diff qiime2/qiime_diversity_core-metrics.xml @ 0:370e0b6e9826 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_diversity_core-metrics.xml	Wed Jul 17 03:05:17 2019 -0400
@@ -0,0 +1,121 @@
+<?xml version="1.0" ?>
+<tool id="qiime_diversity_core-metrics" name="qiime diversity core-metrics" version="2019.4">
+	<description> - Core diversity metrics (non-phylogenetic)</description>
+	<requirements>
+		<requirement type="package" version="2019.4">qiime2</requirement>
+	</requirements>
+	<command><![CDATA[
+qiime diversity core-metrics
+
+--i-table=$itable
+--p-sampling-depth="$psamplingdepth"
+
+#set $pnjobs = '${GALAXY_SLOTS:-4}'
+#if str($pnjobs):
+ --p-n-jobs="$pnjobs"
+#end if
+
+#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 + ',' + d['additional_input'].__getattr__('file_name')
+#end for
+#return $file_list
+#end def
+
+--m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
+
+
+--o-rarefied-table=orarefiedtable
+--o-observed-otus-vector=oobservedotusvector
+--o-shannon-vector=oshannonvector
+--o-evenness-vector=oevennessvector
+--o-jaccard-distance-matrix=ojaccarddistancematrix
+--o-bray-curtis-distance-matrix=obraycurtisdistancematrix
+--o-jaccard-pcoa-results=ojaccardpcoaresults
+--o-bray-curtis-pcoa-results=obraycurtispcoaresults
+--o-jaccard-emperor=ojaccardemperor
+--o-bray-curtis-emperor=obraycurtisemperor
+;
+cp orarefiedtable.qza $orarefiedtable;
+cp oobservedotusvector.qza $oobservedotusvector;
+cp oshannonvector.qza $oshannonvector;
+cp oevennessvector.qza $oevennessvector;
+cp ojaccarddistancematrix.qza $ojaccarddistancematrix;
+cp obraycurtisdistancematrix.qza $obraycurtisdistancematrix;
+cp ojaccardpcoaresults.qza $ojaccardpcoaresults;
+cp obraycurtispcoaresults.qza $obraycurtispcoaresults;
+qiime tools export --input-path ojaccardemperor.qzv --output-path out   && mkdir -p '$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'
+&& cp -r out/* '$obraycurtisemperor.files_path'
+&& mv '$obraycurtisemperor.files_path/index.html' '$obraycurtisemperor';
+	]]></command>
+	<inputs>
+		<param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table containing the samples over which diversity metrics should be computed.        [required]" name="itable" optional="False" type="data"/>
+		<param label="--p-sampling-depth: INTEGER Range(1, None)     The total frequency that each sample should be rarefied to prior to computing diversity metrics. [required]" name="psamplingdepth" optional="False" min="1" value="" type="integer"/>
+
+		<repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
+			<param label="--m-metadata-file: METADATA... (multiple arguments will be merged) The sample metadata to use in the emperor plots. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
+		</repeat>
+
+	</inputs>
+	<outputs>
+		<data format="qza" label="${tool.name} on ${on_string}: rarefiedtable.qza" name="orarefiedtable"/>
+		<data format="qza" label="${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 ${on_string}: jaccarddistancematrix.qza" name="ojaccarddistancematrix"/>
+		<data format="qza" label="${tool.name} on ${on_string}: braycurtisdistancematrix.qza" name="obraycurtisdistancematrix"/>
+		<data format="qza" label="${tool.name} on ${on_string}: jaccardpcoaresults.qza" name="ojaccardpcoaresults"/>
+		<data format="qza" label="${tool.name} on ${on_string}: braycurtispcoaresults.qza" name="obraycurtispcoaresults"/>
+		<data format="html" label="${tool.name} on ${on_string}: jaccardemperor.qzv" name="ojaccardemperor"/>
+		<data format="html" label="${tool.name} on ${on_string}: braycurtisemperor.qzv" name="obraycurtisemperor"/>
+	</outputs>
+	<help><![CDATA[
+Core diversity metrics (non-phylogenetic)
+#########################################
+
+Applies a collection of diversity metrics (non-phylogenetic) to a feature
+table.
+
+Parameters
+----------
+table : FeatureTable[Frequency]
+    The feature table containing the samples over which diversity metrics
+    should be computed.
+sampling_depth : Int % Range(1, None)
+    The total frequency that each sample should be rarefied to prior to
+    computing diversity metrics.
+metadata : Metadata
+    The sample metadata to use in the emperor plots.
+
+Returns
+-------
+rarefied_table : FeatureTable[Frequency]
+    The resulting rarefied feature table.
+observed_otus_vector : SampleData[AlphaDiversity]
+    Vector of Observed OTUs values by sample.
+shannon_vector : SampleData[AlphaDiversity]
+    Vector of Shannon diversity values by sample.
+evenness_vector : SampleData[AlphaDiversity]
+    Vector of Pielou's evenness values by sample.
+jaccard_distance_matrix : DistanceMatrix
+    Matrix of Jaccard distances between pairs of samples.
+bray_curtis_distance_matrix : DistanceMatrix
+    Matrix of Bray-Curtis distances between pairs of samples.
+jaccard_pcoa_results : PCoAResults
+    PCoA matrix computed from Jaccard distances between samples.
+bray_curtis_pcoa_results : PCoAResults
+    PCoA matrix computed from Bray-Curtis distances between samples.
+jaccard_emperor : Visualization
+    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>
+    <import>qiime_citation.xml</import>
+</macros>
+<expand macro="qiime_citation"/>
+</tool>