annotate qiime2-2020.8/qiime_longitudinal_first-distances.xml @ 20:d93d8888f0b0 draft

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<?xml version="1.0" ?>
<tool id="qiime_longitudinal_first-distances" name="qiime longitudinal first-distances"
      version="2020.8">
  <description>Compute first distances or distance from baseline between sequential states</description>
  <requirements>
    <requirement type="package" version="2020.8">qiime2</requirement>
  </requirements>
  <command><![CDATA[
qiime longitudinal first-distances

--i-distance-matrix=$idistancematrix
# 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

#if '__ob__' in str($pstatecolumn):
  #set $pstatecolumn_temp = $pstatecolumn.replace('__ob__', '[')
  #set $pstatecolumn = $pstatecolumn_temp
#end if
#if '__cb__' in str($pstatecolumn):
  #set $pstatecolumn_temp = $pstatecolumn.replace('__cb__', ']')
  #set $pstatecolumn = $pstatecolumn_temp
#end if
#if 'X' in str($pstatecolumn):
  #set $pstatecolumn_temp = $pstatecolumn.replace('X', '\\')
  #set $pstatecolumn = $pstatecolumn_temp
#end if
#if '__sq__' in str($pstatecolumn):
  #set $pstatecolumn_temp = $pstatecolumn.replace('__sq__', "'")
  #set $pstatecolumn = $pstatecolumn_temp
#end if
#if '__db__' in str($pstatecolumn):
  #set $pstatecolumn_temp = $pstatecolumn.replace('__db__', '"')
  #set $pstatecolumn = $pstatecolumn_temp
#end if

--p-state-column=$pstatecolumn


#if '__ob__' in str($pindividualidcolumn):
  #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__ob__', '[')
  #set $pindividualidcolumn = $pindividualidcolumn_temp
#end if
#if '__cb__' in str($pindividualidcolumn):
  #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__cb__', ']')
  #set $pindividualidcolumn = $pindividualidcolumn_temp
#end if
#if 'X' in str($pindividualidcolumn):
  #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('X', '\\')
  #set $pindividualidcolumn = $pindividualidcolumn_temp
#end if
#if '__sq__' in str($pindividualidcolumn):
  #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__sq__', "'")
  #set $pindividualidcolumn = $pindividualidcolumn_temp
#end if
#if '__db__' in str($pindividualidcolumn):
  #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__db__', '"')
  #set $pindividualidcolumn = $pindividualidcolumn_temp
#end if

--p-individual-id-column=$pindividualidcolumn


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

--o-first-distances=ofirstdistances

#if str($examples) != 'None':
--examples=$examples
#end if

;
cp ofirstdistances.qza $ofirstdistances

  ]]></command>
  <inputs>
    <param format="qza,no_unzip.zip" label="--i-distance-matrix: ARTIFACT DistanceMatrix       Matrix of distances between pairs of samples. [required]" name="idistancematrix" optional="False" type="data" />
    <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
      <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA... (multiple            Sample metadata file containing arguments will be   individual-id-column. merged)                                                        [required]" name="additional_input" optional="False" type="data" />
    </repeat>
    <param label="--p-state-column: TEXT  Metadata column containing state (time) variable information.                               [required]" name="pstatecolumn" optional="False" type="text" />
    <param label="--p-individual-id-column: TEXT Metadata column containing IDs for individual subjects.                                  [required]" name="pindividualidcolumn" optional="False" type="text" />
    <param label="--p-baseline: NUMBER    A value listed in the state-column metadata column against which all other states should be compared. Toggles calculation of static distances instead of first distances (which are calculated if no value is given for baseline). If a \'baseline\' value is provided, sample distances 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="False" type="text" />
    <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>
    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
    
  </inputs>

  <outputs>
    <data format="qza" label="${tool.name} on ${on_string}: firstdistances.qza" name="ofirstdistances" />
    
  </outputs>

  <help><![CDATA[
Compute first distances or distance from baseline between sequential states
###############################################################

Calculates first distances between sequential states for samples collected
from individual subjects sampled repeatedly at two or more states. This
method is similar to the "first differences" method, except that it
requires a distance matrix as input and calculates first differences as
distances between successive states. Outputs a data series of first
distances for each individual subject at each sequential pair of states,
labeled by the SampleID of the second state (e.g., paired distances 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 distances across time or
among groups of subjects. Also supports distance from baseline (or other
static comparison state) by setting the "baseline" parameter.

Parameters
----------
distance_matrix : DistanceMatrix
    Matrix of distances between pairs of samples.
metadata : Metadata
    Sample metadata file containing individual_id_column.
state_column : Str
    Metadata column containing state (time) variable information.
individual_id_column : Str
    Metadata column containing IDs for individual subjects.
baseline : Float, optional
    A value listed in the state_column metadata column against which all
    other states should be compared. Toggles calculation of static
    distances instead of first distances (which are calculated if no value
    is given for baseline). If a "baseline" value is provided, sample
    distances at each state are compared against the baseline state,
    instead of the previous state. Must be a value listed in the
    state_column.
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.

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