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diff qiime2/qiime_feature-table_filter-features.xml @ 14:a0a8d77a991c draft

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Uploaded
author florianbegusch
date Thu, 03 Sep 2020 09:51:29 +0000
parents f190567fe3f6
children
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--- a/qiime2/qiime_feature-table_filter-features.xml	Thu Sep 03 09:46:00 2020 +0000
+++ b/qiime2/qiime_feature-table_filter-features.xml	Thu Sep 03 09:51:29 2020 +0000
@@ -1,80 +1,97 @@
 <?xml version="1.0" ?>
-<tool id="qiime_feature-table_filter-features" name="qiime feature-table filter-features" version="2019.7">
-	<description> - Filter features from table</description>
-	<requirements>
-		<requirement type="package" version="2019.7">qiime2</requirement>
-	</requirements>
-	<command><![CDATA[
+<tool id="qiime_feature-table_filter-features" name="qiime feature-table filter-features"
+      version="2020.8">
+  <description>Filter features from table</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
 qiime feature-table filter-features
 
 --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($input_files_mmetadatafile)
-#end if
-
-
-#if str($pminfrequency):
- --p-min-frequency=$pminfrequency
-#end if
+--p-min-frequency=$pminfrequency
 
 #if str($pmaxfrequency):
- --p-max-frequency="$pmaxfrequency"
+  --p-max-frequency=$pmaxfrequency
 #end if
-
-#if str($pminsamples):
- --p-min-samples=$pminsamples
-#end if
+--p-min-samples=$pminsamples
 
 #if str($pmaxsamples):
- --p-max-samples="$pmaxsamples"
+  --p-max-samples=$pmaxsamples
+#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($input_files_mmetadatafile)
+# end if
+
+#if '__ob__' in str($pwhere):
+  #set $pwhere_temp = $pwhere.replace('__ob__', '[')
+  #set $pwhere = $pwhere_temp
 #end if
-
+#if '__cb__' in str($pwhere):
+  #set $pwhere_temp = $pwhere.replace('__cb__', ']')
+  #set $pwhere = $pwhere_temp
+#end if
+#if 'X' in str($pwhere):
+  #set $pwhere_temp = $pwhere.replace('X', '\\')
+  #set $pwhere = $pwhere_temp
+#end if
 #if '__sq__' in str($pwhere):
   #set $pwhere_temp = $pwhere.replace('__sq__', "'")
   #set $pwhere = $pwhere_temp
 #end if
+#if '__db__' in str($pwhere):
+  #set $pwhere_temp = $pwhere.replace('__db__', '"')
+  #set $pwhere = $pwhere_temp
+#end if
 
 #if str($pwhere):
- --p-where="$pwhere"
+  --p-where=$pwhere
 #end if
 
-#if str($pexcludeids):
+#if $pexcludeids:
  --p-exclude-ids
 #end if
 
 --o-filtered-table=ofilteredtable
+
+#if str($examples) != 'None':
+--examples=$examples
+#end if
+
 ;
 cp ofilteredtable.qza $ofilteredtable
-	]]></command>
-	<inputs>
-		<param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table from which features should be filtered.                                    [required]" name="itable" optional="False" type="data"/>
-		<param label="--p-min-frequency: INTEGER The minimum total frequency that a feature must have to be retained.                            [default: 0]" name="pminfrequency" optional="True" type="integer" value="0"/>
-		<param label="--p-max-frequency: INTEGER The maximum total frequency that a feature can have to be retained. If no value is provided this will default to infinity (i.e., no maximum frequency filter will be applied).                                    [optional]" name="pmaxfrequency" optional="True" type="integer"/>
-		<param label="--p-min-samples: INTEGER The minimum number of samples that a feature must be observed in to be retained.                [default: 0]" name="pminsamples" optional="True" type="integer" value="0"/>
-		<param label="--p-max-samples: INTEGER The maximum number of samples that a feature can be observed in to be retained. If no value is provided this will default to infinity (i.e., no maximum sample filter will be applied).                     [optional]" name="pmaxsamples" optional="True" type="integer"/>
-		<param label="--p-where: TEXT       SQLite WHERE clause specifying feature metadata criteria that must be met to be included in the filtered feature table. If not provided, all features in `metadata` that are also in the feature table will be retained.                                 [optional]" name="pwhere" optional="True" type="text"/>
-		<param label="--p-exclude-ids: --p-no-exclude-ids If true, the features selected by `metadata` or `where` parameters will be excluded from the filtered table instead of being retained.       [default: False]" name="pexcludeids" selected="False" type="boolean"/>
 
-		<repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
-			<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[Frequency] The feature table from which features should be filtered.                                    [required]" name="itable" optional="False" type="data" />
+    <param label="--p-min-frequency: INTEGER The minimum total frequency that a feature must have to be retained.                            [default: 0]" name="pminfrequency" optional="True" type="integer" value="0" />
+    <param label="--p-max-frequency: INTEGER The maximum total frequency that a feature can have to be retained. If no value is provided this will default to infinity (i.e., no maximum frequency filter will be applied).                                    [optional]" name="pmaxfrequency" optional="False" type="text" />
+    <param label="--p-min-samples: INTEGER The minimum number of samples that a feature must be observed in to be retained.                [default: 0]" name="pminsamples" optional="True" type="integer" value="0" />
+    <param label="--p-max-samples: INTEGER The maximum number of samples that a feature can be observed in to be retained. If no value is provided this will default to infinity (i.e., no maximum sample filter will be applied).                     [optional]" name="pmaxsamples" optional="False" type="text" />
+    <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
+      <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA... (multiple          Feature metadata used with `where` parameter when arguments will    selecting features to retain, or with `exclude-ids` be merged)        when selecting features to discard.          [optional]" name="additional_input" optional="True" type="data" />
+    </repeat>
+    <param label="--p-where: TEXT       SQLite WHERE clause specifying feature metadata criteria that must be met to be included in the filtered feature table. If not provided, all features in `metadata` that are also in the feature table will be retained.                                 [optional]" name="pwhere" optional="False" type="text" />
+    <param label="--p-exclude-ids: --p-exclude-ids: / --p-no-exclude-ids If true, the features selected by `metadata` or `where` parameters will be excluded from the filtered table instead of being retained.       [default: False]" name="pexcludeids" selected="False" type="boolean" />
+    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
+    
+  </inputs>
 
-	</inputs>
-	<outputs>
-		<data format="qza" label="${tool.name} on ${on_string}: filteredtable.qza" name="ofilteredtable"/>
-	</outputs>
-	<help><![CDATA[
+  <outputs>
+    <data format="qza" label="${tool.name} on ${on_string}: filteredtable.qza" name="ofilteredtable" />
+    
+  </outputs>
+
+  <help><![CDATA[
 Filter features from table
-##########################
+###############################################################
 
 Filter features from table based on frequency and/or metadata. Any samples
 with a frequency of zero after feature filtering will also be removed. See
@@ -113,9 +130,9 @@
 -------
 filtered_table : FeatureTable[Frequency]
     The resulting feature table filtered by feature.
-	]]></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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