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interaction:fixed effects and corrections modified #5928

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Apr 29, 2024
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interaction:fixed effects and corrections modified #5928

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interaction:fixed effects and corrections modified
renu-pal Mar 27, 2024
8fa089e
fixed effects, random effects , corrections methods modified and vers…
renu-pal Apr 17, 2024
bfc500c
maaslin2: test cases added
renu-pal Apr 19, 2024
02ab4b6
maaslin2 : updated fixed and random effects to include just numbers i…
renu-pal Apr 24, 2024
18bb723
Update tools/maaslin2/maaslin2.xml
bgruening Apr 25, 2024
621439a
maaslin2: update correction help
renu-pal Apr 26, 2024
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11 changes: 9 additions & 2 deletions tools/maaslin2/maaslin2.xml
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Expand Up @@ -55,7 +55,7 @@ cd outputFolder && mkdir -p figures/ && cp *.pdf figures
<inputs>
<param name="input_data" type="data" format="tabular" label="Data (or features) file"/>
<param name="input_metadata" type="data" format="tabular" label="Metadata file"/>
<param argument="--fixed_effects" type="select" multiple="true" optional="true" label="Interactions: Fixed effects" help="The fixed effects for the model, comma-delimited for multiple effects">
<param argument="--fixed_effects" type="text" multiple="true" optional="true" label="Interactions: Fixed effects" help="The fixed effects for the model, comma-delimited for multiple effects">
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Why should this be a text paraeter? We should probably fix the help instead?

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We can do that now but if more association factors get added in the future, we might have to make changes again as we are doing now. So instead take it as a text parameter.

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In fact, the fixed_effects as well as the random_effects should be of type: data_column (see:

tools-iuc/tools/bedtools/overlapBed.xml

Line 17 in 4e3719a

<param name="cols" type="data_column" data_ref="input" multiple="true"
for an example).
Since for both multiple columns from the input can be chosen. The original optional values are nonsense, since they hard-coded the column names of the test data.

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I am getting column numbers instead of names after using type="data_column" . Do we have any other type where we can get names of columns directly instead of numbers?

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Have you tried setting numerical=false? https://docs.galaxyproject.org/en/latest/dev/schema.html#id51

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setting numerical="false" did not work instead setting use_header_names="true" worked and UI shows column names now but the test cases are failing. Do not understand why it is still accepting numerical values as valid options for tests. So working on that now.

tool_test_output.json

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I could be wrong, but the use_header_names="true" option is really just cosmetic and for the UI, you still need to give numbers in the tests.

Very good idea to use use_header_names="true"!!!

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hi @renu-pal it was a surprise for me, that there is not easy way to get the column_names available for the command line from Galaxy, however after some fideling I found a way to get them from the input file:

## get column names of fixed and random effect from the input file, since galaxy 
## can only return indices with type="data_column" 

## get header
#set $input = open(str($input_metadata), 'r')
#set $header = $input.readlines()[0].split('\t')

## get fixed effects
#set $fixed_effects_val = []
#for $i in $fixed_effects:
    #silent $fixed_effects_val.append($header[int($i)])
#end for
#set $fixed_effects = ','.join($fixed_effects_val)

## get random effects
#set $random_effects_val = []
#for $i in $random_effects:
    #silent $random_effects_val.append($header[int($i)])
#end for
#set $random_effects = ','.join($random_effects_val)

Maybe let the user know in the help, that the column names must be in the first line of the table or modify the code to skip comments when parsing the header

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forget about that, we need to get the column names in the command line not the cheetah code...

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So update, this way, using awk the file is only parsed on script execution

## get column names of fixed and random effect from the input file, since galaxy 
## can only return indices with type="data_column" 
## using awk so that the file is only parsed on command line execution

#set idx = []
#for $i in $fixed_effects:
    #silent idx.append(f'${i}')
#end for
#set idx_for_awk = ','.join(idx)

fixed_effects=`awk -v OFS=',' -F"\t" 'NR == 1 { print $idx_for_awk}' '$input_metadata'` &&
echo 'Assigned fixed effects as:' \$fixed_effects &&

#set idx = []
#for $i in $random_effects:
    #silent idx.append(f'${i}')
#end for
#set idx_for_awk = ','.join(idx)

random_effects=`awk -v OFS=',' -F"\t" 'NR == 1 { print $idx_for_awk}' '$input_metadata'` &&
echo 'Assigned random effects as:' \$random_effects &&

<option value="diagnosis" selected="true">diagnosis</option>
<option value="dysbiosisnonIBD" selected="true">dysbiosisnonIBD</option>
<option value="dysbiosisUC" selected="true">dysbiosisUC</option>
Expand Down Expand Up @@ -87,7 +87,14 @@ cd outputFolder && mkdir -p figures/ && cp *.pdf figures
<option value="NEGBIN">NEGBIN</option>
<option value="ZINB">ZINB</option>
</param>
<param argument="--correction" type="text" value="BH" optional="true" label="Correction" help="The correction method for computing the q-value"/>
<param argument="--correction" type="select" value="BH" multiple="true" optional="true" label="Correction" help="The correction method for computing the q-value">
<option value="holm">holm</option>
<option value="hochberg">hochberg</option>
<option value="hommel">hommel</option>
<option value="bonferroni">bonferroni</option>
<option value="BH">BH</option>
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Can you add the full names for BH and BY as well, maybe also add a link to the explanation to the help and check if they all work, maybe add a test or two as well

<option value="BY">BY</option>
</param>
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<param argument="--standardize" type="boolean" truevalue="--standardize TRUE" falsevalue="--standardize FALSE" checked="true" label="Apply z-score so continuous metadata are on the same scale"/>
</section>
<section name="output" title="Set Plotting Output" expanded="true">
Expand Down