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more tweaks..
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fubar2 committed Sep 5, 2024
1 parent 336da21 commit 24dcdc2
Showing 1 changed file with 7 additions and 6 deletions.
13 changes: 7 additions & 6 deletions tools/ncbi_egapx/ncbi_egapx.xml
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]]></command>
<inputs>
<conditional name="cond_input_style">
<param name="input_style" type="select" label="Fill in a tool form or use an existing yaml configuration?"
help="Use a pre-prepared yaml if available. Use the tool form if history files are needed for this job">
<param name="input_style" type="select" label="Fill in a tool form or use an existing yaml configuration from the current history?"
help="Use a pre-prepared yaml if available. Use the tool form if history files are needed as rna-seq or reference genome inputs for this job">
<option selected="True" value="history">Use a pre-prepared yaml egapx configuration</option>
<option value="fillform">Provide configuration details for conversion into a configuration yaml</option>
</param>
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<when value="fillform">
<param name="taxid" type="text" optional="false" label="NCBI Taxon ID" help="Used to identify the HMM model files needed"/>
<conditional name="reference_genome">
<param name="genome_type_select" type="select" label="Reference genome source" help="Select a built in, history or remote URI for the reference genome fasta">
<option selected="True" value="indexed">Use a Galaxy server built-in genome</option>
<option value="history">Use a genome fasta file from the current history</option>
<param name="genome_type_select" type="select" label="Reference genome source for mapping supplied RNA-seq reads"
help="Select a built in, history or remote URI for the reference genome fasta">
<option value="indexed">Use a Galaxy server built-in genome</option>
<option value="history" selected="True">Use a genome fasta file from the current history</option>
<option value="uri">Provide a remote web link URI ("https://...") pointing at the required genome reference fasta file</option>
</param>
<when value="indexed">
Expand Down Expand Up @@ -135,7 +136,7 @@ This wrapper is designed to allow measuring how *inefficient* it is in terms of
required to convert Nextflow DDL into tools and WF logic. Balancing these competing requirements is a fundamental Galaxy challenge.
EGAPx requires very substantial resources to run with real data. *128GB and 32 cores* are the minimum requirement; *256GB and 64 cores* are recommended.
EGAPx requires very substantial resources to run with real data. *132GB and 32 cores* are the minimum requirement; *256GB and 64 cores* are recommended.
A special minimal example that can be run in 6GB with 4 cores is provided as a yaml configuration and is used for the tool test.
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