Mercurial > repos > florianbegusch > qiime2_suite

diff qiime2/qiime_longitudinal_nmit.xml @ 14:a0a8d77a991c draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author florianbegusch
date Thu, 03 Sep 2020 09:51:29 +0000
parents f190567fe3f6
children
line wrap: on
line diff
--- a/qiime2/qiime_longitudinal_nmit.xml	Thu Sep 03 09:46:00 2020 +0000
+++ b/qiime2/qiime_longitudinal_nmit.xml	Thu Sep 03 09:51:29 2020 +0000
@@ -1,80 +1,96 @@
 <?xml version="1.0" ?>
-<tool id="qiime_longitudinal_nmit" name="qiime longitudinal nmit" version="2019.7">
-	<description> - Nonparametric microbial interdependence test</description>
-	<requirements>
-		<requirement type="package" version="2019.7">qiime2</requirement>
-	</requirements>
-	<command><![CDATA[
+<tool id="qiime_longitudinal_nmit" name="qiime longitudinal nmit"
+      version="2020.8">
+  <description>Nonparametric microbial interdependence test</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
 qiime longitudinal nmit
 
 --i-table=$itable
-
+# 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 '__ob__' in str($pindividualidcolumn):
+  #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__ob__', '[')
+  #set $pindividualidcolumn = $pindividualidcolumn_temp
+#end if
+#if '__cb__' in str($pindividualidcolumn):
+  #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__cb__', ']')
+  #set $pindividualidcolumn = $pindividualidcolumn_temp
+#end if
+#if 'X' in str($pindividualidcolumn):
+  #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('X', '\\')
+  #set $pindividualidcolumn = $pindividualidcolumn_temp
+#end if
 #if '__sq__' in str($pindividualidcolumn):
   #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__sq__', "'")
   #set $pindividualidcolumn = $pindividualidcolumn_temp
 #end if
-
-#if str($pindividualidcolumn):
- --p-individual-id-column="$pindividualidcolumn"
+#if '__db__' in str($pindividualidcolumn):
+  #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__db__', '"')
+  #set $pindividualidcolumn = $pindividualidcolumn_temp
 #end if
 
-
+--p-individual-id-column=$pindividualidcolumn
 
 
 #if str($pcorrmethod) != 'None':
- --p-corr-method=$pcorrmethod
+--p-corr-method=$pcorrmethod
 #end if
 
 #if str($pdistmethod) != 'None':
- --p-dist-method=$pdistmethod
+--p-dist-method=$pdistmethod
 #end if
 
+--o-distance-matrix=odistancematrix
 
-#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($input_files_mmetadatafile)
+#if str($examples) != 'None':
+--examples=$examples
 #end if
 
-
---o-distance-matrix=odistancematrix
 ;
 cp odistancematrix.qza $odistancematrix
-	]]></command>
-	<inputs>
-		<param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[RelativeFrequency] Feature table to use for microbial interdependence test.                                       [required]" name="itable" optional="False" type="data"/>
-		<param label="--p-individual-id-column: TEXT Metadata column containing IDs for individual subjects.                                   [required]" name="pindividualidcolumn" optional="False" type="text"/>
-		<param label="--p-corr-method: " name="pcorrmethod" optional="True" type="select">
-			<option selected="True" value="None">Selection is Optional</option>
-			<option value="kendall">kendall</option>
-			<option value="pearson">pearson</option>
-			<option value="spearman">spearman</option>
-		</param>
-		<param label="--p-dist-method: " name="pdistmethod" optional="True" type="select">
-			<option selected="True" value="None">Selection is Optional</option>
-			<option value="fro">fro</option>
-			<option value="nuc">nuc</option>
-		</param>
 
-		<repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file  [required]">
-			<param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge 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[RelativeFrequency] Feature table to use for microbial interdependence test.                                       [required]" name="itable" 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 file containing individual-id-column. arguments will be merged)                                                        [required]" name="additional_input" optional="False" type="data" />
+    </repeat>
+    <param label="--p-individual-id-column: TEXT Metadata column containing IDs for individual subjects.                                   [required]" name="pindividualidcolumn" optional="False" type="text" />
+    <param label="--p-corr-method: " name="pcorrmethod" optional="True" type="select">
+      <option selected="True" value="None">Selection is Optional</option>
+      <option value="kendall">kendall</option>
+      <option value="pearson">pearson</option>
+      <option value="spearman">spearman</option>
+    </param>
+    <param label="--p-dist-method: " name="pdistmethod" optional="True" type="select">
+      <option selected="True" value="None">Selection is Optional</option>
+      <option value="fro">fro</option>
+      <option value="nuc">nuc</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 ${on_string}: distancematrix.qza" name="odistancematrix"/>
-	</outputs>
-	<help><![CDATA[
+  <outputs>
+    <data format="qza" label="${tool.name} on ${on_string}: distancematrix.qza" name="odistancematrix" />
+    
+  </outputs>
+
+  <help><![CDATA[
 Nonparametric microbial interdependence test
-############################################
+###############################################################
 
 Perform nonparametric microbial interdependence test to determine
 longitudinal sample similarity as a function of temporal microbial
@@ -98,9 +114,9 @@
 -------
 distance_matrix : DistanceMatrix
     The resulting distance matrix.
-	]]></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