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diff qiime2/qiime_longitudinal_first-distances.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_longitudinal_first-distances.xml	Thu Sep 03 09:46:00 2020 +0000
+++ b/qiime2/qiime_longitudinal_first-distances.xml	Thu Sep 03 09:51:29 2020 +0000
@@ -1,64 +1,116 @@
 <?xml version="1.0" ?>
-<tool id="qiime_longitudinal_first-distances" name="qiime longitudinal first-distances" version="2019.7">
-	<description> - Compute first distances or distance from baseline between sequential states</description>
-	<requirements>
-		<requirement type="package" version="2019.7">qiime2</requirement>
-	</requirements>
-	<command><![CDATA[
+<tool id="qiime_longitudinal_first-distances" name="qiime longitudinal first-distances"
+      version="2020.8">
+  <description>Compute first distances or distance from baseline between sequential states</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
 qiime longitudinal first-distances
 
 --i-distance-matrix=$idistancematrix
---p-state-column="$pstatecolumn"
---p-individual-id-column="$pindividualidcolumn"
+# 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 str($pbaseline):
- --p-baseline="$pbaseline"
+#if '__ob__' in str($pstatecolumn):
+  #set $pstatecolumn_temp = $pstatecolumn.replace('__ob__', '[')
+  #set $pstatecolumn = $pstatecolumn_temp
+#end if
+#if '__cb__' in str($pstatecolumn):
+  #set $pstatecolumn_temp = $pstatecolumn.replace('__cb__', ']')
+  #set $pstatecolumn = $pstatecolumn_temp
+#end if
+#if 'X' in str($pstatecolumn):
+  #set $pstatecolumn_temp = $pstatecolumn.replace('X', '\\')
+  #set $pstatecolumn = $pstatecolumn_temp
+#end if
+#if '__sq__' in str($pstatecolumn):
+  #set $pstatecolumn_temp = $pstatecolumn.replace('__sq__', "'")
+  #set $pstatecolumn = $pstatecolumn_temp
+#end if
+#if '__db__' in str($pstatecolumn):
+  #set $pstatecolumn_temp = $pstatecolumn.replace('__db__', '"')
+  #set $pstatecolumn = $pstatecolumn_temp
 #end if
 
-#if str($preplicatehandling) != 'None':
- --p-replicate-handling=$preplicatehandling
-#end if
+--p-state-column=$pstatecolumn
 
 
-#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($input_files_mmetadatafile)
+#if '__ob__' in str($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 = $pindividualidcolumn_temp
+#end if
+#if '__db__' in str($pindividualidcolumn):
+  #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__db__', '"')
+  #set $pindividualidcolumn = $pindividualidcolumn_temp
 #end if
 
+--p-individual-id-column=$pindividualidcolumn
+
+
+#if str($pbaseline):
+  --p-baseline=$pbaseline
+#end if
+#if str($preplicatehandling) != 'None':
+--p-replicate-handling=$preplicatehandling
+#end if
 
 --o-first-distances=ofirstdistances
+
+#if str($examples) != 'None':
+--examples=$examples
+#end if
+
 ;
 cp ofirstdistances.qza $ofirstdistances
-	]]></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-state-column: TEXT  Metadata column containing state (time) variable information.                               [required]" name="pstatecolumn" optional="False" type="text"/>
-		<param label="--p-individual-id-column: TEXT Metadata column containing IDs for individual subjects.                                  [required]" name="pindividualidcolumn" optional="False" type="text"/>
-		<param label="--p-baseline: NUMBER    A value listed in the state-column metadata column against which all other states should be compared. Toggles calculation of static distances instead of first distances (which are calculated if no value is given for baseline). If a 'baseline' value is provided, sample distances at each state are compared against the baseline state, instead of the previous state. Must be a value listed in the state-column. [optional]" name="pbaseline" optional="True" type="float"/>
-		<param label="--p-replicate-handling: " name="preplicatehandling" optional="True" type="select">
-			<option selected="True" value="None">Selection is Optional</option>
-			<option value="error">error</option>
-			<option value="random">random</option>
-			<option value="drop">drop</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-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 file containing arguments will be   individual-id-column. merged)                                                        [required]" name="additional_input" optional="False" type="data" />
+    </repeat>
+    <param label="--p-state-column: TEXT  Metadata column containing state (time) variable information.                               [required]" name="pstatecolumn" optional="False" type="text" />
+    <param label="--p-individual-id-column: TEXT Metadata column containing IDs for individual subjects.                                  [required]" name="pindividualidcolumn" optional="False" type="text" />
+    <param label="--p-baseline: NUMBER    A value listed in the state-column metadata column against which all other states should be compared. Toggles calculation of static distances instead of first distances (which are calculated if no value is given for baseline). If a \'baseline\' value is provided, sample distances at each state are compared against the baseline state, instead of the previous state. Must be a value listed in the state-column. [optional]" name="pbaseline" optional="False" type="text" />
+    <param label="--p-replicate-handling: " name="preplicatehandling" optional="True" type="select">
+      <option selected="True" value="None">Selection is Optional</option>
+      <option value="error">error</option>
+      <option value="random">random</option>
+      <option value="drop">drop</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 ${on_string}: firstdistances.qza" name="ofirstdistances"/>
-	</outputs>
-	<help><![CDATA[
+  <outputs>
+    <data format="qza" label="${tool.name} on ${on_string}: firstdistances.qza" name="ofirstdistances" />
+    
+  </outputs>
+
+  <help><![CDATA[
 Compute first distances or distance from baseline between sequential states
-###########################################################################
+###############################################################
 
 Calculates first distances between sequential states for samples collected
 from individual subjects sampled repeatedly at two or more states. This
@@ -101,9 +153,9 @@
 -------
 first_distances : SampleData[FirstDifferences]
     Series of first distances.
-	]]></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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