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diff qiime2/qiime_longitudinal_pairwise-differences.xml @ 14:a0a8d77a991c draft

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author florianbegusch
date Thu, 03 Sep 2020 09:51:29 +0000
parents f190567fe3f6
children
line wrap: on
line diff
--- a/qiime2/qiime_longitudinal_pairwise-differences.xml	Thu Sep 03 09:46:00 2020 +0000
+++ b/qiime2/qiime_longitudinal_pairwise-differences.xml	Thu Sep 03 09:51:29 2020 +0000
@@ -1,34 +1,104 @@
 <?xml version="1.0" ?>
-<tool id="qiime_longitudinal_pairwise-differences" name="qiime longitudinal pairwise-differences" version="2019.7">
-	<description> - Paired difference testing and boxplots</description>
-	<requirements>
-		<requirement type="package" version="2019.7">qiime2</requirement>
-	</requirements>
-	<command><![CDATA[
+<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
 
---p-metric="$pmetric"
---p-state-column="$pstatecolumn"
---p-state-1="$pstate1"
---p-state-2="$pstate2"
+#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 = $pindividualidcolumn_temp
 #end if
-#if str($pindividualidcolumn):
- --p-individual-id-column="$pindividualidcolumn"
+#if '__db__' in str($pindividualidcolumn):
+  #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__db__', '"')
+  #set $pindividualidcolumn = $pindividualidcolumn_temp
 #end if
 
+--p-individual-id-column=$pindividualidcolumn
 
 
-#if str($itable) != 'None':
- --i-table=$itable
+#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"
+  --p-group-column=$pgroupcolumn
 #end if
 
 #if $pparametric:
@@ -36,91 +106,91 @@
 #end if
 
 #if str($ppalette) != 'None':
- --p-palette=$ppalette
+--p-palette=$ppalette
 #end if
 
 #if str($preplicatehandling) != 'None':
- --p-replicate-handling=$preplicatehandling
+--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($input_files_mmetadatafile)
-#end if
-
-
 --o-visualization=ovisualization
+
+#if str($examples) != 'None':
+--examples=$examples
+#end if
+
 ;
-qiime tools export --input-path ovisualization.qzv --output-path out   && mkdir -p '$ovisualization.files_path'
+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 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>
+&& mv '$ovisualization.files_path/index.html' '$ovisualization'
 
-		<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>
+  ]]></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>
 
-	</inputs>
-	<outputs>
-		<data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
-	</outputs>
-	<help><![CDATA[
+  <outputs>
+    <data format="html" label="${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
+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.
+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
 ----------
@@ -146,7 +216,7 @@
 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
+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,
@@ -159,9 +229,9 @@
 Returns
 -------
 visualization : Visualization
-	]]></help>
-<macros>
+  ]]></help>
+  <macros>
     <import>qiime_citation.xml</import>
-</macros>
-<expand macro="qiime_citation"/>
-</tool>
+  </macros>
+  <expand macro="qiime_citation"/>
+</tool>
\ No newline at end of file