--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_longitudinal_pairwise-differences.xml	Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,237 @@
+<?xml version="1.0" ?>
+<tool id="qiime_longitudinal_pairwise-differences" name="qiime longitudinal pairwise-differences"
+      version="2020.8">
+  <description>Paired difference testing and boxplots</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
+qiime longitudinal pairwise-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($input_files_mmetadatafile)
+# end if
+
+--p-metric=$pmetric
+
+#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
+
+
+--p-state-1=$pstate1
+
+--p-state-2=$pstate2
+
+#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 '__ob__' in str($pgroupcolumn):
+  #set $pgroupcolumn_temp = $pgroupcolumn.replace('__ob__', '[')
+  #set $pgroupcolumn = $pgroupcolumn_temp
+#end if
+#if '__cb__' in str($pgroupcolumn):
+  #set $pgroupcolumn_temp = $pgroupcolumn.replace('__cb__', ']')
+  #set $pgroupcolumn = $pgroupcolumn_temp
+#end if
+#if 'X' in str($pgroupcolumn):
+  #set $pgroupcolumn_temp = $pgroupcolumn.replace('X', '\\')
+  #set $pgroupcolumn = $pgroupcolumn_temp
+#end if
+#if '__sq__' in str($pgroupcolumn):
+  #set $pgroupcolumn_temp = $pgroupcolumn.replace('__sq__', "'")
+  #set $pgroupcolumn = $pgroupcolumn_temp
+#end if
+#if '__db__' in str($pgroupcolumn):
+  #set $pgroupcolumn_temp = $pgroupcolumn.replace('__db__', '"')
+  #set $pgroupcolumn = $pgroupcolumn_temp
+#end if
+
+#if str($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=$preplicatehandling
+#end if
+
+--o-visualization=ovisualization
+
+#if str($examples) != 'None':
+--examples=$examples
+#end if
+
+;
+cp odistancematrix.qza $odistancematrix
+
+;
+qiime tools export  ovisualization.qzv --output-path out
+&& mkdir -p '$ovisualization.files_path'
+&& cp -r out/* '$ovisualization.files_path'
+&& mv '$ovisualization.files_path/index.html' '$ovisualization'
+
+  ]]></command>
+  <inputs>
+    <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[RelativeFrequency] Feature table to optionally use for paired comparisons.                               [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-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 label="--p-group-column: TEXT  Metadata column on which to separate groups for comparison                                 [optional]" name="pgroupcolumn" optional="False" type="text" />
+    <param label="--p-parametric: --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>
+      <option value="cividis">cividis</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>
+    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
+    
+  </inputs>
+
+  <outputs>
+    <data format="html" label="${tool.name} on ${on_string}: visualization.html" 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 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. Note
+that "metric" can be derived from a feature table or metadata.
+
+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', 'cividis'), 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>
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