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diff qiime2/qiime_diversity_alpha-rarefaction.xml @ 14:a0a8d77a991c draft

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author florianbegusch
date Thu, 03 Sep 2020 09:51:29 +0000
parents f190567fe3f6
children
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--- a/qiime2/qiime_diversity_alpha-rarefaction.xml	Thu Sep 03 09:46:00 2020 +0000
+++ b/qiime2/qiime_diversity_alpha-rarefaction.xml	Thu Sep 03 09:51:29 2020 +0000
@@ -1,104 +1,107 @@
 <?xml version="1.0" ?>
-<tool id="qiime_diversity_alpha-rarefaction" name="qiime diversity alpha-rarefaction" version="2019.7">
-	<description> - Alpha rarefaction curves</description>
-	<requirements>
-		<requirement type="package" version="2019.7">qiime2</requirement>
-	</requirements>
-	<command><![CDATA[
+<tool id="qiime_diversity_alpha-rarefaction" name="qiime diversity alpha-rarefaction"
+      version="2020.8">
+  <description>Alpha rarefaction curves</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
 qiime diversity alpha-rarefaction
 
 --i-table=$itable
 
-
-#if str($pmaxdepth):
- --p-max-depth="$pmaxdepth"
-#end if
-
 #if str($iphylogeny) != 'None':
- --i-phylogeny=$iphylogeny
-#end if
-
-#if str($pmetrics) != 'None':
- --p-metrics=$pmetrics
-#end if
-
-
-#if str($pmindepth):
- --p-min-depth=$pmindepth
+--i-phylogeny=$iphylogeny
 #end if
 
-#if str($psteps):
- --p-steps=$psteps
+--p-max-depth=$pmaxdepth
+
+#if str($pmetrics) != 'None':
+--p-metrics=$pmetrics
 #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 str($piterations):
- --p-iterations=$piterations
+--p-min-depth=$pmindepth
+
+--p-steps=$psteps
+
+--p-iterations=$piterations
+
+--o-visualization=ovisualization
+
+#if str($examples) != 'None':
+--examples=$examples
 #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
+;
+cp oalphadiversity.qza $oalphadiversity
 
---o-visualization=ovisualization
 ;
-qiime tools export --input-path ovisualization.qzv --output-path out   && mkdir -p '$ovisualization.files_path'
+qiime tools export  ovisualization.qzv --output-path out
+&& mkdir -p '$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[Frequency] Feature table to compute rarefaction curves from. [required]" name="itable" optional="False" type="data"/>
-		<param label="--p-max-depth: INTEGER   The maximum rarefaction depth. Must be greater than Range(1, None)        min-depth.                                [required]" name="pmaxdepth" optional="False" min="1" value="" type="integer"/>
-		<param format="qza,no_unzip.zip" label="--i-phylogeny: ARTIFACT  Optional phylogeny for phylogenetic metrics. Phylogeny[Rooted]                                               [optional]" name="iphylogeny" optional="True" type="data"/>
-		<param label="--p-metrics: " name="pmetrics" optional="True" type="select">
-			<option selected="True" value="None">Selection is Optional</option>
-			<option value="dominance">dominance</option>
-			<option value="ace">ace</option>
-			<option value="brillouin_d">brillouin_d</option>
-			<option value="margalef">margalef</option>
-			<option value="menhinick">menhinick</option>
-			<option value="mcintosh_d">mcintosh_d</option>
-			<option value="berger_parker_d">berger_parker_d</option>
-			<option value="enspie">enspie</option>
-			<option value="doubles">doubles</option>
-			<option value="lladser_pe">lladser_pe</option>
-			<option value="observed_otus">observed_otus</option>
-			<option value="faith_pd">faith_pd</option>
-			<option value="simpson_e">simpson_e</option>
-			<option value="robbins">robbins</option>
-			<option value="shannon">shannon</option>
-			<option value="pielou_e">pielou_e</option>
-			<option value="singles">singles</option>
-			<option value="michaelis_menten_fit">michaelis_menten_fit</option>
-			<option value="heip_e">heip_e</option>
-			<option value="mcintosh_e">mcintosh_e</option>
-			<option value="fisher_alpha">fisher_alpha</option>
-			<option value="goods_coverage">goods_coverage</option>
-			<option value="chao1">chao1</option>
-			<option value="gini_index">gini_index</option>
-			<option value="simpson">simpson</option>
-		</param>
-		<param label="--p-min-depth: INTEGER   The minimum rarefaction depth. Range(1, None)                                                [default: 1]" name="pmindepth" optional="True" type="integer" min="1" value="1"/>
-		<param label="--p-steps: INTEGER       The number of rarefaction depths to include between Range(2, None)        min-depth and max-depth.               [default: 10]" name="psteps" optional="True" type="integer" min="2" value="10"/>
-		<param label="--p-iterations: INTEGER  The number of rarefied feature tables to compute at Range(1, None)        each step.                             [default: 10]" name="piterations" optional="True" type="integer" min="1" value="10"/>
 
-		<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. The sample 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[Frequency] Feature table to compute rarefaction curves from. [required]" name="itable" optional="False" type="data" />
+    <param format="qza,no_unzip.zip" label="--i-phylogeny: ARTIFACT  Optional phylogeny for phylogenetic metrics. Phylogeny[Rooted]                                               [optional]" name="iphylogeny" optional="False" type="data" />
+    <param label="--p-max-depth: INTEGER   The maximum rarefaction depth. Must be greater than Range(1, None)        min-depth.                                [required]" name="pmaxdepth" optional="False" type="text" />
+    <param label="--p-metrics: " multiple="True" name="pmetrics" optional="True" type="select">
+      <option selected="True" value="None">Selection is Optional</option>
+      <option value="observed_features">observed_features</option>
+      <option value="heip_e">heip_e</option>
+      <option value="dominance">dominance</option>
+      <option value="goods_coverage">goods_coverage</option>
+      <option value="ace">ace</option>
+      <option value="gini_index">gini_index</option>
+      <option value="simpson_e">simpson_e</option>
+      <option value="pielou_e">pielou_e</option>
+      <option value="mcintosh_e">mcintosh_e</option>
+      <option value="berger_parker_d">berger_parker_d</option>
+      <option value="shannon">shannon</option>
+      <option value="enspie">enspie</option>
+      <option value="mcintosh_d">mcintosh_d</option>
+      <option value="lladser_pe">lladser_pe</option>
+      <option value="brillouin_d">brillouin_d</option>
+      <option value="menhinick">menhinick</option>
+      <option value="simpson">simpson</option>
+      <option value="margalef">margalef</option>
+      <option value="robbins">robbins</option>
+      <option value="doubles">doubles</option>
+      <option value="chao1">chao1</option>
+      <option value="michaelis_menten_fit">michaelis_menten_fit</option>
+      <option value="singles">singles</option>
+      <option value="faith_pd">faith_pd</option>
+      <option value="fisher_alpha">fisher_alpha</option>
+    </param>
+    <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
+      <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA... (multiple arguments   The sample metadata. will be merged)                                                [optional]" name="additional_input" optional="True" type="data" />
+    </repeat>
+    <param label="--p-min-depth: INTEGER   The minimum rarefaction depth. Range(1, None)                                                [default: 1]" min="1" name="pmindepth" optional="True" type="integer" value="1" />
+    <param label="--p-steps: INTEGER       The number of rarefaction depths to include between Range(2, None)        min-depth and max-depth.               [default: 10]" min="2" name="psteps" optional="True" type="integer" value="10" />
+    <param label="--p-iterations: INTEGER  The number of rarefied feature tables to compute at Range(1, None)        each step.                             [default: 10]" min="1" name="piterations" optional="True" type="integer" value="10" />
+    <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[
 Alpha rarefaction curves
-########################
+###############################################################
 
 Generate interactive alpha rarefaction curves by computing rarefactions
 between `min_depth` and `max_depth`. The number of intermediate depths to
@@ -114,9 +117,9 @@
     The maximum rarefaction depth. Must be greater than min_depth.
 phylogeny : Phylogeny[Rooted], optional
     Optional phylogeny for phylogenetic metrics.
-metrics : Set[Str % Choices('pielou_e', 'simpson_e', 'shannon', 'margalef', 'menhinick', 'brillouin_d', 'mcintosh_e', 'doubles', 'robbins', 'simpson', 'enspie', 'fisher_alpha', 'heip_e', 'singles', 'michaelis_menten_fit', 'observed_otus', 'gini_index', 'dominance', 'goods_coverage', 'mcintosh_d', 'faith_pd', 'ace', 'chao1', 'lladser_pe', 'berger_parker_d')], optional
-    The metrics to be measured. By default computes observed_otus, shannon,
-    and if phylogeny is provided, faith_pd.
+metrics : Set[Str % Choices('mcintosh_e', 'chao1', 'observed_features', 'ace', 'margalef', 'berger_parker_d', 'simpson_e', 'doubles', 'gini_index', 'heip_e', 'michaelis_menten_fit', 'enspie', 'faith_pd', 'menhinick', 'pielou_e', 'shannon', 'singles', 'simpson', 'fisher_alpha', 'dominance', 'robbins', 'lladser_pe', 'mcintosh_d', 'brillouin_d', 'goods_coverage')], optional
+    The metrics to be measured. By default computes observed_features,
+    shannon, and if phylogeny is provided, faith_pd.
 metadata : Metadata, optional
     The sample metadata.
 min_depth : Int % Range(1, None), optional
@@ -130,9 +133,9 @@
 Returns
 -------
 visualization : Visualization
-	]]></help>
-<macros>
+  ]]></help>
+  <macros>
     <import>qiime_citation.xml</import>
-</macros>
-<expand macro="qiime_citation"/>
-</tool>
+  </macros>
+  <expand macro="qiime_citation"/>
+</tool>
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