diff qiime2-2020.8/qiime_longitudinal_first-differences.xml @ 20:d93d8888f0b0 draft

Uploaded

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+++ b/qiime2-2020.8/qiime_longitudinal_first-differences.xml	Fri Sep 04 12:44:24 2020 +0000
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+<?xml version="1.0" ?>
+<tool id="qiime_longitudinal_first-differences" name="qiime longitudinal first-differences"
+      version="2020.8">
+  <description>Compute first differences or difference from baseline between sequential states</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
+qiime longitudinal first-differences
+
+#if str($itable) != 'None':
+--i-table=$itable
+#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($input_files_mmetadatafile)
+# end if
+
+#if '__ob__' in str($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
+
+
+--p-metric=$pmetric
+
+#if str($preplicatehandling) != 'None':
+--p-replicate-handling=$preplicatehandling
+#end if
+
+#if str($pbaseline):
+  --p-baseline=$pbaseline
+#end if
+--o-first-differences=ofirstdifferences
+
+#if str($examples) != 'None':
+--examples=$examples
+#end if
+
+;
+cp ofirstdifferences.qza $ofirstdifferences
+
+  ]]></command>
+  <inputs>
+    <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[RelativeFrequency] Feature table to optionally use for computing first differences.                               [optional]" name="itable" 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-metric: TEXT        Numerical metadata or artifact column to test. [required]" name="pmetric" 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="--p-baseline: NUMBER    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="False" type="text" />
+    <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}: firstdifferences.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
+----------
+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.
+metric : Str
+    Numerical metadata or artifact column to test.
+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.
+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.
+table : FeatureTable[RelativeFrequency], optional
+    Feature table to optionally use for computing first differences.
+
+Returns
+-------
+first_differences : SampleData[FirstDifferences]
+    Series of first differences.
+  ]]></help>
+  <macros>
+    <import>qiime_citation.xml</import>
+  </macros>
+  <expand macro="qiime_citation"/>
+</tool>
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