Staramr add DM and update tool with database information #6609
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…e only thing missing is the test database
This reverts commit d63371f. Back with db repo with index information
…9f_plasmidfinder_3e77502/update/plasmidfinder/' content from commit 4add28296 git-subtree-dir: tools/staramr/test-data/resfinder_d1e607b_pointfinder_694919f_plasmidfinder_3e77502/update/plasmidfinder git-subtree-split: 4add282963c788762cdc3c6e91eb46c3d109f19b
…ramr/test-data/resfinder_d1e607b_pointfinder_694919f_plasmidfinder_3e77502/update/plasmidfinder'
…9f_plasmidfinder_3e77502/update/resfinder/' content from commit e0525f203 git-subtree-dir: tools/staramr/test-data/resfinder_d1e607b_pointfinder_694919f_plasmidfinder_3e77502/update/resfinder git-subtree-split: e0525f203e43bcd6dc91348e561a2cb09fd4014b
…ramr/test-data/resfinder_d1e607b_pointfinder_694919f_plasmidfinder_3e77502/update/resfinder'
…9f_plasmidfinder_3e77502/update/pointfinder/' content from commit 694919f59 git-subtree-dir: tools/staramr/test-data/resfinder_d1e607b_pointfinder_694919f_plasmidfinder_3e77502/update/pointfinder git-subtree-split: 694919f59a38980204009e7ade76bf319cb7df0b
…ramr/test-data/resfinder_d1e607b_pointfinder_694919f_plasmidfinder_3e77502/update/pointfinder'
…rch, used only for test with hidden parameter
…into staramr_add
| @@ -0,0 +1,12 @@ | |||
| name: data_manager_build_staramr | |||
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You could update the shed.yml file for the data mananger. Currently it reads as for the tool.
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| <stdio> | ||
| <exit_code range=":-1" level="fatal" description="Error: Cannot open file"/> | ||
| <exit_code range="1:" level="fatal" description="Error"/> | ||
| </stdio> | ||
| <command><![CDATA[ |
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equivalent:
Suggested change
| <stdio> | |
| <exit_code range=":-1" level="fatal" description="Error: Cannot open file"/> | |
| <exit_code range="1:" level="fatal" description="Error"/> | |
| </stdio> | |
| <command><![CDATA[ | |
| <command detect_errors="exit_code"><![CDATA[ |
| <command><![CDATA[ | ||
| #import re | ||
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| #set $match_resfinder = re.search(r'^resfinder_(?:[^_]*_)?([0-9a-z]*)_[0-9]{4}-[0-9]{2}-[0-9]{2}$', str($resfinder.resfinder_database_select)) |
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You could simplify parsing by make the values a comma-separated string (then you can just use split). Of course any other character will do as well.
| "staramr_database":[ | ||
| { | ||
| "value": "staramr_downloaded_#echo date.today().strftime('%d%m%Y')#_resfinder_${resfinder_commit}_pointfinder_${pointfinder_commit}_plasmidfinder_${plasmidfinder_commit}", | ||
| "name": "starAMR databases with ResFinder: ${resfinder_tag_commit_date}, PointFinder: ${pointfinder_tag_commit_date}, PlasmidFinder: ${plasmidfinder_tag_commit_date}", |
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Does this info shown to the user contain the hash? Maybe do not show it?
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| #set $named_genomes = '' | ||
| #for $genome in $genomes | ||
| #set $_named_genome = re.sub(r'(\s|\(|\)|\/)', '_', '"{}.fasta"'.format($genome.element_identifier)) |
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Maybe better something like
tools-iuc/tools/seqsero2/seqsero2.xml
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| +------------+---------------------+---------------+---------+---------+---------+---------+---------+---------+----------+ | ||
| | Isolate ID | Scheme | Sequence Type | Locus 1 | Locus 2 | Locus 3 | Locus 4 | Locus 5 | Locus 6 | Locus 7 | | ||
| +============+=====================+===============+=========+=========+=========+=========+=========+=========+==========+ | ||
| | SRR1952908 | senterica_achtman_2 | 11 | aroC(5) | dnaN(2) | hemD(3) | hisD(7) | purE(6) | sucA(6) | thrA(11) | | ||
| | SRR1952926 | senterica_achtman_2 | 11 | aroC(5) | dnaN(2) | hemD(3) | hisD(7) | purE(6) | sucA(6) | thrA(11) | | ||
| +------------+---------------------+---------------+---------+---------+---------+---------+---------+---------+----------+ |
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My preference would be a list of column definitions instead of an example. Up to you.
| </section> | ||
| </inputs> | ||
| <outputs> | ||
| <data format="tabular" name="mlst" label="${tool.name} on ${on_string}: MLST report" /> |
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Quite a few outputs .. maybe make some optional by using filters?
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| <conditional name="complex_mutations"> | ||
| <param name="complex_mutations_condition" type="select" label="Provide a custom list of complex mutations"> | ||
| <option value="default" selected="true">Use default list of complex mutations</option> | ||
| <option value="custom">Provide a custom list of complex mutations</option> | ||
| </param> | ||
| <when value="default" /> | ||
| <when value="custom"> | ||
| <param type="data" name="complex_mutations_file" format="txt,tabular" label="Complex mutations file" help="Pass a file containing a list of complex mutations to group (if present) in the PointFinder results" /> | ||
| </when> | ||
| </conditional> |
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Instead of the conditional one could just use an optional data parameter? Problem with conditionals is that they are fixed in workflows.
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| <param argument="--genome-size-lower-bound" type="integer" label="The lower bound for our genome size for the quality metrics" value="4000000" /> | ||
| <param argument="--genome-size-upper-bound" type="integer" label="The upper bound for our genome size for the quality metrics" value="6000000" /> | ||
| <param argument="--minimum-N50-value" type="integer" label="The minimum N50 value for the quality metrics" value="10000" /> | ||
| <param argument="--minimum-contig-length" type="integer" label="The minimum contig length for the quality metrics" value="300" /> |
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These integers could also have a min, or? Maybe 0?
| ]]></command> | ||
| <inputs> | ||
| <param name="hide_db_build" type="hidden" value="" /> | ||
| <param type="data" name="genomes" format="fasta" multiple="true"/> |
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Is fasta.gz also possible?
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FOR CONTRIBUTOR: