wrappers for ppanggolin all and ppanggolin msa #6645
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tools/ppanggolin/.shed.yml
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| homepage_url: https://ppanggolin.readthedocs.io/en/latest/ | ||
| long_description: | | ||
| Depicting microbial species diversity via a Partitioned PanGenome Graph Of Linked Neighbors. | ||
| remote_repository_url: https://github.com/labgem/PPanGGOLiN |
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I think this should point to the IUC repo. Use this one for homepage_url. The readthedocs URL might be cool to mention in the tool's help section.
| remote_repository_url: https://github.com/labgem/PPanGGOLiN | ||
| type: unrestricted | ||
| categories: | ||
| - Genome annotation |
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Is this a good category for the tool?
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I think so but I am not sure. Roary (a tool with overlapping functionalities) is classified in "Genomics Analysis -> Annotation" in https://usegalaxy.fr/ and in "Genome Analysis Tools -> Genome annotation" in https://galaxy.migale.inrae.fr/. Is there a list of categories and/or a guideline to choose the right category for the tool ?
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It's just the toolshed categories. You can see all of them here: https://toolshed.g2.bx.psu.edu/
tools/ppanggolin/ppanggolin_all.xml
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| <tool id="ppanggolin_all" name="PPanGGOLiN all" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> | |||
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Maybe a newer profile, e.g. 23.0?
tools/ppanggolin/ppanggolin_all.xml
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| <tool id="ppanggolin_all" name="PPanGGOLiN all" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> | |||
| <description>generates a partitioned pangenome graph with predicted RGP, spots and modules.</description> | |||
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- Remove the
. - Can you shorten this as much as possible? The
tool name: descriptionwill be shown in Galaxy's tool menu.
tools/ppanggolin/ppanggolin_all.xml
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| echo -n > "./tmp_ppanggolin/organism_list/organism.list" && | ||
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| #for $i, $file in enumerate($input_type.genomes): | ||
| #set base_name = str($file.name).split('.')[0] |
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$file.element_identifier is preferred instead of $file.name
tools/ppanggolin/ppanggolin_all.xml
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| <conditional name="input_nb_of_partitions"> | ||
| <param name="choice_nb_of_partitions" type="select" label="Number of partitions"> | ||
| <option value="automatic" selected="true">Automatic</option> | ||
| <option value="manually_set_to">Manually set to:</option> | ||
| </param> | ||
| <when value="automatic"/> | ||
| <when value="manually_set_to"> | ||
| <param argument="-K" name="nb_of_partitions" type="integer" value="3" min="2" max="20" label="Number of partitions"/> | ||
| </when> | ||
| </conditional> |
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Also here, you could make nb_of_partitions an optional parameter instead and document that empty means automatic and 3 as a good choice.
tools/ppanggolin/ppanggolin_all.xml
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| <option value="32">32 - Balanophoraceae Plastid</option> | ||
| <option value="33">33 - Cephalodiscidae Mitochondrial</option> | ||
| </param> | ||
| <param name="do_defrag" type="boolean" checked="true" label="Gene family defragmentation"/> |
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You can add truevalue="" falsevalue="--no_defrag" and just use $do_defrag in the command section, i.e. remove the #if.
tools/ppanggolin/ppanggolin_all.xml
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| </param> | ||
| <param name="do_defrag" type="boolean" checked="true" label="Gene family defragmentation"/> | ||
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| <section name="basic_pangenome_output_files" title="Basic pangenome output files" expanded="False"> |
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I would not add sections for single parameters. The space used for expanded="False" should be about the same for a single parameter. Maybe one "advanced parameters" section for all of them?
tools/ppanggolin/ppanggolin_msa.xml
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| mkdir -p "./tmp_ppanggolin/tmpdir_msa" && | ||
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| ppanggolin msa | ||
| --pangenome $pangenome_h5 |
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Add single quotes (always for data and text inputs as well as output files).
tools/ppanggolin/ppanggolin_msa.xml
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| <option value="dna">DNA</option> | ||
| </param> | ||
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| <param argument="--phylo" name="do_phylo" type="boolean" checked="true" label="Writes a whole genome msa file for additional phylogenetic analysis (recommended)"/> |
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truevalue/falsevalue for all booleans?
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Thanks @bernt-matthias , I implemented your suggestions, does it look good to you ? I couldn't get the validator to work for checking the consistency of the input files format, I didn't find a way to loop through multiple datasets or dataset collection and didn't find an example of such a validator. I implemented this check in the section by raising an exception. Best, Thomas |
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