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patch krakentools beta_diversity.xml #6553

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merged 11 commits into from
Nov 22, 2024
Merged

patch krakentools beta_diversity.xml #6553

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972ab77
patch krakentools beta_diversity.xml
Nov 12, 2024
d030b29
Merge branch 'galaxyproject:main' into kraken_beta_diversity_patch
mthang Nov 13, 2024
4f9dac2
add re.sub to beta_diversity.xml
Nov 13, 2024
3fabc97
Merge branch 'galaxyproject:main' into kraken_beta_diversity_patch
mthang Nov 15, 2024
25b1b41
patch beta_diversity.xml
Nov 15, 2024
5816c1f
update test unit in beta_diversity.xml
Nov 15, 2024
ad1217d
make output tabular and improve assertions
bernt-matthias Nov 15, 2024
1df8ee0
Merge branch 'galaxyproject:main' into kraken_beta_diversity_patch
mthang Nov 18, 2024
852b59c
Merge branch 'galaxyproject:main' into kraken_beta_diversity_patch
mthang Nov 19, 2024
d1eb0fd
fix re.sub in beta diversity
Nov 19, 2024
0faff71
Update tools/krakentools/beta_diversity.xml
bernt-matthias Nov 19, 2024
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13 changes: 11 additions & 2 deletions tools/krakentools/beta_diversity.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -7,10 +7,19 @@
<expand macro="requirements"/>
<expand macro="version"/>
<command detect_errors="exit_code"><![CDATA[
#import re
#set input_names=[]

#for $input in $inputs
#set identifier = re.sub('[^\s\w\-\\.]', '_', str($input.element_identifier))
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I guess ..

Suggested change
#set identifier = re.sub('[^\s\w\-\\.]', '_', str($input.element_identifier))
#set identifier = re.sub('[^\s\w\-\.]', '_', str($input.element_identifier))

or just

Suggested change
#set identifier = re.sub('[^\s\w\-\\.]', '_', str($input.element_identifier))
#set identifier = re.sub('[^\s\w-.]', '_', str($input.element_identifier))

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Seems to be the former one. Wanted to make some experiments yesterday which version is correct (we have all of them in the repo).. but did not finish yet.

#silent $input_names.append($identifier)
ln -s '$input' '${identifier}' &&
#end for

beta_diversity.py
--inputs
#for $input in $inputs
'$input'
#for $input_name in $input_names
'${input_name}'
#end for
--type '$sample.type'
#if $sample.type == 'kreport'
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