Mercurial > repos > florianbegusch > qiime2_suite

diff qiime2/qiime_diversity_adonis.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_adonis.xml	Thu Sep 03 09:46:00 2020 +0000
+++ b/qiime2/qiime_diversity_adonis.xml	Thu Sep 03 09:51:29 2020 +0000
@@ -1,67 +1,72 @@
 <?xml version="1.0" ?>
-<tool id="qiime_diversity_adonis" name="qiime diversity adonis" version="2019.7">
-	<description> - adonis PERMANOVA test for beta group significance</description>
-	<requirements>
-		<requirement type="package" version="2019.7">qiime2</requirement>
-	</requirements>
-	<command><![CDATA[
+<tool id="qiime_diversity_adonis" name="qiime diversity adonis"
+      version="2020.8">
+  <description>adonis PERMANOVA test for beta group significance</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
 qiime diversity adonis
 
 --i-distance-matrix=$idistancematrix
-
+# 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 $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($input_files_mmetadatafile)
-#end if
+--p-formula=$pformula
+
+--p-permutations=$ppermutations
 
-
+--p-n-jobs=$pnjobs
 
-#if '__sq__' in str($pformula):
-  #set $pformula_temp = $pformula.replace('__sq__', "'")
-  #set $pformula = $pformula_temp
+--o-visualization=ovisualization
+
+#if str($examples) != 'None':
+--examples=$examples
 #end if
 
---p-formula="$pformula"
-
-
-
-#if str($ppermutations):
- --p-permutations=$ppermutations
-#end if
+;
+cp osubsampledsequences.qza $osubsampledsequences
 
-#set $pnjobs = '${GALAXY_SLOTS:-4}'
-#if str($pnjobs):
- --p-n-jobs="$pnjobs"
-#end if
+;
+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'
 
---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-distance-matrix: ARTIFACT DistanceMatrix     Matrix of distances between pairs of samples. [required]" name="idistancematrix" optional="False" type="data"/>
-		<param label="--p-formula: TEXT     Model formula containing only independent terms contained in the sample metadata. These can be continuous variables or factors, and they can have interactions as in a typical R formula. E.g., the formula 'treatment+block' would test whether the input distance matrix partitions based on 'treatment' and 'block' sample metadata. The formula 'treatment*block' would test both of those effects as well as their interaction. Enclose formulae in quotes to avoid unpleasant surprises.                        [required]" name="pformula" optional="False" type="text"/>
-		<param label="--p-permutations: INTEGER Range(1, None)     The number of permutations to be run when computing p-values.                                [default: 999]" name="ppermutations" optional="True" min="1" type="integer" value="999"/>
 
-		<repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file  [required]">
-			<param format="tabular" label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [required]" name="additional_input" type="data"/>
-		</repeat>
-	</inputs>
-	<outputs>
-		<data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
-	</outputs>
-	<help><![CDATA[
+  ]]></command>
+  <inputs>
+    <param format="qza,no_unzip.zip" label="--i-distance-matrix: ARTIFACT DistanceMatrix     Matrix of distances between pairs of samples. [required]" name="idistancematrix" optional="False" type="data" />
+    <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
+      <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA... (multiple          Sample metadata containing formula terms. arguments will be merged)                                                     [required]" name="additional_input" optional="False" type="data" />
+    </repeat>
+    <param label="--p-formula: TEXT     Model formula containing only independent terms contained in the sample metadata. These can be continuous variables or factors, and they can have interactions as in a typical R formula. E.g., the formula \'treatment+block\' would test whether the input distance matrix partitions based on \'treatment\' and \'block\' sample metadata. The formula \'treatment*block\' would test both of those effects as well as their interaction. Enclose formulae in quotes to avoid unpleasant surprises.                        [required]" name="pformula" optional="False" type="text" />
+    <param label="--p-permutations: INTEGER Range(1, None)     The number of permutations to be run when computing p-values.                                [default: 999]" min="1" name="ppermutations" optional="True" type="integer" value="999" />
+    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
+    
+  </inputs>
+
+  <outputs>
+    <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
+    
+  </outputs>
+
+  <help><![CDATA[
 adonis PERMANOVA test for beta group significance
-##################################################
+###############################################################
 
 Determine whether groups of samples are significantly different from one
 another using the ADONIS permutation-based statistical test in vegan-R. The
@@ -89,13 +94,15 @@
     surprises.
 permutations : Int % Range(1, None), optional
     The number of permutations to be run when computing p-values.
+n_jobs : Int % Range(1, None), optional
+    Number of parallel processes to run.
 
 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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