diff qiime2/qiime_longitudinal_first-differences.xml @ 14:a0a8d77a991c draft

Uploaded

--- a/qiime2/qiime_longitudinal_first-differences.xml	Thu Sep 03 09:46:00 2020 +0000
+++ b/qiime2/qiime_longitudinal_first-differences.xml	Thu Sep 03 09:51:29 2020 +0000
@@ -1,78 +1,122 @@
 <?xml version="1.0" ?>
-<tool id="qiime_longitudinal_first-differences" name="qiime longitudinal first-differences" version="2019.7">
-	<description> - Compute first differences or difference from baseline between sequential states</description>
-	<requirements>
-		<requirement type="package" version="2019.7">qiime2</requirement>
-	</requirements>
-	<command><![CDATA[
+<tool id="qiime_longitudinal_first-differences" name="qiime longitudinal first-differences"
+      version="2020.8">
+  <description>Compute first differences or difference from baseline between sequential states</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
 qiime longitudinal first-differences
 
---p-state-column="$pstatecolumn"
---p-metric="$pmetric"
+#if str($itable) != 'None':
+--i-table=$itable
+#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)
+# end if
 
+#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 = $pstatecolumn_temp
+#end if
+
+--p-state-column=$pstatecolumn
 
 
-#if '__pd__' in str($pindividualidcolumn):
-	#set $pwhere_temp = $pindividualidcolumn.replace('__pd__', "#")
-	#set $pindividualidcolumn = $pwhere_temp
+#if '__ob__' in str($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 = $pindividualidcolumn_temp
 #end if
---p-individual-id-column="$pindividualidcolumn"
+#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($itable) != 'None':
- --i-table=$itable
-#end if
+--p-metric=$pmetric
 
 #if str($preplicatehandling) != 'None':
- --p-replicate-handling=$preplicatehandling
+--p-replicate-handling=$preplicatehandling
 #end if
 
 #if str($pbaseline):
- --p-baseline="$pbaseline"
+  --p-baseline=$pbaseline
+#end if
+--o-first-differences=ofirstdifferences
+
+#if str($examples) != 'None':
+--examples=$examples
 #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)
-#end if
-
-
---o-first-differences=ofirstdifferences
 ;
 cp ofirstdifferences.qza $ofirstdifferences
-	]]></command>
-	<inputs>
-		<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-metric: TEXT        Numerical metadata or artifact column to test. [required]" name="pmetric" optional="False" type="text"/>
-		<param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[RelativeFrequency] Feature table to optionally use for computing first differences.                               [optional]" name="itable" optional="True" type="data"/>
-		<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="--p-baseline: NUMBER    A value listed in the state-column metadata column against which all other states should be compared. Toggles calculation of static differences instead of first differences (which are calculated if no value is given for baseline). If a 'baseline' value is provided, sample differences 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"/>
 
-		<repeat name="input_files_mmetadatafile" optional="False" 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 optionally use for computing first differences.                               [optional]" 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 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-metric: TEXT        Numerical metadata or artifact column to test. [required]" name="pmetric" 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="--p-baseline: NUMBER    A value listed in the state-column metadata column against which all other states should be compared. Toggles calculation of static differences instead of first differences (which are calculated if no value is given for baseline). If a \'baseline\' value is provided, sample differences 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="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
+    
+  </inputs>
 
-	</inputs>
-	<outputs>
-		<data format="qza" label="${tool.name} on ${on_string}: firstdifferences.qza" name="ofirstdifferences"/>
-	</outputs>
-	<help><![CDATA[
+  <outputs>
+    <data format="qza" label="${tool.name} on ${on_string}: firstdifferences.qza" name="ofirstdifferences" />
+    
+  </outputs>
+
+  <help><![CDATA[
 Compute first differences or difference from baseline between sequential states
-###############################################################################
+###############################################################
+
 
 Calculates first differences in "metric" between sequential states for
 samples collected from individual subjects sampled repeatedly at two or
@@ -117,9 +161,9 @@
 -------
 first_differences : SampleData[FirstDifferences]
     Series of first differences.
-	]]></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