maaslin2: maaslin2.xml annotate

annotate maaslin2.xml @ 3:43ccbef89f1d draft

planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5

author	iuc
date	Wed, 26 Jun 2024 09:40:13 +0000
parents	faacef62bb54
children

rev	line source
0 c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	1 <tool id="maaslin2" name="MaAsLin 2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	2 <description>Microbiome Multivariable Association with Linear Models</description>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	3 <macros>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	4 <import>macros.xml</import>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	5 </macros>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	6 <expand macro="edam_ontology"/>
1 ef2cace85809 planemo upload for repository https://github.com/biobakery/Maaslin2 commit 1bed0ce83796932c1a21006f0c657656b49ccd8f iuc parents: 0 diff changeset	7 <expand macro="xrefs"/>
0 c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	8 <expand macro="requirements"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	9 <command detect_errors="exit_code"><![CDATA[
2 faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	10
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	11 ## get column names of fixed and random effect from the input file, since galaxy
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	12 ## can only return indices with type="data_column"
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	13 ## using awk so that the file is only parsed on command line execution
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	14
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	15 #if $fixed_effects
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	16 #set idx = []
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	17 #for $i in $fixed_effects:
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	18 #silent idx.append(f'${i}')
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	19 #end for
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	20 #set idx_for_awk = ','.join(idx)
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	21
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	22 fixed_effects=`awk -v OFS=',' -F"\t" 'NR == 1 { print $idx_for_awk}' '$input_metadata'` &&
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	23 echo 'Assigned fixed effects as:' \$fixed_effects &&
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	24 #end if
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	25
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	26
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	27 #if $random_effects
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	28 #set idx = []
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	29 #for $i in $random_effects:
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	30 #silent idx.append(f'${i}')
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	31 #end for
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	32 #set idx_for_awk = ','.join(idx)
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	33
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	34 random_effects=`awk -v OFS=',' -F"\t" 'NR == 1 { print $idx_for_awk}' '$input_metadata'` &&
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	35 echo 'Assigned random effects as:' \$random_effects &&
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	36 #end if
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	37
0 c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	38 ln -s '$input_data' 'input_data.tsv'
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	39 &&
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	40 ln -s '$input_metadata' 'input_metadata.tsv'
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	41 &&
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	42 Maaslin2.R
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	43 #if $additional_options.min_abundance
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	44 --min_abundance '$additional_options.min_abundance'
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	45 #end if
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	46 #if $additional_options.min_prevalence
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	47 --min_prevalence '$additional_options.min_prevalence'
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	48 #end if
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	49 #if $additional_options.max_significance
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	50 --max_significance '$additional_options.max_significance'
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	51 #end if
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	52 #if $additional_options.normalization
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	53 --normalization '$additional_options.normalization'
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	54 #end if
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	55 #if $additional_options.transform
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	56 --transform '$additional_options.transform'
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	57 #end if
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	58 #if $additional_options.analysis_method
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	59 --analysis_method '$additional_options.analysis_method'
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	60 #end if
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	61 #if $random_effects
2 faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	62 --random_effects \$random_effects
0 c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	63 #end if
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	64 #if $fixed_effects
2 faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	65 --fixed_effects \$fixed_effects
0 c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	66 #end if
3 43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5 iuc parents: 2 diff changeset	67 #if $reference
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5 iuc parents: 2 diff changeset	68 --reference '$reference'
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5 iuc parents: 2 diff changeset	69 #end if
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5 iuc parents: 2 diff changeset	70
0 c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	71 #if $additional_options.correction
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	72 --correction '$additional_options.correction'
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	73 #end if
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	74 $additional_options.standardize
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	75 $output.plot_heatmap
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	76 #if $output.heatmap_first_n
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	77 --heatmap_first_n '$output.heatmap_first_n'
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	78 #end if
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	79 $output.plot_scatter
3 43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5 iuc parents: 2 diff changeset	80 --cores 1
0 c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	81 'input_data.tsv'
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	82 'input_metadata.tsv'
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	83 'outputFolder'
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	84 &&
3 43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5 iuc parents: 2 diff changeset	85 zip -r out.zip outputFolder &&
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5 iuc parents: 2 diff changeset	86 cd outputFolder &&
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5 iuc parents: 2 diff changeset	87 mkdir -p figures/ &&
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5 iuc parents: 2 diff changeset	88 cp *.pdf figures
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5 iuc parents: 2 diff changeset	89
2 faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	90
0 c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	91 ]]></command>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	92 <inputs>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	93 <param name="input_data" type="data" format="tabular" label="Data (or features) file"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	94 <param name="input_metadata" type="data" format="tabular" label="Metadata file"/>
2 faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	95 <param argument="--fixed_effects" type="data_column" data_ref="input_metadata" use_header_names="true" multiple="true" optional="true" label="Interactions: Fixed effects" help="The fixed effects for the model, comma-delimited for multiple effects, Default value: All " />
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	96 <param argument="--random_effects" type="data_column" data_ref="input_metadata" use_header_names="true" multiple="true" optional="true" label="Random effects" help="The random effects for the model, comma-delimited for multiple effects, Default: None" />
3 43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5 iuc parents: 2 diff changeset	97 <param argument="--reference" type="text" label="Reference" help="Reference for a variable with more than two levels provided as a string of 'variable,reference' comma delimited for multiple variables. " />
0 c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	98 <section name="additional_options" title="Additional Options" expanded="true">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	99 <param argument="--min_abundance" type="float" value="0.0" optional="true" label="Minimum abundance" help="The minimum abundance for each feature"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	100 <param argument="--min_prevalence" type="float" value="0.1" optional="true" label="Minimum prevalence" help="The minimum percent of samples for which a feature is detected at minimum abundance"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	101 <param argument="--max_significance" type="float" value="0.25" optional="true" label="Maximum significance" help="The q-value threshold for significance"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	102 <param argument="--normalization" type="select" optional="true" label="The normalization method to apply">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	103 <option value="TSS" selected="true">TSS</option>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	104 <option value="CLR">CLR</option>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	105 <option value="CSS">CSS</option>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	106 <option value="NONE">NONE</option>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	107 <option value="TMM">TMM</option>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	108 </param>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	109 <param argument="--transform" type="select" optional="true" label="The transform to apply">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	110 <option value="LOG" selected="true">LOG</option>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	111 <option value="LOGIT">LOGIT</option>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	112 <option value="AST">AST</option>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	113 <option value="NONE">NONE</option>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	114 </param>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	115 <param argument="--analysis_method" type="select" optional="true" label="The analysis method to apply">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	116 <option value="LM" selected="true">LM</option>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	117 <option value="CPLM">CPLM</option>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	118 <option value="NEGBIN">NEGBIN</option>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	119 <option value="ZINB">ZINB</option>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	120 </param>
2 faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	121 <param argument="--correction" type="select" value="BH" optional="true" label="Correction" help="The correction method for computing the q-value, Default: BH ">
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	122 <option value="BH">Benjamini-Hochberg(BH)</option>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	123 <option value="BY">Benjamini-Yekutieli(BY)</option>
3 43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5 iuc parents: 2 diff changeset	124 <option value="Bonferroni">Bonferroni</option>
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5 iuc parents: 2 diff changeset	125 <option value="Holm">Holm</option>
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5 iuc parents: 2 diff changeset	126 <option value="Hochberg">Hochberg</option>
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5 iuc parents: 2 diff changeset	127 <option value="Hommel">Hommel</option>
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5 iuc parents: 2 diff changeset	128 </param>
0 c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	129 <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"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	130 </section>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	131 <section name="output" title="Set Plotting Output" expanded="true">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	132 <param argument="--plot_heatmap" type="boolean" truevalue="--plot_heatmap TRUE" falsevalue="--plot_heatmap FALSE" checked="true" label="Generate a heatmap for the significant associations"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	133 <param argument="--heatmap_first_n" type="integer" value="50" optional="true" label="Heatmap plot first N" help="In heatmap, plot top N features with significant associations"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	134 <param argument="--plot_scatter" type="boolean" truevalue="--plot_scatter TRUE" falsevalue="--plot_scatter FALSE" checked="true" label="Generate scatter plots for the significant associations"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	135 <param name="residuals_output" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Output data frame with residuals for each feature"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	136 </section>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	137 </inputs>
3 43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5 iuc parents: 2 diff changeset	138 <outputs>
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5 iuc parents: 2 diff changeset	139 <data name="archive_output" format="zip" from_work_dir="out.zip" label="${tool.name} on ${on_string}: zip of the complete output" />
0 c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	140 <data name="all_results" format="tabular" from_work_dir="outputFolder/all_results.tsv" label="All results ordered by increasing q-value"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	141 <data name="significant_results" format="tabular" from_work_dir="outputFolder/significant_results.tsv" label="Q-values smaller than or equal to the threshold"/>
3 43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5 iuc parents: 2 diff changeset	142 <data name="residuals" format="rdata" from_work_dir="outputFolder/fits/residuals.rds" label="Data frame with residuals for each feature">
0 c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	143 <filter>output['residuals_output'] is True</filter>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	144 </data>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	145 <data format="pdf" name="headmap" from_work_dir="outputFolder/figures/heatmap.pdf" label="Heatmap of the significant associations" >
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	146 <filter>output['plot_heatmap'] is True</filter>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	147 </data>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	148 <collection name="figures_pdfs" type="list" label="Plots" >
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	149 <discover_datasets pattern="(?P<designation>.+)" directory="outputFolder/figures/" format="pdf"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	150 <filter>output['plot_scatter'] is True</filter>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	151 </collection>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	152 </outputs>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	153 <tests>
3 43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5 iuc parents: 2 diff changeset	154 <test expect_num_outputs="6">
0 c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	155 <param name="input_data" value="HMP2_taxonomy.tsv"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	156 <param name="input_metadata" value="HMP2_metadata.tsv"/>
2 faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	157 <param name="random_effects" value= "2,5"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	158 <param name="fixed_effects" value="4,9,10,11,6,3"/>
3 43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5 iuc parents: 2 diff changeset	159 <param name="reference" value="diagnosis,nonIBD"/>
0 c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	160 <section name="additional_options">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	161 <param name="min_abundance" value="0.0"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	162 <param name="min_prevalence" value="0.1"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	163 <param name="max_significance" value="0.25"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	164 <param name="normalization" value="NONE"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	165 <param name="transform" value="AST"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	166 <param name="analysis_method" value="LM"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	167 <param name="correction" value="BH"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	168 <param name="standardize" value="false"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	169 </section>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	170 <section name="output">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	171 <param name="plot_heatmap" value="true"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	172 <param name="heatmap_first_n" value="50"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	173 <param name="plot_scatter" value="true"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	174 <param name="residuals_output" value="true"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	175 </section>
3 43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5 iuc parents: 2 diff changeset	176 <output name="archive_output">
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5 iuc parents: 2 diff changeset	177 <assert_contents>
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5 iuc parents: 2 diff changeset	178 <has_size value="15005328" delta="1000000" />
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5 iuc parents: 2 diff changeset	179 </assert_contents>
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5 iuc parents: 2 diff changeset	180 </output>
0 c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	181 <output name="all_results">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	182 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	183 <has_text text="feature"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	184 <has_n_lines n="610"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	185 <has_n_columns n="9"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	186 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	187 </output>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	188 <output name="significant_results">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	189 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	190 <has_text text="dysbiosisCD"/>
3 43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5 iuc parents: 2 diff changeset	191 <has_n_lines n="159" delta="10"/>
0 c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	192 <has_n_columns n="9"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	193 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	194 </output>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	195 <output name="residuals">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	196 <assert_contents>
3 43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5 iuc parents: 2 diff changeset	197 <has_size value="462386" />
0 c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	198 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	199 </output>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	200 <output name="headmap">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	201 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	202 <has_size value="7373" delta="1000" />
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	203 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	204 </output>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	205 <output_collection name="figures_pdfs" type="list">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	206 <element name="heatmap.pdf" ftype="pdf">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	207 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	208 <has_size value="7373" delta="1000" />
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	209 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	210 </element>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	211 <element name="age.pdf" ftype="pdf">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	212 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	213 <has_size value="407859" delta="100000" />
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	214 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	215 </element>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	216 <element name="antibiotics.pdf" ftype="pdf">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	217 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	218 <has_size value="1590476" delta="1000000" />
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	219 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	220 </element>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	221 <element name="diagnosis.pdf" ftype="pdf">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	222 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	223 <has_size value="1407572" delta="1000000" />
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	224 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	225 </element>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	226 <element name="dysbiosisCD.pdf" ftype="pdf">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	227 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	228 <has_size value="2328523" delta="1000000" />
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	229 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	230 </element>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	231 <element name="dysbiosisnonIBD.pdf" ftype="pdf">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	232 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	233 <has_size value="1032602" delta="1000000" />
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	234 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	235 </element>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	236 <element name="dysbiosisUC.pdf" ftype="pdf">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	237 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	238 <has_size value="1037005" delta="1000000" />
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	239 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	240 </element>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	241 </output_collection>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	242 </test>
3 43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5 iuc parents: 2 diff changeset	243 <test expect_num_outputs="6">
0 c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	244 <param name="input_data" value="HMP2_taxonomy.tsv"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	245 <param name="input_metadata" value="HMP2_metadata.tsv"/>
2 faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	246 <param name="fixed_effects" value="4,9"/>
3 43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5 iuc parents: 2 diff changeset	247 <param name="reference" value="diagnosis,nonIBD"/>
0 c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	248 <section name="additional_options">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	249 <param name="min_abundance" value="0.0"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	250 <param name="min_prevalence" value="0.1"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	251 <param name="max_significance" value="0.25"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	252 <param name="normalization" value="NONE"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	253 <param name="transform" value="AST"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	254 <param name="analysis_method" value="LM"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	255 <param name="correction" value="BH"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	256 <param name="standardize" value="false"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	257 </section>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	258 <section name="output">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	259 <param name="plot_heatmap" value="true"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	260 <param name="heatmap_first_n" value="50"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	261 <param name="plot_scatter" value="true"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	262 <param name="residuals_output" value="true"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	263 </section>
3 43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5 iuc parents: 2 diff changeset	264 <output name="archive_output">
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5 iuc parents: 2 diff changeset	265 <assert_contents>
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5 iuc parents: 2 diff changeset	266 <has_size value="12630049" delta="1000000" />
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5 iuc parents: 2 diff changeset	267 </assert_contents>
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5 iuc parents: 2 diff changeset	268 </output>
0 c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	269 <output name="all_results">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	270 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	271 <has_text text="feature"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	272 <has_n_lines n="262"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	273 <has_n_columns n="9"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	274 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	275 </output>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	276 <output name="significant_results">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	277 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	278 <has_text text="diagnosis"/>
3 43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5 iuc parents: 2 diff changeset	279 <has_n_lines n="175" delta="5"/>
0 c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	280 <has_n_columns n="9"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	281 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	282 </output>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	283 <output name="residuals">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	284 <assert_contents>
3 43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5 iuc parents: 2 diff changeset	285 <has_size value="366875"/>
0 c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	286 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	287 </output>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	288 <output_collection name="figures_pdfs" type="list">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	289 <element name="diagnosis.pdf" ftype="pdf">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	290 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	291 <has_size value="6234127" delta="1000000" />
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	292 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	293 </element>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	294 </output_collection>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	295 </test>
3 43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5 iuc parents: 2 diff changeset	296 <test expect_num_outputs="6">
0 c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	297 <param name="input_data" value="HMP2_taxonomy.tsv"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	298 <param name="input_metadata" value="HMP2_metadata.tsv"/>
3 43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5 iuc parents: 2 diff changeset	299 <param name="fixed_effects" value="2,4"/>
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5 iuc parents: 2 diff changeset	300 <param name="reference" value="site,Cedars-Sinai,diagnosis,UC"/>
0 c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	301 <section name="additional_options">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	302 <param name="min_abundance" value="0.0001"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	303 <param name="min_prevalence" value="0.1"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	304 <param name="max_significance" value="0.25"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	305 <param name="normalization" value="NONE"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	306 <param name="transform" value="AST"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	307 <param name="analysis_method" value="LM"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	308 <param name="correction" value="BH"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	309 <param name="standardize" value="false"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	310 </section>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	311 <section name="output">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	312 <param name="plot_heatmap" value="true"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	313 <param name="heatmap_first_n" value="50"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	314 <param name="plot_scatter" value="true"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	315 <param name="residuals_output" value="true"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	316 </section>
3 43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5 iuc parents: 2 diff changeset	317 <output name="archive_output">
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5 iuc parents: 2 diff changeset	318 <assert_contents>
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5 iuc parents: 2 diff changeset	319 <has_size value="18278259" delta="1000000" />
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5 iuc parents: 2 diff changeset	320 </assert_contents>
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5 iuc parents: 2 diff changeset	321 </output>
0 c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	322 <output name="all_results">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	323 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	324 <has_text text="feature"/>
3 43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5 iuc parents: 2 diff changeset	325 <has_n_lines n="415" delta="10"/>
0 c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	326 <has_n_columns n="9"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	327 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	328 </output>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	329 <output name="significant_results">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	330 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	331 <has_text text="diagnosis"/>
3 43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5 iuc parents: 2 diff changeset	332 <has_n_lines n="300" delta="15"/>
0 c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	333 <has_n_columns n="9"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	334 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	335 </output>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	336 <output name="residuals">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	337 <assert_contents>
3 43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5 iuc parents: 2 diff changeset	338 <has_size value="363118"/>
0 c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	339 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	340 </output>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	341 <output name="headmap">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	342 <assert_contents>
3 43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5 iuc parents: 2 diff changeset	343 <has_size value="7000" delta="1000" />
0 c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	344 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	345 </output>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	346 <output_collection name="figures_pdfs" type="list">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	347 <element name="heatmap.pdf" ftype="pdf">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	348 <assert_contents>
3 43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5 iuc parents: 2 diff changeset	349 <has_size value="7693" delta="100" />
0 c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	350 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	351 </element>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	352 <element name="diagnosis.pdf" ftype="pdf">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	353 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	354 <has_size value="6061545" delta="1000000" />
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	355 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	356 </element>
3 43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5 iuc parents: 2 diff changeset	357
0 c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	358 </output_collection>
3 43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5 iuc parents: 2 diff changeset	359 </test>
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5 iuc parents: 2 diff changeset	360 <test expect_num_outputs="6">
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5 iuc parents: 2 diff changeset	361 <param name="input_data" value="HMP2_taxonomy.tsv"/>
2 faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	362 <param name="input_metadata" value="HMP2_metadata.tsv"/>
3 43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5 iuc parents: 2 diff changeset	363 <param name="fixed_effects" value="7,9"/>
2 faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	364 <param name="random_effects" value="3" />
3 43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5 iuc parents: 2 diff changeset	365
2 faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	366 <section name="additional_options">
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	367 <param name="min_abundance" value="0.0"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	368 <param name="min_prevalence" value="0.1"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	369 <param name="max_significance" value="0.25"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	370 <param name="normalization" value="TSS"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	371 <param name="transform" value="LOG"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	372 <param name="analysis_method" value="LM"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	373 <param name="correction" value="BY"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	374 <param name="standardize" value="True"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	375 </section>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	376 <section name="output">
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	377 <param name="plot_heatmap" value="true"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	378 <param name="heatmap_first_n" value="50"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	379 <param name="plot_scatter" value="true"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	380 <param name="residuals_output" value="true"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	381 </section>
3 43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5 iuc parents: 2 diff changeset	382 <output name="archive_output">
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5 iuc parents: 2 diff changeset	383 <assert_contents>
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5 iuc parents: 2 diff changeset	384 <has_size value="8567935" delta="1000000" />
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5 iuc parents: 2 diff changeset	385 </assert_contents>
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5 iuc parents: 2 diff changeset	386 </output>
2 faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	387 <output name="all_results">
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	388 <assert_contents>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	389 <has_text text="feature"/>
3 43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5 iuc parents: 2 diff changeset	390 <has_n_lines n="175" delta="10"/>
2 faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	391 <has_n_columns n="9"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	392 </assert_contents>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	393 </output>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	394 <output name="significant_results">
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	395 <assert_contents>
3 43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5 iuc parents: 2 diff changeset	396 <has_text text="dysbiosisnonIBD"/>
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5 iuc parents: 2 diff changeset	397 <has_n_lines n="95" delta="5"/>
2 faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	398 <has_n_columns n="9"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	399 </assert_contents>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	400 </output>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	401 <output name="residuals">
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	402 <assert_contents>
3 43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5 iuc parents: 2 diff changeset	403 <has_size value="434087"/>
2 faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	404 </assert_contents>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	405 </output>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	406 <output_collection name="figures_pdfs" type="list">
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	407 <element name="heatmap.pdf" ftype="pdf">
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	408 <assert_contents>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	409 <has_size value="7000" delta="1000" />
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	410 </assert_contents>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	411 </element>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	412 </output_collection>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	413 </test>
3 43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5 iuc parents: 2 diff changeset	414
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5 iuc parents: 2 diff changeset	415
0 c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	416 </tests>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	417 <help><![CDATA[
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	418 @HELP_HEADER@
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	419 MaAsLin 2
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	420 =========
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	421 MaAsLin2 is the next generation of MaAsLin (Microbiome Multivariable Association with Linear Models).
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	422
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	423 Input
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	424 =====
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	425 MaAsLin2 requires two input files:
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	426
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	427 - Data (or features) tabular file
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	428 - This file is tab-delimited.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	429 - Formatted with features as columns and samples as rows.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	430 - The transpose of this format is also okay.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	431 - Possible features in this file include taxonomy or genes.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	432 - Metadata tabular file
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	433 - This file is tab-delimited.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	434 - Formatted with features as columns and samples as rows.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	435 - The transpose of this format is also okay.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	436 - Possible metadata in this file include gender or age.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	437
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	438 The data file can contain samples not included in the metadata file (along with the reverse case). For both cases, those samples not included in both files will be removed from the analysis. Also the samples do not need to be in the same order in the two files.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	439
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	440 Output
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	441 ======
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	442 1- Data output files
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	443 - All results ordered by increasing q-value (tabular file)
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	444 - Full list of associations that pass MaAsLin2's significance threshold, ordered by increasing q-values
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	445 - This includes the same data as the data.frame returned.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	446 - This file contains all results ordered by increasing q-value.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	447 - The first columns are the metadata and feature names.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	448 - The next two columns are the value and coefficient from the model.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	449 - The next column is the standard deviation from the model.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	450 - The N column is the total number of data points.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	451 - The N.not.zero column is the total of non-zero data points.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	452 - The pvalue from the calculation is the second to last column.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	453 - The qvalue is computed with p.adjust with the correction method.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	454 - Q-values smaller than or equal to the threshold (tabular file)
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	455 - This file is a subset of the results in the first file.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	456 - It only includes associations with q-values <= to the threshold.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	457 - Data frame with residuals for each feature (R data file)
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	458 - This file contains a data frame with residuals for each feature.
2 faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	459
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	460 Correction methods to compute the q-value : https://www.rdocumentation.org/packages/stats/versions/3.6.2/topics/p.adjust
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	461
0 c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	462 2- Visualization output files
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	463 - Heatmap of the significant associations (PDF file)
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	464 - This file contains a heatmap of the significant associations.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	465 - A plot for every significant association found (PDF file(s))
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	466 - A plot is generated for each significant association.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	467 - Scatter plots are used for continuous metadata.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	468 - Box plots are for categorical data.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	469 - Data points plotted are after normalization, filtering, and transform.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	470
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	471 ]]></help>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	472 <citations>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	473 <citation type="doi">10.1101/2021.01.20.427420</citation>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	474 </citations>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	475 </tool>

Mercurial > repos > iuc > maaslin2

annotate maaslin2.xml @ 3:43ccbef89f1d draft