Add galaxy tool wrapper for IRMA #6494
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bgruening
reviewed
Oct 28, 2024
bgruening
reviewed
Oct 28, 2024
tools/irma/IRMA.xml
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| <param name="TMP" type="text" value="/tmp" label="Define temp directory" /> | ||
| </section> | ||
| <section name="reference" title="General settings" expanded="false"> | ||
| <param name="SKIP_E" type="select" label="Skip elongation?"> |
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@aaronKol as @bgruening points out there is no need to implement this as a select param. type="boolean" is clearer here.
Same everywhere else where you just have a Yes/No choice. Only exception is where the choice represents a conditional param and determines what's shown in the rest of the tool interface. Booleans are not allowed to cause such a change, i.e. then and only then would a type="select" be appropriate.
| </conditional> | ||
| <param name="module" value="FLU-utr" /> | ||
| <param name="optional_outputs" value="vcf,bam"/> | ||
| <output_collection name="consensus_collection" type="list"> |
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how many elements are in this collection, I guess you can use count to test for it
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tools/irma/IRMA.xml
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| </output_collection> | ||
| </test> | ||
| </tests> | ||
| <help><
wm75
reviewed
Oct 29, 2024
wm75
reviewed
Oct 29, 2024
wm75
reviewed
Oct 29, 2024
wm75
reviewed
Oct 29, 2024
wm75
reviewed
Oct 29, 2024
wm75
reviewed
Oct 29, 2024
wm75
reviewed
Oct 29, 2024
wm75
reviewed
Oct 29, 2024
wm75
reviewed
Oct 29, 2024
…ipped files; fixed env variables
bgruening
reviewed
Oct 31, 2024
tools/irma/createMissingFiles.py
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| for file in os.listdir(dirPrefix): | ||
| if file.endswith(".fasta"): | ||
| presentSegments.append(file.split('.')[0]) | ||
| print(presentSegments) |
tools/irma/IRMA.xml
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| #if $input_type_conditional.fastq_input.forward.is_of_type('fastq.gz') | ||
| ln -sf '${input_type_conditional.fastq_input.forward}' file1.fastq.gz && | ||
| ln -sf '${input_type_conditional.fastq_input.reverse}' file2.fastq.gz && | ||
| #end if |
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Suggested change
| #if $input_type_conditional.fastq_input.forward.is_of_type('fastq.gz') | |
| ln -sf '${input_type_conditional.fastq_input.forward}' file1.fastq.gz && | |
| ln -sf '${input_type_conditional.fastq_input.reverse}' file2.fastq.gz && | |
| #end if | |
| #if $input_type_conditional.fastq_input.forward.is_of_type('fastq.gz') | |
| ln -sf '${input_type_conditional.fastq_input.forward}' file1.fastq.gz && | |
| ln -sf '${input_type_conditional.fastq_input.reverse}' file2.fastq.gz && | |
| #end if |
tools/irma/IRMA.xml
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| #if $input_type_conditional.fastq_input1.is_of_type('fastq.gz') | ||
| file1.fastq.gz | ||
| #else | ||
| '${input_type_conditional.fastq_input1}' | ||
| #end if |
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Suggested change
| #if $input_type_conditional.fastq_input1.is_of_type('fastq.gz') | |
| file1.fastq.gz | |
| #else | |
| '${input_type_conditional.fastq_input1}' | |
| #end if | |
| #if $input_type_conditional.fastq_input1.is_of_type('fastq.gz') | |
| file1.fastq.gz | |
| #else | |
| '${input_type_conditional.fastq_input1}' | |
| #end if |
tools/irma/IRMA.xml
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| #if $input_type_conditional.fastq_input.forward.is_of_type('fastq.gz') | ||
| file1.fastq.gz | ||
| file2.fastq.gz | ||
| #else | ||
| '${input_type_conditional.fastq_input.forward}' | ||
| '${input_type_conditional.fastq_input.reverse}' | ||
| #end if |
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Suggested change
| #if $input_type_conditional.fastq_input.forward.is_of_type('fastq.gz') | |
| file1.fastq.gz | |
| file2.fastq.gz | |
| #else | |
| '${input_type_conditional.fastq_input.forward}' | |
| '${input_type_conditional.fastq_input.reverse}' | |
| #end if | |
| #if $input_type_conditional.fastq_input.forward.is_of_type('fastq.gz') | |
| file1.fastq.gz | |
| file2.fastq.gz | |
| #else | |
| '${input_type_conditional.fastq_input.forward}' | |
| '${input_type_conditional.fastq_input.reverse}' | |
| #end if |
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Adding a wrapper for the tool IRMA (Iterative Refinement Meta-Assembler).
Problem: The IRMA variable
SINGLE_LOCAL_PROCdoesnt set the thread usage. IRMA will start a subprocess for every (8) virus segment. The variableSINGLE_LOCAL_PROCdetermines on how many threads each of these subprocess should run. E.g.SINGLE_LOCAL_PROC=4would yield 4 times 8 = 32 subprocesses.I did not find a way to restrict cores used by irma.
FOR CONTRIBUTOR: