maaslin2: maaslin2.xml annotate

annotate maaslin2.xml @ 2:faacef62bb54 draft

planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3

author	iuc
date	Mon, 29 Apr 2024 10:33:48 +0000
parents	ef2cace85809
children	43ccbef89f1d

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
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	67 #if $additional_options.correction
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	68 --correction '$additional_options.correction'
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	69 #end if
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	70 $additional_options.standardize
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	71 $output.plot_heatmap
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	72 #if $output.heatmap_first_n
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	73 --heatmap_first_n '$output.heatmap_first_n'
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	74 #end if
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	75 $output.plot_scatter
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	76 --cores \${GALAXY_SLOTS:-4}
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	77 'input_data.tsv'
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	78 'input_metadata.tsv'
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	79 'outputFolder'
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	80 &&
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	81 cd outputFolder && mkdir -p figures/ && cp *.pdf figures
2 faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	82
0 c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	83 ]]></command>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	84 <inputs>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	85 <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	86 <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	87 <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	88
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	89 <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" />
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	90
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	91
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	92
0 c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	93 <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	94 <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	95 <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	96 <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	97 <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	98 <option value="TSS" selected="true">TSS</option>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	99 <option value="CLR">CLR</option>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	100 <option value="CSS">CSS</option>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	101 <option value="NONE">NONE</option>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	102 <option value="TMM">TMM</option>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	103 </param>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	104 <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	105 <option value="LOG" selected="true">LOG</option>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	106 <option value="LOGIT">LOGIT</option>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	107 <option value="AST">AST</option>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	108 <option value="NONE">NONE</option>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	109 </param>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	110 <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	111 <option value="LM" selected="true">LM</option>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	112 <option value="CPLM">CPLM</option>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	113 <option value="NEGBIN">NEGBIN</option>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	114 <option value="ZINB">ZINB</option>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	115 </param>
2 faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	116 <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	117
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	118 <option value="BH">Benjamini-Hochberg(BH)</option>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	119 <option value="BY">Benjamini-Yekutieli(BY)</option>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	120 </param>
0 c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	121 <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	122 </section>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	123 <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	124 <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	125 <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	126 <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	127 <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	128 </section>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	129 </inputs>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	130 <outputs>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	131 <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	132 <data name="significant_results" format="tabular" from_work_dir="outputFolder/significant_results.tsv" label="Q-values smaller than or equal to the threshold"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	133 <data name="residuals" format="rdata" from_work_dir="outputFolder/residuals.rds" label="Data frame with residuals for each feature">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	134 <filter>output['residuals_output'] is True</filter>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	135 </data>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	136 <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	137 <filter>output['plot_heatmap'] is True</filter>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	138 </data>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	139 <collection name="figures_pdfs" type="list" label="Plots" >
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	140 <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	141 <filter>output['plot_scatter'] is True</filter>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	142 </collection>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	143 </outputs>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	144 <tests>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	145 <test expect_num_outputs="5">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	146 <param name="input_data" value="HMP2_taxonomy.tsv"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	147 <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	148 <param name="random_effects" value= "2,5"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	149 <param name="fixed_effects" value="4,9,10,11,6,3"/>
0 c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	150 <section name="additional_options">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	151 <param name="min_abundance" value="0.0"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	152 <param name="min_prevalence" value="0.1"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	153 <param name="max_significance" value="0.25"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	154 <param name="normalization" value="NONE"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	155 <param name="transform" value="AST"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	156 <param name="analysis_method" value="LM"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	157 <param name="correction" value="BH"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	158 <param name="standardize" value="false"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	159 </section>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	160 <section name="output">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	161 <param name="plot_heatmap" value="true"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	162 <param name="heatmap_first_n" value="50"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	163 <param name="plot_scatter" value="true"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	164 <param name="residuals_output" value="true"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	165 </section>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	166 <output name="all_results">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	167 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	168 <has_text text="feature"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	169 <has_n_lines n="610"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	170 <has_n_columns n="9"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	171 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	172 </output>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	173 <output name="significant_results">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	174 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	175 <has_text text="dysbiosisCD"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	176 <has_n_lines n="159"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	177 <has_n_columns n="9"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	178 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	179 </output>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	180 <output name="residuals">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	181 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	182 <has_size value="462746" delta="1000"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	183 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	184 </output>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	185 <output name="headmap">
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 <has_size value="7373" delta="1000" />
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	188 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	189 </output>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	190 <output_collection name="figures_pdfs" type="list">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	191 <element name="heatmap.pdf" ftype="pdf">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	192 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	193 <has_size value="7373" delta="1000" />
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	194 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	195 </element>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	196 <element name="age.pdf" ftype="pdf">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	197 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	198 <has_size value="407859" delta="100000" />
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	199 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	200 </element>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	201 <element name="antibiotics.pdf" ftype="pdf">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	202 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	203 <has_size value="1590476" delta="1000000" />
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	204 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	205 </element>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	206 <element name="diagnosis.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="1407572" delta="1000000" />
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="dysbiosisCD.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="2328523" delta="1000000" />
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="dysbiosisnonIBD.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="1032602" 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="dysbiosisUC.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="1037005" 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 </output_collection>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	227 </test>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	228 <test expect_num_outputs="5">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	229 <param name="input_data" value="HMP2_taxonomy.tsv"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	230 <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	231 <param name="fixed_effects" value="4,9"/>
0 c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	232 <section name="additional_options">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	233 <param name="min_abundance" value="0.0"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	234 <param name="min_prevalence" value="0.1"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	235 <param name="max_significance" value="0.25"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	236 <param name="normalization" value="NONE"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	237 <param name="transform" value="AST"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	238 <param name="analysis_method" value="LM"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	239 <param name="correction" value="BH"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	240 <param name="standardize" value="false"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	241 </section>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	242 <section name="output">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	243 <param name="plot_heatmap" value="true"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	244 <param name="heatmap_first_n" value="50"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	245 <param name="plot_scatter" value="true"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	246 <param name="residuals_output" value="true"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	247 </section>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	248 <output name="all_results">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	249 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	250 <has_text text="feature"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	251 <has_n_lines n="262"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	252 <has_n_columns n="9"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	253 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	254 </output>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	255 <output name="significant_results">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	256 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	257 <has_text text="diagnosis"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	258 <has_n_lines n="175"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	259 <has_n_columns n="9"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	260 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	261 </output>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	262 <output name="residuals">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	263 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	264 <has_size value="367224" delta="1000"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	265 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	266 </output>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	267 <output_collection name="figures_pdfs" type="list">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	268 <element name="diagnosis.pdf" ftype="pdf">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	269 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	270 <has_size value="6234127" delta="1000000" />
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	271 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	272 </element>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	273 </output_collection>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	274 </test>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	275 <test expect_num_outputs="5">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	276 <param name="input_data" value="HMP2_taxonomy.tsv"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	277 <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	278 <param name="fixed_effects" value="4,9"/>
0 c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	279 <section name="additional_options">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	280 <param name="min_abundance" value="0.0001"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	281 <param name="min_prevalence" value="0.1"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	282 <param name="max_significance" value="0.25"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	283 <param name="normalization" value="NONE"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	284 <param name="transform" value="AST"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	285 <param name="analysis_method" value="LM"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	286 <param name="correction" value="BH"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	287 <param name="standardize" value="false"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	288 </section>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	289 <section name="output">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	290 <param name="plot_heatmap" value="true"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	291 <param name="heatmap_first_n" value="50"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	292 <param name="plot_scatter" value="true"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	293 <param name="residuals_output" value="true"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	294 </section>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	295 <output name="all_results">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	296 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	297 <has_text text="feature"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	298 <has_n_lines n="250"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	299 <has_n_columns n="9"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	300 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	301 </output>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	302 <output name="significant_results">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	303 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	304 <has_text text="diagnosis"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	305 <has_n_lines n="172"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	306 <has_n_columns n="9"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	307 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	308 </output>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	309 <output name="residuals">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	310 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	311 <has_size value="359943" delta="1000"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	312 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	313 </output>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	314 <output name="headmap">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	315 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	316 <has_size value="6554" delta="1000" />
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	317 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	318 </output>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	319 <output_collection name="figures_pdfs" type="list">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	320 <element name="heatmap.pdf" ftype="pdf">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	321 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	322 <has_size value="6554" delta="1000" />
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 </element>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	325 <element name="diagnosis.pdf" ftype="pdf">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	326 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	327 <has_size value="6061545" delta="1000000" />
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	328 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	329 </element>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	330 <element name="dysbiosisnonIBD.pdf" ftype="pdf">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	331 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	332 <has_size value="2599373" delta="1000000" />
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	333 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	334 </element>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	335 </output_collection>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	336 </test>
2 faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	337 <test expect_num_outputs="5">
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	338 <param name="input_data" value="HMP2_taxonomy.tsv"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	339 <param name="input_metadata" value="HMP2_metadata.tsv"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	340 <param name="random_effects" value="3" />
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	341 <section name="additional_options">
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	342 <param name="min_abundance" value="0.0"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	343 <param name="min_prevalence" value="0.1"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	344 <param name="max_significance" value="0.25"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	345 <param name="normalization" value="TSS"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	346 <param name="transform" value="LOG"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	347 <param name="analysis_method" value="LM"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	348 <param name="correction" value="BY"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	349 <param name="standardize" value="True"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	350 </section>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	351 <section name="output">
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	352 <param name="plot_heatmap" value="true"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	353 <param name="heatmap_first_n" value="50"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	354 <param name="plot_scatter" value="true"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	355 <param name="residuals_output" value="true"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	356 </section>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	357 <output name="all_results">
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	358 <assert_contents>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	359 <has_text text="feature"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	360 <has_n_lines n="8092"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	361 <has_n_columns n="9"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	362 </assert_contents>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	363 </output>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	364 <output name="significant_results">
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	365 <assert_contents>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	366 <has_text text="subject"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	367 <has_n_lines n="216" delta="5"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	368 <has_n_columns n="9"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	369 </assert_contents>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	370 </output>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	371 <output name="residuals">
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	372 <assert_contents>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	373 <has_size value="671142" delta="1000"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	374 </assert_contents>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	375 </output>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	376 <output_collection name="figures_pdfs" type="list">
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	377 <element name="heatmap.pdf" ftype="pdf">
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	378 <assert_contents>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	379 <has_size value="7000" delta="1000" />
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	380 </assert_contents>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	381 </element>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	382 </output_collection>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	383 </test>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	384 <test expect_num_outputs="5">
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	385 <param name="input_data" value="HMP2_taxonomy.tsv"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	386 <param name="input_metadata" value="HMP2_metadata.tsv"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	387
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	388 <section name="additional_options">
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	389 <param name="min_abundance" value="0.0"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	390 <param name="min_prevalence" value="0.1"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	391 <param name="max_significance" value="0.25"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	392 <param name="normalization" value="TSS"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	393 <param name="transform" value="LOG"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	394 <param name="analysis_method" value="LM"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	395 <param name="correction" value="BH"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	396 <param name="standardize" value="True"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	397 </section>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	398 <section name="output">
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	399 <param name="plot_heatmap" value="true"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	400 <param name="heatmap_first_n" value="50"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	401 <param name="plot_scatter" value="true"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	402 <param name="residuals_output" value="true"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	403 </section>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	404 <output name="all_results">
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	405 <assert_contents>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	406 <has_text text="feature"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	407 <has_n_lines n="8092"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	408 <has_n_columns n="9"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	409 </assert_contents>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	410 </output>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	411 <output name="significant_results">
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	412 <assert_contents>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	413 <has_text text="subject"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	414 <has_n_lines n="880"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	415 <has_n_columns n="9"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	416 </assert_contents>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	417 </output>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	418 <output name="residuals">
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	419 <assert_contents>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	420 <has_size value="670759" delta="1000"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	421 </assert_contents>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	422 </output>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	423 <output_collection name="figures_pdfs" type="list">
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	424 <element name="heatmap.pdf" ftype="pdf">
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	425 <assert_contents>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	426 <has_size value="7900" delta="1000" />
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	427 </assert_contents>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	428 </element>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	429 </output_collection>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	430 </test>
0 c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	431 </tests>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	432 <help><![CDATA[
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	433 @HELP_HEADER@
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	434 MaAsLin 2
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	435 =========
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	436 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	437
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	438 Input
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 MaAsLin2 requires two input files:
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 - Data (or features) tabular file
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	443 - This file is tab-delimited.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	444 - 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	445 - The transpose of this format is also okay.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	446 - 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	447 - Metadata tabular file
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	448 - This file is tab-delimited.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	449 - 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	450 - The transpose of this format is also okay.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	451 - 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	452
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	453 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	454
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	455 Output
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	456 ======
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	457 1- Data output files
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	458 - 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	459 - 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	460 - 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	461 - 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	462 - 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	463 - 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	464 - 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	465 - 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	466 - 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	467 - 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	468 - 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	469 - 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	470 - 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	471 - 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	472 - 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	473 - 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	474
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 iuc parents: 1 diff changeset	475 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	476
0 c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	477 2- Visualization output files
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	478 - Heatmap of the significant associations (PDF file)
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	479 - 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	480 - 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	481 - A plot is generated for each significant association.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	482 - Scatter plots are used for continuous metadata.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	483 - Box plots are for categorical data.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	484 - 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	485
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	486 ]]></help>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	487 <citations>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	488 <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	489 </citations>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28" iuc parents: diff changeset	490 </tool>

Mercurial > repos > iuc > maaslin2

annotate maaslin2.xml @ 2:faacef62bb54 draft