<?xml version="1.0" ?>
<tool id="qiime_longitudinal_first-differences" name="qiime longitudinal first-differences" version="2018.4">
	<description> - Compute first differences or difference from baseline between sequential states</description>
	<requirements>
		<requirement type="package" version="2018.4">qiime2</requirement>
	</requirements>
	<command>
	<![CDATA[	
	
	qiime longitudinal first-differences --p-state-column="$pstatecolumn"
	
	#if '__pd__' in str($pindividualidcolumn):
		#set $pwhere_temp = $pindividualidcolumn.replace('__pd__', "#")
		#set $pindividualidcolumn = $pwhere_temp
	#end if

	#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) --p-individual-id-column="$pindividualidcolumn" --p-metric="$pmetric"
	#if str($itable) != 'None':
	 --i-table=$itable
	#end if

	#if str($cmdconfig) != 'None':
	 --cmd-config=$cmdconfig
	#end if

	#if str($preplicatehandling) != 'None':
	 --p-replicate-handling=$preplicatehandling
	#end if
	 --o-first-differences=ofirstdifferences
	#if str($pbaseline):
	 --p-baseline="$pbaseline"
	#end if
	;
	cp ofirstdifferences.qza $ofirstdifferences;
	]]>
	</command>
	<inputs>
		<repeat name="input_files_mmetadatafile" optional="False" 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. Sample metadata file containing individual_id_column.  [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
		</repeat>

		<param label="--p-state-column: Metadata column containing state (e.g., Time) across which samples are paired. [required]" name="pstatecolumn" optional="False" type="text"/>
		<param label="--p-individual-id-column: Metadata column containing IDs for individual subjects.  [required]" name="pindividualidcolumn" optional="False" type="text"/>

		<param label="--p-metric: Numerical metadata or artifact column to test.  [required]" name="pmetric" optional="False" type="text"/>

		<param label="--p-replicate-handling: 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.  [default: error]" 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>

		<param label="--p-baseline: A value listed in the state_column metadata column against which all other states should be compared. Toggles calculation of static differences instead of first differences (which are calculated if no value is given for baseline). If a 'baseline' value is provided, sample differences at each state are compared against the baseline state, instead of the previous state. Must be a value listed in the state_column. [optional]" name="pbaseline" optional="True" type="text"/>

		<param format="qza,no_unzip.zip" label="--i-table: FeatureTable[RelativeFrequency] Feature table to optionally use for computing first differences.  [optional]" name="itable" optional="True" type="data"/>

		<param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
	</inputs>
	<outputs>
		<data format="qza" label="${tool.name} on ${on_string}: first-differences.qza" name="ofirstdifferences"/>
	</outputs>
	<help>
		<![CDATA[
Compute first differences or difference from baseline between sequential states
--------------------------------------------------------------------------------

Calculates first differences in "metric" between sequential states for
samples collected from individual subjects sampled repeatedly at two or
more states. First differences can be performed on a metadata column
(including artifacts that can be input as metadata) or a feature in a
feature table. Outputs a data series of first differences for each
individual subject at each sequential pair of states, labeled by the
SampleID of the second state (e.g., paired differences between time 0 and
time 1 would be labeled by the SampleIDs at time 1). This file can be used
as input to linear mixed effects models or other longitudinal or diversity
methods to compare changes in first differences across time or among groups
of subjects. Also supports differences from baseline (or other static
comparison state) by setting the "baseline" parameter.

Parameters
----------
table : FeatureTable[RelativeFrequency], optional
    Feature table to optionally use for computing first differences.
metadata : Metadata
    Sample metadata file containing individual_id_column.
state_column : Str
    Metadata column containing state (e.g., Time) across which samples are
    paired.
individual_id_column : Str
    Metadata column containing IDs for individual subjects.
metric : Str
    Numerical metadata or artifact column to test.
replicate_handling : Str % Choices({'drop', 'error', 'random'}), 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.
baseline : Float, optional
    A value listed in the state_column metadata column against which all
    other states should be compared. Toggles calculation of static
    differences instead of first differences (which are calculated if no
    value is given for baseline). If a "baseline" value is provided, sample
    differences at each state are compared against the baseline state,
    instead of the previous state. Must be a value listed in the
    state_column.

Returns
-------
first_differences : SampleData[FirstDifferences]
    Series of first differences.
		]]>
	</help>
<macros>
	<import>qiime_citation.xml</import>
</macros>
<expand macro="qiime_citation" />
</tool>