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diff qiime2/qiime_diversity_core-metrics-phylogenetic.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_core-metrics-phylogenetic.xml	Thu Sep 03 09:46:00 2020 +0000
+++ b/qiime2/qiime_diversity_core-metrics-phylogenetic.xml	Thu Sep 03 09:51:29 2020 +0000
@@ -1,114 +1,139 @@
 <?xml version="1.0" ?>
-<tool id="qiime_diversity_core-metrics-phylogenetic" name="qiime diversity core-metrics-phylogenetic" version="2019.7">
-	<description> - Core diversity metrics (phylogenetic and non- phylogenetic)</description>
-	<requirements>
-		<requirement type="package" version="2019.7">qiime2</requirement>
-	</requirements>
-	<command><![CDATA[
+<tool id="qiime_diversity_core-metrics-phylogenetic" name="qiime diversity core-metrics-phylogenetic"
+      version="2020.8">
+  <description>Core diversity metrics (phylogenetic and non- phylogenetic)</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
 qiime diversity core-metrics-phylogenetic
 
 --i-table=$itable
+
 --i-phylogeny=$iphylogeny
 
-#if str($psamplingdepth):
- --p-sampling-depth="$psamplingdepth"
-#end if
-
-#set $pnjobs = '${GALAXY_SLOTS:-4}'
-#if str($pnjobs):
- --p-n-jobs="$pnjobs"
-#end if
-
+--p-sampling-depth=$psamplingdepth
+# 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($input_files_mmetadatafile)
+#if str($pnjobsorthreads) != 'None':
+--p-n-jobs-or-threads=$pnjobsorthreads
 #end if
 
-
-
 --o-rarefied-table=orarefiedtable
+
 --o-faith-pd-vector=ofaithpdvector
---o-observed-otus-vector=oobservedotusvector
+
+--o-observed-features-vector=oobservedfeaturesvector
+
 --o-shannon-vector=oshannonvector
+
 --o-evenness-vector=oevennessvector
+
 --o-unweighted-unifrac-distance-matrix=ounweightedunifracdistancematrix
+
 --o-weighted-unifrac-distance-matrix=oweightedunifracdistancematrix
+
 --o-jaccard-distance-matrix=ojaccarddistancematrix
+
 --o-bray-curtis-distance-matrix=obraycurtisdistancematrix
+
 --o-unweighted-unifrac-pcoa-results=ounweightedunifracpcoaresults
+
 --o-weighted-unifrac-pcoa-results=oweightedunifracpcoaresults
+
 --o-jaccard-pcoa-results=ojaccardpcoaresults
+
 --o-bray-curtis-pcoa-results=obraycurtispcoaresults
+
 --o-unweighted-unifrac-emperor=ounweightedunifracemperor
+
 --o-weighted-unifrac-emperor=oweightedunifracemperor
+
 --o-jaccard-emperor=ojaccardemperor
+
 --o-bray-curtis-emperor=obraycurtisemperor
+
+#if str($examples) != 'None':
+--examples=$examples
+#end if
+
 ;
-cp orarefiedtable.qza $orarefiedtable;
-cp ofaithpdvector.qza $ofaithpdvector;
-cp oobservedotusvector.qza $oobservedotusvector;
-cp oshannonvector.qza $oshannonvector;
-cp oevennessvector.qza $oevennessvector;
-cp ounweightedunifracdistancematrix.qza $ounweightedunifracdistancematrix;
-cp oweightedunifracdistancematrix.qza $oweightedunifracdistancematrix;
-cp ojaccarddistancematrix.qza $ojaccarddistancematrix;
-cp obraycurtisdistancematrix.qza $obraycurtisdistancematrix;
-cp ounweightedunifracpcoaresults.qza $ounweightedunifracpcoaresults;
-cp oweightedunifracpcoaresults.qza $oweightedunifracpcoaresults;
-cp ojaccardpcoaresults.qza $ojaccardpcoaresults;
-cp obraycurtispcoaresults.qza $obraycurtispcoaresults;
-qiime tools export --input-path ounweightedunifracemperor.qzv --output-path out   && mkdir -p '$ounweightedunifracemperor.files_path'
+cp obraycurtispcoaresults.qza $obraycurtispcoaresults
+
+;
+qiime tools export  ounweightedunifracemperor.qzv --output-path out
+&& mkdir -p '$ounweightedunifracemperor.files_path'
 && cp -r out/* '$ounweightedunifracemperor.files_path'
-&& mv '$ounweightedunifracemperor.files_path/index.html' '$ounweightedunifracemperor';
-qiime tools export --input-path oweightedunifracemperor.qzv --output-path out   && mkdir -p '$oweightedunifracemperor.files_path'
+&& mv '$ounweightedunifracemperor.files_path/index.html' '$ounweightedunifracemperor'
+
+;
+qiime tools export  oweightedunifracemperor.qzv --output-path out
+&& mkdir -p '$oweightedunifracemperor.files_path'
 && cp -r out/* '$oweightedunifracemperor.files_path'
-&& mv '$oweightedunifracemperor.files_path/index.html' '$oweightedunifracemperor';
-qiime tools export --input-path ojaccardemperor.qzv --output-path out   && mkdir -p '$ojaccardemperor.files_path'
+&& mv '$oweightedunifracemperor.files_path/index.html' '$oweightedunifracemperor'
+
+;
+qiime tools export  ojaccardemperor.qzv --output-path out
+&& mkdir -p '$ojaccardemperor.files_path'
 && cp -r out/* '$ojaccardemperor.files_path'
-&& mv '$ojaccardemperor.files_path/index.html' '$ojaccardemperor';
-qiime tools export --input-path obraycurtisemperor.qzv --output-path out   && mkdir -p '$obraycurtisemperor.files_path'
+&& mv '$ojaccardemperor.files_path/index.html' '$ojaccardemperor'
+
+;
+qiime tools export  obraycurtisemperor.qzv --output-path out
+&& mkdir -p '$obraycurtisemperor.files_path'
 && cp -r out/* '$obraycurtisemperor.files_path'
-&& mv '$obraycurtisemperor.files_path/index.html' '$obraycurtisemperor';
-	]]></command>
-	<inputs>
-		<param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table containing the samples over which diversity metrics should be computed.     [required]" name="itable" optional="False" type="data"/>
-		<param format="qza,no_unzip.zip" label="--i-phylogeny: ARTIFACT  Phylogenetic tree containing tip identifiers that Phylogeny[Rooted]     correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree.                  [required]" name="iphylogeny" optional="False" type="data"/>
-		<param label="--p-sampling-depth: INTEGER Range(1, None)        The total frequency that each sample should be rarefied to prior to computing diversity metrics. [required]" name="psamplingdepth" optional="False" min="1" value="" type="integer"/>
+&& mv '$obraycurtisemperor.files_path/index.html' '$obraycurtisemperor'
 
-		<repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file [required]">
-			<param label="--m-metadata-file:  (multiple arguments will be merged) The sample metadata to use in the emperor plots. [required]" name="additional_input" optional="False" type="data" format="tabular,qza,no_unzip.zip" />
-		</repeat>
+  ]]></command>
+  <inputs>
+    <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table containing the samples over which diversity metrics should be computed.     [required]" name="itable" optional="False" type="data" />
+    <param format="qza,no_unzip.zip" label="--i-phylogeny: ARTIFACT  Phylogenetic tree containing tip identifiers that Phylogeny[Rooted]     correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree.                  [required]" name="iphylogeny" optional="False" type="data" />
+    <param label="--p-sampling-depth: INTEGER Range(1, None)        The total frequency that each sample should be rarefied to prior to computing diversity metrics. [required]" name="psamplingdepth" optional="False" type="text" />
+    <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
+      <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA... (multiple arguments   The sample metadata to use in the emperor plots. will be merged)                                                [required]" name="additional_input" optional="False" type="data" />
+    </repeat>
+    <param label="--p-n-jobs-or-threads: " name="pnjobsorthreads" optional="True" type="select">
+      <option selected="True" value="None">Selection is Optional</option>
+      <option value="Int % Range(1">Int % Range(1</option>
+      <option value="None">None</option>
+    </param>
+    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
+    
+  </inputs>
 
-	</inputs>
-	<outputs>
-		<data format="qza" label="${tool.name} on ${on_string}: rarefiedtable.qza" name="orarefiedtable"/>
-		<data format="qza" label="${tool.name} on ${on_string}: faithpdvector.qza" name="ofaithpdvector"/>
-		<data format="qza" label="${tool.name} on ${on_string}: observedotusvector.qza" name="oobservedotusvector"/>
-		<data format="qza" label="${tool.name} on ${on_string}: shannonvector.qza" name="oshannonvector"/>
-		<data format="qza" label="${tool.name} on ${on_string}: evennessvector.qza" name="oevennessvector"/>
-		<data format="qza" label="${tool.name} on ${on_string}: unweightedunifracdistancematrix.qza" name="ounweightedunifracdistancematrix"/>
-		<data format="qza" label="${tool.name} on ${on_string}: weightedunifracdistancematrix.qza" name="oweightedunifracdistancematrix"/>
-		<data format="qza" label="${tool.name} on ${on_string}: jaccarddistancematrix.qza" name="ojaccarddistancematrix"/>
-		<data format="qza" label="${tool.name} on ${on_string}: braycurtisdistancematrix.qza" name="obraycurtisdistancematrix"/>
-		<data format="qza" label="${tool.name} on ${on_string}: unweightedunifracpcoaresults.qza" name="ounweightedunifracpcoaresults"/>
-		<data format="qza" label="${tool.name} on ${on_string}: weightedunifracpcoaresults.qza" name="oweightedunifracpcoaresults"/>
-		<data format="qza" label="${tool.name} on ${on_string}: jaccardpcoaresults.qza" name="ojaccardpcoaresults"/>
-		<data format="qza" label="${tool.name} on ${on_string}: braycurtispcoaresults.qza" name="obraycurtispcoaresults"/>
-		<data format="html" label="${tool.name} on ${on_string}: unweightedunifracemperor.qzv" name="ounweightedunifracemperor"/>
-		<data format="html" label="${tool.name} on ${on_string}: weightedunifracemperor.qzv" name="oweightedunifracemperor"/>
-		<data format="html" label="${tool.name} on ${on_string}: jaccardemperor.qzv" name="ojaccardemperor"/>
-		<data format="html" label="${tool.name} on ${on_string}: braycurtisemperor.qzv" name="obraycurtisemperor"/>
-	</outputs>
-	<help><![CDATA[
-Core diversity metrics (phylogenetic and non-phylogenetic)
-##########################################################
+  <outputs>
+    <data format="qza" label="${tool.name} on ${on_string}: rarefiedtable.qza" name="orarefiedtable" />
+    <data format="qza" label="${tool.name} on ${on_string}: faithpdvector.qza" name="ofaithpdvector" />
+    <data format="qza" label="${tool.name} on ${on_string}: observedfeaturesvector.qza" name="oobservedfeaturesvector" />
+    <data format="qza" label="${tool.name} on ${on_string}: shannonvector.qza" name="oshannonvector" />
+    <data format="qza" label="${tool.name} on ${on_string}: evennessvector.qza" name="oevennessvector" />
+    <data format="qza" label="${tool.name} on ${on_string}: unweightedunifracdistancematrix.qza" name="ounweightedunifracdistancematrix" />
+    <data format="qza" label="${tool.name} on ${on_string}: weightedunifracdistancematrix.qza" name="oweightedunifracdistancematrix" />
+    <data format="qza" label="${tool.name} on ${on_string}: jaccarddistancematrix.qza" name="ojaccarddistancematrix" />
+    <data format="qza" label="${tool.name} on ${on_string}: braycurtisdistancematrix.qza" name="obraycurtisdistancematrix" />
+    <data format="qza" label="${tool.name} on ${on_string}: unweightedunifracpcoaresults.qza" name="ounweightedunifracpcoaresults" />
+    <data format="qza" label="${tool.name} on ${on_string}: weightedunifracpcoaresults.qza" name="oweightedunifracpcoaresults" />
+    <data format="qza" label="${tool.name} on ${on_string}: jaccardpcoaresults.qza" name="ojaccardpcoaresults" />
+    <data format="qza" label="${tool.name} on ${on_string}: braycurtispcoaresults.qza" name="obraycurtispcoaresults" />
+    <data format="html" label="${tool.name} on ${on_string}: unweightedunifracemperor.html" name="ounweightedunifracemperor" />
+    <data format="html" label="${tool.name} on ${on_string}: weightedunifracemperor.html" name="oweightedunifracemperor" />
+    <data format="html" label="${tool.name} on ${on_string}: jaccardemperor.html" name="ojaccardemperor" />
+    <data format="html" label="${tool.name} on ${on_string}: braycurtisemperor.html" name="obraycurtisemperor" />
+    
+  </outputs>
+
+  <help><![CDATA[
+Core diversity metrics (phylogenetic and non- phylogenetic)
+###############################################################
 
 Applies a collection of diversity metrics (both phylogenetic and non-
 phylogenetic) to a feature table.
@@ -128,6 +153,13 @@
     computing diversity metrics.
 metadata : Metadata
     The sample metadata to use in the emperor plots.
+n_jobs_or_threads : Int % Range(1, None) | Str % Choices('auto'), optional
+    [beta/beta-phylogenetic methods only] - The number of concurrent jobs
+    or CPU threads to use in performing this calculation. Individual
+    methods will create jobs/threads as implemented in q2-diversity-lib
+    dependencies. May not exceed the number of available physical cores. If
+    n_jobs_or_threads = 'auto', one thread/job will be created for each
+    identified CPU core on the host.
 
 Returns
 -------
@@ -135,8 +167,8 @@
     The resulting rarefied feature table.
 faith_pd_vector : SampleData[AlphaDiversity]
     Vector of Faith PD values by sample.
-observed_otus_vector : SampleData[AlphaDiversity]
-    Vector of Observed OTUs values by sample.
+observed_features_vector : SampleData[AlphaDiversity]
+    Vector of Observed Features values by sample.
 shannon_vector : SampleData[AlphaDiversity]
     Vector of Shannon diversity values by sample.
 evenness_vector : SampleData[AlphaDiversity]
@@ -165,9 +197,9 @@
     Emperor plot of the PCoA matrix computed from Jaccard.
 bray_curtis_emperor : Visualization
     Emperor plot of the PCoA matrix computed from Bray-Curtis.
-	]]></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