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diff qiime2/qiime_diversity_mantel.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_mantel.xml	Thu Sep 03 09:46:00 2020 +0000
+++ b/qiime2/qiime_diversity_mantel.xml	Thu Sep 03 09:51:29 2020 +0000
@@ -1,76 +1,73 @@
 <?xml version="1.0" ?>
-<tool id="qiime_diversity_mantel" name="qiime diversity mantel" version="2019.7">
-	<description> - Apply the Mantel test to two distance matrices</description>
-	<requirements>
-		<requirement type="package" version="2019.7">qiime2</requirement>
-	</requirements>
-	<command><![CDATA[
+<tool id="qiime_diversity_mantel" name="qiime diversity mantel"
+      version="2020.8">
+  <description>Apply the Mantel test to two distance matrices</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
 qiime diversity mantel
 
 --i-dm1=$idm1
+
 --i-dm2=$idm2
 
 #if str($pmethod) != 'None':
- --p-method=$pmethod
+--p-method=$pmethod
 #end if
 
-#if str($ppermutations):
- --p-permutations=$ppermutations
-#end if
+--p-permutations=$ppermutations
 
 #if $pintersectids:
  --p-intersect-ids
 #end if
 
-
-
-#if '__sq__' in str($plabel1):
-  #set $plabel1_temp = $plabel1.replace('__sq__', "'")
-  #set $plabel1 = $plabel1_temp
-#end if
-
 #if str($plabel1):
- --p-label1="$plabel1"
+  --p-label1=$plabel1
 #end if
-
-
+#if str($plabel2):
+  --p-label2=$plabel2
+#end if
+--o-visualization=ovisualization
 
-#if '__sq__' in str($plabel2):
-  #set $plabel2_temp = $plabel2.replace('__sq__', "'")
-  #set $plabel2 = $plabel2_temp
-#end if
-
-#if str($plabel2):
- --p-label2="$plabel2"
+#if str($examples) != 'None':
+--examples=$examples
 #end if
 
-
+;
+cp ofiltereddistancematrix.qza $ofiltereddistancematrix
 
---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' '$ovisualization';
-	]]></command>
-	<inputs>
-		<param format="qza,no_unzip.zip" label="--i-dm1: ARTIFACT     Matrix of distances between pairs of samples. DistanceMatrix                                                  [required]" name="idm1" optional="False" type="data"/>
-		<param format="qza,no_unzip.zip" label="--i-dm2: ARTIFACT     Matrix of distances between pairs of samples. DistanceMatrix                                                  [required]" name="idm2" optional="False" type="data"/>
-		<param label="--p-method: " name="pmethod" optional="True" type="select">
-			<option selected="True" value="None">Selection is Optional</option>
-			<option value="spearman">spearman</option>
-			<option value="pearson">pearson</option>
-		</param>
-		<param label="--p-permutations: INTEGER Range(0, None)     The number of permutations to be run when computing p-values. Supplying a value of zero will disable permutation testing and p-values will not be calculated (this results in *much* quicker execution time if p-values are not desired).               [default: 999]" name="ppermutations" optional="True" type="integer" min="0" value="999"/>
-		<param label="--p-intersect-ids: --p-no-intersect-ids If supplied, IDs that are not found in both distance matrices will be discarded before applying the Mantel test. Default behavior is to error on any mismatched IDs.                                   [default: False]" name="pintersectids" selected="False" type="boolean"/>
-		<param label="--p-label1: TEXT      Label for `dm1` in the output visualization. [default: 'Distance Matrix 1']" name="plabel1" optional="True" type="text" value="Distance Matrix 1"/>
-		<param label="--p-label2: TEXT      Label for `dm2` in the output visualization. [default: 'Distance Matrix 2']" name="plabel2" optional="True" type="text" value="Distance Matrix 2"/>
-	</inputs>
-	<outputs>
-		<data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
-	</outputs>
-	<help><![CDATA[
+&& mv '$ovisualization.files_path/index.html' '$ovisualization'
+
+  ]]></command>
+  <inputs>
+    <param format="qza,no_unzip.zip" label="--i-dm1: ARTIFACT     Matrix of distances between pairs of samples. DistanceMatrix                                                  [required]" name="idm1" optional="False" type="data" />
+    <param format="qza,no_unzip.zip" label="--i-dm2: ARTIFACT     Matrix of distances between pairs of samples. DistanceMatrix                                                  [required]" name="idm2" optional="False" type="data" />
+    <param label="--p-method: " name="pmethod" optional="True" type="select">
+      <option selected="True" value="None">Selection is Optional</option>
+      <option value="spearman">spearman</option>
+      <option value="pearson">pearson</option>
+    </param>
+    <param label="--p-permutations: INTEGER Range(0, None)     The number of permutations to be run when computing p-values. Supplying a value of zero will disable permutation testing and p-values will not be calculated (this results in *much* quicker execution time if p-values are not desired).               [default: 999]" min="0" name="ppermutations" optional="True" type="integer" value="999" />
+    <param label="--p-intersect-ids: --p-intersect-ids: / --p-no-intersect-ids If supplied, IDs that are not found in both distance matrices will be discarded before applying the Mantel test. Default behavior is to error on any mismatched IDs.                                   [default: False]" name="pintersectids" selected="False" type="boolean" />
+    <param label="--p-label1: TEXT      Label for `dm1` in the output visualization. [default: \'Distance Matrix 1\']" name="plabel1" optional="False" type="text" value="\'Distance Matrix 1\'" />
+    <param label="--p-label2: TEXT      Label for `dm2` in the output visualization. [default: \'Distance Matrix 2\']" name="plabel2" optional="False" type="text" value="\'Distance Matrix 2\'" />
+    <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[
 Apply the Mantel test to two distance matrices
-##############################################
+###############################################################
 
 Apply a two-sided Mantel test to identify correlation between two distance
 matrices.  Note: the directionality of the comparison has no bearing on the
@@ -79,7 +76,7 @@
 distance matrices does not need to be the same; the distance matrices will
 be reordered before applying the Mantel test.  See the scikit-bio docs for
 more details about the Mantel test:  http://scikit-
-bio.org/docs/latest/generated/generated/skbio.stats.distance.mantel.html
+bio.org/docs/latest/generated/skbio.stats.distance.mantel
 
 Parameters
 ----------
@@ -106,9 +103,9 @@
 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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