A completely refurbished taxonomy tools collection #463
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…ng devteam taxonomy tool_collection. devteam tools will be put into legacy folder. These tools can be used with blast, diamond, and kraken and visualize directly in krona using iuc's krona wrapper.
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@nekrut if you give me commit access to your repository I will do my review on the fly. For example adding sha256sum is annoying and I can help with this. |
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| <?xml version="1.0"?> | |||
| <tool_dependency> | |||
| <package name="ghostscript" version="9.10"> | |||
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This file needs to be properly indented.
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@bgruening : I gave you push access to my repo |
…nto taxonomy_tools
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@bgruening @nsoranzo @peterjc pls take a look |
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| <tool id="lca1" name="Find lowest diagnostic rank (LCA)" version="1.2.0"> | |||
| <description>in a taxonomy</description> | |||
| <command interpreter="python"> | |||
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This tool uses sort to we want to depend on gnu-coreutils?
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Also set LC_ALL=C for reproducibility?
| </command> | ||
| <inputs> | ||
| <param name="input1" format="tabular" type="data" label="Input File"/> | ||
| <param name="input2" type="integer" value="2" label="First Column"/> |
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@nekrut any reason to not use data_column here?
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| Drawing the tree with default parameters (without changing anything in the interface) will produce this tree: | ||
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| .. image:: https://galaxyproject.org/tool_images/taxonomy/t2ps_ideal.png |
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My main problem with local images is that they just don't work for local testing. They may work once the tools migrates to toolshed. So I would like to keep the URLs for now
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Yeah, this should be fixed in Galaxy and planemo.
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so for now, let me have them as remote URLs. They are also committed to galaxy ansible playbook
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Should we include all images locally or are web-urls ok? |
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I think that embedding remote images is fine if they are part of the upstream documentation, but in this case I'd vote to include them in the repository. |
| tool (aka Taxonomy format) as the input. | ||
| name: lca_wrapper | ||
| owner: iuc | ||
| remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/packages/tool_collections/taxonomy/lca_wrapper |
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/packages/tool_collections/ -> /tool_collections/
…nto taxonomy_tools
…into taxonomy_tools
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@bgruening @nsoranzo @yhoogstrate @peterjc pls, take a look and merge if you don't have major objections |
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Please don't merge! Sorry Anton, here is something wrong with the merge you removed packages. |
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Yes. I see. Probably I did something stupid. |
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closing in favor of #501 |
This completely replaces devteam's taxonomy tool_collection. Devteam tools will be put into legacy folder. These tools can be used with blast, diamond, and kraken and visualize directly in krona using iuc's krona wrapper.