view qiime2/qiime_longitudinal_pairwise-differences.xml @ 4:914fa4daf16a draft

Fixes

<?xml version="1.0" ?>
<tool id="qiime_longitudinal_pairwise-differences" name="qiime longitudinal pairwise-differences" version="2019.4">
	<description> - Paired difference testing and boxplots</description>
	<requirements>
		<requirement type="package" version="2019.4">qiime2</requirement>
	</requirements>
	<command><![CDATA[
qiime longitudinal pairwise-differences

--p-metric="$pmetric"
--p-state-column="$pstatecolumn"
--p-state-1="$pstate1"
--p-state-2="$pstate2"


#if '__sq__' in str($pindividualidcolumn):
  #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__sq__', "'")
  #set $pindividualidcolumn = $pindividualidcolumn_temp
#end if
#if str($pindividualidcolumn):
 --p-individual-id-column="$pindividualidcolumn"
#end if



#if str($itable) != 'None':
 --i-table=$itable
#end if

#if str($pgroupcolumn):
 --p-group-column="$pgroupcolumn"
#end if

#if $pparametric:
 --p-parametric
#end if

#if str($ppalette) != 'None':
 --p-palette=$ppalette
#end if

#if str($preplicatehandling) != 'None':
 --p-replicate-handling=$preplicatehandling
#end if


#if $input_files_mmetadatafile:
#def list_dict_to_string(list_dict):
	#set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
	#for d in list_dict[1:]:
		#set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
	#end for
	#return $file_list
#end def
 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
#end if


--o-visualization=ovisualization
;
qiime tools export --input-path ovisualization.qzv --output-path out   && mkdir -p '$ovisualization.files_path'
&& cp -r out/* '$ovisualization.files_path'
&& mv '$ovisualization.files_path/index.html' '$ovisualization';
	]]></command>
	<inputs>
		<param label="--p-metric: TEXT        Numerical metadata or artifact column to test. [required]" name="pmetric" optional="False" type="text"/>
		<param label="--p-state-column: TEXT  Metadata column containing state (e.g., Time) across which samples are paired.                  [required]" name="pstatecolumn" optional="False" type="text"/>
		<param label="--p-state-1: TEXT       Baseline state column value.               [required]" name="pstate1" optional="False" type="text"/>
		<param label="--p-state-2: TEXT       State column value to pair with baseline.  [required]" name="pstate2" optional="False" type="text"/>
		<param label="--p-individual-id-column: TEXT Metadata column containing subject IDs to use for pairing samples. WARNING: if replicates exist for an individual ID at either state-1 or state-2, that subject will be dropped and reported in standard output by default. Set replicate_handling='random' to instead randomly select one member.        [required]" name="pindividualidcolumn" optional="False" type="text"/>
		<param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[RelativeFrequency] Feature table to optionally use for paired comparisons.                               [optional]" name="itable" optional="True" type="data"/>
		<param label="--p-group-column: TEXT  Metadata column on which to separate groups for comparison                                 [optional]" name="pgroupcolumn" optional="True" type="text"/>
		<param label="--p-parametric: --p-no-parametric Perform parametric (ANOVA and t-tests) or non-parametric (Kruskal-Wallis, Wilcoxon, and Mann-Whitney U tests) statistical tests. [default: False]" name="pparametric" selected="False" type="boolean"/>
		<param label="--p-palette: " name="ppalette" optional="True" type="select">
			<option selected="True" value="None">Selection is Optional</option>
			<option value="Set1">Set1</option>
			<option value="Set2">Set2</option>
			<option value="Set3">Set3</option>
			<option value="Pastel1">Pastel1</option>
			<option value="Pastel2">Pastel2</option>
			<option value="Paired">Paired</option>
			<option value="Accent">Accent</option>
			<option value="Dark2">Dark2</option>
			<option value="tab10">tab10</option>
			<option value="tab20">tab20</option>
			<option value="tab20b">tab20b</option>
			<option value="tab20c">tab20c</option>
			<option value="viridis">viridis</option>
			<option value="plasma">plasma</option>
			<option value="inferno">inferno</option>
			<option value="magma">magma</option>
			<option value="terrain">terrain</option>
			<option value="rainbow">rainbow</option>
		</param>
		<param label="--p-replicate-handling: " name="preplicatehandling" optional="True" type="select">
			<option selected="True" value="None">Selection is Optional</option>
			<option value="error">error</option>
			<option value="random">random</option>
			<option value="drop">drop</option>
		</param>

		<repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
			<param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
		</repeat>

	</inputs>
	<outputs>
		<data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
	</outputs>
	<help><![CDATA[
Paired difference testing and boxplots
######################################

Performs paired difference testing between samples from each subject.
Sample pairs may represent a typical intervention study, e.g., samples
collected pre- and post-treatment; paired samples from two different
timepoints (e.g., in a longitudinal study design), or identical samples
receiving different two different treatments. This action tests whether the
change in a numeric metadata value "metric" differs from zero and differs
between groups (e.g., groups of subjects receiving different treatments),
and produces boxplots of paired difference distributions for each group. A
feature table artifact is required input, though whether "metric" is
derived from the feature table or metadata is optional.

Parameters
----------
metadata : Metadata
    Sample metadata file containing individual_id_column.
metric : Str
    Numerical metadata or artifact column to test.
state_column : Str
    Metadata column containing state (e.g., Time) across which samples are
    paired.
state_1 : Str
    Baseline state column value.
state_2 : Str
    State column value to pair with baseline.
individual_id_column : Str
    Metadata column containing subject IDs to use for pairing samples.
    WARNING: if replicates exist for an individual ID at either state_1 or
    state_2, that subject will be dropped and reported in standard output
    by default. Set replicate_handling="random" to instead randomly select
    one member.
group_column : Str, optional
    Metadata column on which to separate groups for comparison
parametric : Bool, optional
    Perform parametric (ANOVA and t-tests) or non-parametric (Kruskal-
    Wallis, Wilcoxon, and Mann-Whitney U tests) statistical tests.
palette : Str % Choices('Set1', 'Set2', 'Set3', 'Pastel1', 'Pastel2', 'Paired', 'Accent', 'Dark2', 'tab10', 'tab20', 'tab20b', 'tab20c', 'viridis', 'plasma', 'inferno', 'magma', 'terrain', 'rainbow'), optional
    Color palette to use for generating boxplots.
replicate_handling : Str % Choices('error', 'random', 'drop'), optional
    Choose how replicate samples are handled. If replicates are detected,
    "error" causes method to fail; "drop" will discard all replicated
    samples; "random" chooses one representative at random from among
    replicates.
table : FeatureTable[RelativeFrequency], optional
    Feature table to optionally use for paired comparisons.

Returns
-------
visualization : Visualization
	]]></help>
<macros>
    <import>qiime_citation.xml</import>
</macros>
<expand macro="qiime_citation"/>
</tool>