Add new tool: mapDamage #7081
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Add new tool: mapDamage #7081
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SaimMomin12
reviewed
Jun 27, 2025
Co-authored-by: Saim Momin <[email protected]>
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| sbam_file='$sbam_file' && ## This line would fit better inside the if statement, but for some reason doing that breaks everything when using --rescale. | ||
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| file_extension=\${sbam_file\#\#*.} && |
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This will always be .dat.
Just use $sbam_file.ext.
bgruening
reviewed
Jun 28, 2025
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| ## RENAMING INPUT FILE SO THAT OUTPUT ALWAYS HAS SAME NAME (essential for fasta and rescaled bam, whose name depends on input). | ||
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| sbam_file='$sbam_file' && ## This line would fit better inside the if statement, but for some reason doing that breaks everything when using --rescale. | ||
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| file_extension=\${sbam_file\#\#*.} && | ||
| ln -s '$sbam_file' alignment.\${file_extension} && |
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Suggested change
| ## RENAMING INPUT FILE SO THAT OUTPUT ALWAYS HAS SAME NAME (essential for fasta and rescaled bam, whose name depends on input). | |
| sbam_file='$sbam_file' && ## This line would fit better inside the if statement, but for some reason doing that breaks everything when using --rescale. | |
| file_extension=\${sbam_file\#\#*.} && | |
| ln -s '$sbam_file' alignment.\${file_extension} && | |
| ln -s '$sbam_file' alignment.$sbam_file.ext && |
That should work. .ext is the Galaxy datatype, in your case either bam or `sam
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FOR CONTRIBUTOR:
Hello!
I'm submitting this PR to add the ancient DNA authentication tool mapDamage, as announced in issue #7076 .
This is my first time making a wrapper, so I'm not 100% sure if I handled the data tables perfectly, I'd be really grateful if someone could double-check.
Have a nice day!