm installing the bioconda package I'm getting Python 3.8 anyway.
Am I missing sth here or is this just some historic artifact?
| <inputs> | ||
| <param name="input" type="data" format="fasta" label="input fasta,fasta.gz file"/> | ||
| <param name="taxonomy_filter" type="select" multiple="true" optional="true" label="Write sequences to fasta,fasta.gz files specified in the arguments to this option." help="all refers to all classes present in input fasta (to separate fasta files)."> | ||
| <param name="taxonomy_filter" type="select" multiple="true" optional="true" label="Write sequences to fasta,fasta.gz files specified in the arguments to this option." help="Select one or more target types of sequences to write to separate FASTA files."> |
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Instead of making this param optional (and producing an empty collection if the user selects nothing), I would rather make the param required, but put it inside a conditional and after a choice param that asks whether split fasta output should be produced at all.
Then, in outputs, you'd create the collection only if the user selected Yes.
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@wm75 @bgruening following the #1808.
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.