--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_longitudinal_pairwise-differences.xml	Wed Jul 17 03:05:17 2019 -0400
@@ -0,0 +1,157 @@
+<?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"
+--p-individual-id-column="$pindividualidcolumn"
+
+#if str($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>