--- a/qiime2-2020.8/qiime_alignment_mafft-add.xml	Thu Sep 03 09:33:04 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,79 +0,0 @@
-<?xml version="1.0" ?>
-<tool id="qiime_alignment_mafft-add" name="qiime alignment mafft-add"
-      version="2020.8">
-  <description>Add sequences to multiple sequence alignment with MAFFT.</description>
-  <requirements>
-    <requirement type="package" version="2020.8">qiime2</requirement>
-  </requirements>
-  <command><![CDATA[
-qiime alignment mafft-add
-
---i-alignment=$ialignment
-
---i-sequences=$isequences
-
-#if str($pnthreads) != 'None':
---p-n-threads=$pnthreads
-#end if
-
-#if $pparttree:
- --p-parttree
-#end if
-
---o-expanded-alignment=oexpandedalignment
-
-#if str($examples) != 'None':
---examples=$examples
-#end if
-
-;
-cp oexpandedalignment.qza $oexpandedalignment
-
-  ]]></command>
-  <inputs>
-    <param format="qza,no_unzip.zip" label="--i-alignment: ARTIFACT FeatureData[AlignedSequence] The alignment to which sequences should be added. [required]" name="ialignment" optional="False" type="data" />
-    <param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT FeatureData[Sequence] The sequences to be added.                [required]" name="isequences" optional="False" type="data" />
-    <param label="--p-n-threads: " name="pnthreads" optional="True" type="select">
-      <option selected="True" value="None">Selection is Optional</option>
-      <option value="Int % Range(1">Int % Range(1</option>
-      <option value="None">None</option>
-    </param>
-    <param label="--p-parttree: --p-parttree: / --p-no-parttree This flag is required if the number of sequences being aligned are larger than 1000000. Disabled by default                             [default: False]" name="pparttree" selected="False" type="boolean" />
-    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
-    
-  </inputs>
-
-  <outputs>
-    <data format="qza" label="${tool.name} on ${on_string}: expandedalignment.qza" name="oexpandedalignment" />
-    
-  </outputs>
-
-  <help><![CDATA[
-Add sequences to multiple sequence alignment with MAFFT.
-###############################################################
-
-Add new sequences to an existing alignment with MAFFT.
-
-Parameters
-----------
-alignment : FeatureData[AlignedSequence]
-    The alignment to which sequences should be added.
-sequences : FeatureData[Sequence]
-    The sequences to be added.
-n_threads : Int % Range(1, None) | Str % Choices('auto'), optional
-    The number of threads. (Use `auto` to automatically use all available
-    cores)
-parttree : Bool, optional
-    This flag is required if the number of sequences being aligned are
-    larger than 1000000. Disabled by default
-
-Returns
--------
-expanded_alignment : FeatureData[AlignedSequence]
-    Alignment containing the provided aligned and unaligned sequences.
-  ]]></help>
-  <macros>
-    <import>qiime_citation.xml</import>
-  </macros>
-  <expand macro="qiime_citation"/>
-</tool>
\ No newline at end of file

--- a/qiime2-2020.8/qiime_alignment_mafft.xml	Thu Sep 03 09:33:04 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,74 +0,0 @@
-<?xml version="1.0" ?>
-<tool id="qiime_alignment_mafft" name="qiime alignment mafft"
-      version="2020.8">
-  <description>De novo multiple sequence alignment with MAFFT</description>
-  <requirements>
-    <requirement type="package" version="2020.8">qiime2</requirement>
-  </requirements>
-  <command><![CDATA[
-qiime alignment mafft
-
---i-sequences=$isequences
-
-#if str($pnthreads) != 'None':
---p-n-threads=$pnthreads
-#end if
-
-#if $pparttree:
- --p-parttree
-#end if
-
---o-alignment=oalignment
-
-#if str($examples) != 'None':
---examples=$examples
-#end if
-
-;
-cp oalignment.qza $oalignment
-
-  ]]></command>
-  <inputs>
-    <param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT FeatureData[Sequence] The sequences to be aligned.              [required]" name="isequences" optional="False" type="data" />
-    <param label="--p-n-threads: " name="pnthreads" optional="True" type="select">
-      <option selected="True" value="None">Selection is Optional</option>
-      <option value="Int % Range(1">Int % Range(1</option>
-      <option value="None">None</option>
-    </param>
-    <param label="--p-parttree: --p-parttree: / --p-no-parttree This flag is required if the number of sequences being aligned are larger than 1000000. Disabled by default                             [default: False]" name="pparttree" selected="False" type="boolean" />
-    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
-    
-  </inputs>
-
-  <outputs>
-    <data format="qza" label="${tool.name} on ${on_string}: alignment.qza" name="oalignment" />
-    
-  </outputs>
-
-  <help><![CDATA[
-De novo multiple sequence alignment with MAFFT
-###############################################################
-
-Perform de novo multiple sequence alignment using MAFFT.
-
-Parameters
-----------
-sequences : FeatureData[Sequence]
-    The sequences to be aligned.
-n_threads : Int % Range(1, None) | Str % Choices('auto'), optional
-    The number of threads. (Use `auto` to automatically use all available
-    cores)
-parttree : Bool, optional
-    This flag is required if the number of sequences being aligned are
-    larger than 1000000. Disabled by default
-
-Returns
--------
-alignment : FeatureData[AlignedSequence]
-    The aligned sequences.
-  ]]></help>
-  <macros>
-    <import>qiime_citation.xml</import>
-  </macros>
-  <expand macro="qiime_citation"/>
-</tool>
\ No newline at end of file

--- a/qiime2-2020.8/qiime_alignment_mask.xml	Thu Sep 03 09:33:04 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,74 +0,0 @@
-<?xml version="1.0" ?>
-<tool id="qiime_alignment_mask" name="qiime alignment mask"
-      version="2020.8">
-  <description>Positional conservation and gap filtering.</description>
-  <requirements>
-    <requirement type="package" version="2020.8">qiime2</requirement>
-  </requirements>
-  <command><![CDATA[
-qiime alignment mask
-
---i-alignment=$ialignment
-
---p-max-gap-frequency=$pmaxgapfrequency
-
---p-min-conservation=$pminconservation
-
---o-masked-alignment=omaskedalignment
-
-#if str($examples) != 'None':
---examples=$examples
-#end if
-
-;
-cp omaskedalignment.qza $omaskedalignment
-
-  ]]></command>
-  <inputs>
-    <param format="qza,no_unzip.zip" label="--i-alignment: ARTIFACT FeatureData[AlignedSequence] The alignment to be masked.               [required]" name="ialignment" optional="False" type="data" />
-    <param exclude_max="False" label="--p-max-gap-frequency: PROPORTION Range(0, 1, inclusive_end=True) The maximum relative frequency of gap characters in a column for the column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive), where 0.0 retains only those columns without gap characters, and 1.0 retains all columns regardless of gap character frequency. [default: 1.0]" max="1" min="0" name="pmaxgapfrequency" optional="True" type="float" value="1.0" />
-    <param exclude_max="False" label="--p-min-conservation: PROPORTION Range(0, 1, inclusive_end=True) The minimum relative frequency of at least one non-gap character in a column for that column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive). For example, if a value of 0.4 is provided, a column will only be retained if it contains at least one character that is present in at least 40% of the sequences. [default: 0.4]" max="1" min="0" name="pminconservation" optional="True" type="float" value="0.4" />
-    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
-    
-  </inputs>
-
-  <outputs>
-    <data format="qza" label="${tool.name} on ${on_string}: maskedalignment.qza" name="omaskedalignment" />
-    
-  </outputs>
-
-  <help><![CDATA[
-Positional conservation and gap filtering.
-###############################################################
-
-Mask (i.e., filter) unconserved and highly gapped columns from an
-alignment. Default min_conservation was chosen to reproduce the mask
-presented in Lane (1991).
-
-Parameters
-----------
-alignment : FeatureData[AlignedSequence]
-    The alignment to be masked.
-max_gap_frequency : Float % Range(0, 1, inclusive_end=True), optional
-    The maximum relative frequency of gap characters in a column for the
-    column to be retained. This relative frequency must be a number between
-    0.0 and 1.0 (inclusive), where 0.0 retains only those columns without
-    gap characters, and 1.0 retains all columns regardless of gap character
-    frequency.
-min_conservation : Float % Range(0, 1, inclusive_end=True), optional
-    The minimum relative frequency of at least one non-gap character in a
-    column for that column to be retained. This relative frequency must be
-    a number between 0.0 and 1.0 (inclusive). For example, if a value of
-    0.4 is provided, a column will only be retained if it contains at least
-    one character that is present in at least 40% of the sequences.
-
-Returns
--------
-masked_alignment : FeatureData[AlignedSequence]
-    The masked alignment.
-  ]]></help>
-  <macros>
-    <import>qiime_citation.xml</import>
-  </macros>
-  <expand macro="qiime_citation"/>
-</tool>
\ No newline at end of file

--- a/qiime2-2020.8/qiime_composition_add-pseudocount.xml	Thu Sep 03 09:33:04 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,59 +0,0 @@
-<?xml version="1.0" ?>
-<tool id="qiime_composition_add-pseudocount" name="qiime composition add-pseudocount"
-      version="2020.8">
-  <description>Add pseudocount to table</description>
-  <requirements>
-    <requirement type="package" version="2020.8">qiime2</requirement>
-  </requirements>
-  <command><![CDATA[
-qiime composition add-pseudocount
-
---i-table=$itable
-
---p-pseudocount=$ppseudocount
-
---o-composition-table=ocompositiontable
-
-#if str($examples) != 'None':
---examples=$examples
-#end if
-
-;
-cp ocompositiontable.qza $ocompositiontable
-
-  ]]></command>
-  <inputs>
-    <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table to which pseudocounts should be added.                                       [required]" name="itable" optional="False" type="data" />
-    <param label="--p-pseudocount: INTEGER The value to add to all counts in the feature table. [default: 1]" name="ppseudocount" optional="True" type="integer" value="1" />
-    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
-    
-  </inputs>
-
-  <outputs>
-    <data format="qza" label="${tool.name} on ${on_string}: compositiontable.qza" name="ocompositiontable" />
-    
-  </outputs>
-
-  <help><![CDATA[
-Add pseudocount to table
-###############################################################
-
-Increment all counts in table by pseudocount.
-
-Parameters
-----------
-table : FeatureTable[Frequency]
-    The feature table to which pseudocounts should be added.
-pseudocount : Int, optional
-    The value to add to all counts in the feature table.
-
-Returns
--------
-composition_table : FeatureTable[Composition]
-    The resulting feature table.
-  ]]></help>
-  <macros>
-    <import>qiime_citation.xml</import>
-  </macros>
-  <expand macro="qiime_citation"/>
-</tool>
\ No newline at end of file

--- a/qiime2-2020.8/qiime_composition_ancom.xml	Thu Sep 03 09:33:04 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,126 +0,0 @@
-<?xml version="1.0" ?>
-<tool id="qiime_composition_ancom" name="qiime composition ancom"
-      version="2020.8">
-  <description>Apply ANCOM to identify features that differ in abundance.</description>
-  <requirements>
-    <requirement type="package" version="2020.8">qiime2</requirement>
-  </requirements>
-  <command><![CDATA[
-qiime composition ancom
-
---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($input_files_mmetadatafile)
-# end if
-
-#if '__ob__' in str($mmetadatacolumn):
-  #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__ob__', '[')
-  #set $mmetadatacolumn = $mmetadatacolumn_temp
-#end if
-#if '__cb__' in str($mmetadatacolumn):
-  #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__cb__', ']')
-  #set $mmetadatacolumn = $mmetadatacolumn_temp
-#end if
-#if 'X' in str($mmetadatacolumn):
-  #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('X', '\\')
-  #set $mmetadatacolumn = $mmetadatacolumn_temp
-#end if
-#if '__sq__' in str($mmetadatacolumn):
-  #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__sq__', "'")
-  #set $mmetadatacolumn = $mmetadatacolumn_temp
-#end if
-#if '__db__' in str($mmetadatacolumn):
-  #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__db__', '"')
-  #set $mmetadatacolumn = $mmetadatacolumn_temp
-#end if
-
---m-metadata-column=$mmetadatacolumn
-
-
-#if str($ptransformfunction) != 'None':
---p-transform-function=$ptransformfunction
-#end if
-
-#if str($pdifferencefunction) != 'None':
---p-difference-function=$pdifferencefunction
-#end if
-
---o-visualization=ovisualization
-
-#if str($examples) != 'None':
---examples=$examples
-#end if
-
-;
-cp ocompositiontable.qza $ocompositiontable
-
-;
-qiime tools export  ovisualization.qzv --output-path out
-&& mkdir -p '$ovisualization.files_path'
-&& cp -r out/* '$ovisualization.files_path'
-&& mv '$ovisualization.files_path/index.html' '$ovisualization'
-
-  ]]></command>
-  <inputs>
-    <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Composition] The feature table to be used for ANCOM computation. [required]" name="itable" optional="False" type="data" />
-    <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
-      <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA" name="additional_input" optional="True" type="data" />
-    </repeat>
-    <param label="--m-metadata-column: COLUMN  MetadataColumn[Categorical] The categorical sample metadata column to test for differential abundance across.               [required]" name="mmetadatacolumn" optional="False" type="text" />
-    <param label="--p-transform-function: " name="ptransformfunction" optional="True" type="select">
-      <option selected="True" value="None">Selection is Optional</option>
-      <option value="sqrt">sqrt</option>
-      <option value="log">log</option>
-      <option value="clr">clr</option>
-    </param>
-    <param label="--p-difference-function: " name="pdifferencefunction" optional="True" type="select">
-      <option selected="True" value="None">Selection is Optional</option>
-      <option value="mean_difference">mean_difference</option>
-      <option value="f_statistic">f_statistic</option>
-    </param>
-    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
-    
-  </inputs>
-
-  <outputs>
-    <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
-    
-  </outputs>
-
-  <help><![CDATA[
-Apply ANCOM to identify features that differ in abundance.
-###############################################################
-
-Apply Analysis of Composition of Microbiomes (ANCOM) to identify features
-that are differentially abundant across groups.
-
-Parameters
-----------
-table : FeatureTable[Composition]
-    The feature table to be used for ANCOM computation.
-metadata : MetadataColumn[Categorical]
-    The categorical sample metadata column to test for differential
-    abundance across.
-transform_function : Str % Choices('sqrt', 'log', 'clr'), optional
-    The method applied to transform feature values before generating
-    volcano plots.
-difference_function : Str % Choices('mean_difference', 'f_statistic'), optional
-    The method applied to visualize fold difference in feature abundances
-    across groups for volcano plots.
-
-Returns
--------
-visualization : Visualization
-  ]]></help>
-  <macros>
-    <import>qiime_citation.xml</import>
-  </macros>
-  <expand macro="qiime_citation"/>
-</tool>
\ No newline at end of file

--- a/qiime2-2020.8/qiime_cutadapt_demux-paired.xml	Thu Sep 03 09:33:04 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,170 +0,0 @@
-<?xml version="1.0" ?>
-<tool id="qiime_cutadapt_demux-paired" name="qiime cutadapt demux-paired"
-      version="2020.8">
-  <description>Demultiplex paired-end sequence data with barcodes in- sequence.</description>
-  <requirements>
-    <requirement type="package" version="2020.8">qiime2</requirement>
-  </requirements>
-  <command><![CDATA[
-qiime cutadapt demux-paired
-
---i-seqs=$iseqs
-# if $input_files_mforwardbarcodesfile:
-  # 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-forward-barcodes-file=' + d['additional_input'].__getattr__('file_name')
-    # end for
-    # return $file_list
-  # end def
---m-forward-barcodes-file=$list_dict_to_string($input_files_mforwardbarcodesfile)
-# end if
-
-#if '__ob__' in str($mforwardbarcodescolumn):
-  #set $mforwardbarcodescolumn_temp = $mforwardbarcodescolumn.replace('__ob__', '[')
-  #set $mforwardbarcodescolumn = $mforwardbarcodescolumn_temp
-#end if
-#if '__cb__' in str($mforwardbarcodescolumn):
-  #set $mforwardbarcodescolumn_temp = $mforwardbarcodescolumn.replace('__cb__', ']')
-  #set $mforwardbarcodescolumn = $mforwardbarcodescolumn_temp
-#end if
-#if 'X' in str($mforwardbarcodescolumn):
-  #set $mforwardbarcodescolumn_temp = $mforwardbarcodescolumn.replace('X', '\\')
-  #set $mforwardbarcodescolumn = $mforwardbarcodescolumn_temp
-#end if
-#if '__sq__' in str($mforwardbarcodescolumn):
-  #set $mforwardbarcodescolumn_temp = $mforwardbarcodescolumn.replace('__sq__', "'")
-  #set $mforwardbarcodescolumn = $mforwardbarcodescolumn_temp
-#end if
-#if '__db__' in str($mforwardbarcodescolumn):
-  #set $mforwardbarcodescolumn_temp = $mforwardbarcodescolumn.replace('__db__', '"')
-  #set $mforwardbarcodescolumn = $mforwardbarcodescolumn_temp
-#end if
-
---m-forward-barcodes-column=$mforwardbarcodescolumn
-
-# if $input_files_mreversebarcodesfile:
-  # 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-reverse-barcodes-file=' + d['additional_input'].__getattr__('file_name')
-    # end for
-    # return $file_list
-  # end def
---m-reverse-barcodes-file=$list_dict_to_string($input_files_mreversebarcodesfile)
-# end if
-
-#if '__ob__' in str($mreversebarcodescolumn):
-  #set $mreversebarcodescolumn_temp = $mreversebarcodescolumn.replace('__ob__', '[')
-  #set $mreversebarcodescolumn = $mreversebarcodescolumn_temp
-#end if
-#if '__cb__' in str($mreversebarcodescolumn):
-  #set $mreversebarcodescolumn_temp = $mreversebarcodescolumn.replace('__cb__', ']')
-  #set $mreversebarcodescolumn = $mreversebarcodescolumn_temp
-#end if
-#if 'X' in str($mreversebarcodescolumn):
-  #set $mreversebarcodescolumn_temp = $mreversebarcodescolumn.replace('X', '\\')
-  #set $mreversebarcodescolumn = $mreversebarcodescolumn_temp
-#end if
-#if '__sq__' in str($mreversebarcodescolumn):
-  #set $mreversebarcodescolumn_temp = $mreversebarcodescolumn.replace('__sq__', "'")
-  #set $mreversebarcodescolumn = $mreversebarcodescolumn_temp
-#end if
-#if '__db__' in str($mreversebarcodescolumn):
-  #set $mreversebarcodescolumn_temp = $mreversebarcodescolumn.replace('__db__', '"')
-  #set $mreversebarcodescolumn = $mreversebarcodescolumn_temp
-#end if
-
-#if str($mreversebarcodescolumn):
-  --m-reverse-barcodes-column=$mreversebarcodescolumn
-#end if
-
---p-error-rate=$perrorrate
-
---p-minimum-length=$pminimumlength
-
-#if $pmixedorientation:
- --p-mixed-orientation
-#end if
-
---o-per-sample-sequences=opersamplesequences
-
---o-untrimmed-sequences=ountrimmedsequences
-
-#if str($examples) != 'None':
---examples=$examples
-#end if
-
-;
-cp ountrimmedsequences.qza $ountrimmedsequences
-
-  ]]></command>
-  <inputs>
-    <param format="qza,no_unzip.zip" label="--i-seqs: ARTIFACT MultiplexedPairedEndBarcodeInSequence The paired-end sequences to be demultiplexed. [required]" name="iseqs" optional="False" type="data" />
-    <repeat name="input_files_mforwardbarcodesfile" optional="True" title="--m-forward-barcodes-file">
-      <param format="tabular,qza,no_unzip.zip" label="--m-forward-barcodes-file: METADATA" name="additional_input" optional="True" type="data" />
-    </repeat>
-    <param label="--m-forward-barcodes-column: COLUMN  MetadataColumn[Categorical] The sample metadata column listing the per-sample barcodes for the forward reads.           [required]" name="mforwardbarcodescolumn" optional="False" type="text" />
-    <repeat name="input_files_mreversebarcodesfile" optional="True" title="--m-reverse-barcodes-file">
-      <param format="tabular,qza,no_unzip.zip" label="--m-reverse-barcodes-file: METADATA" name="additional_input" optional="True" type="data" />
-    </repeat>
-    <param label="--m-reverse-barcodes-column: COLUMN  MetadataColumn[Categorical] The sample metadata column listing the per-sample barcodes for the reverse reads.           [optional]" name="mreversebarcodescolumn" optional="False" type="text" />
-    <param exclude_max="False" label="--p-error-rate: PROPORTION Range(0, 1, inclusive_end=True) The level of error tolerance, specified as the maximum allowable error rate.         [default: 0.1]" max="1" min="0" name="perrorrate" optional="True" type="float" value="0.1" />
-    <param label="--p-minimum-length: INTEGER Range(1, None)        Discard reads shorter than specified value. Note, the cutadapt default of 0 has been overridden, because that value produces empty sequence records. [default: 1]" min="1" name="pminimumlength" optional="True" type="integer" value="1" />
-    <param label="--p-mixed-orientation: --p-mixed-orientation: / --p-no-mixed-orientation Handle demultiplexing of mixed orientation reads (i.e. when forward and reverse reads coexist in the same file).                         [default: False]" name="pmixedorientation" selected="False" type="boolean" />
-    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
-    
-  </inputs>
-
-  <outputs>
-    <data format="qza" label="${tool.name} on ${on_string}: persamplesequences.qza" name="opersamplesequences" />
-    <data format="qza" label="${tool.name} on ${on_string}: untrimmedsequences.qza" name="ountrimmedsequences" />
-    
-  </outputs>
-
-  <help><![CDATA[
-Demultiplex paired-end sequence data with barcodes in- sequence.
-###############################################################
-
-Demultiplex sequence data (i.e., map barcode reads to sample ids). Barcodes
-are expected to be located within the sequence data (versus the header, or
-a separate barcode file).
-
-Parameters
-----------
-seqs : MultiplexedPairedEndBarcodeInSequence
-    The paired-end sequences to be demultiplexed.
-forward_barcodes : MetadataColumn[Categorical]
-    The sample metadata column listing the per-sample barcodes for the
-    forward reads.
-reverse_barcodes : MetadataColumn[Categorical], optional
-    The sample metadata column listing the per-sample barcodes for the
-    reverse reads.
-error_rate : Float % Range(0, 1, inclusive_end=True), optional
-    The level of error tolerance, specified as the maximum allowable error
-    rate.
-batch_size : Int % Range(0, None), optional
-    The number of samples cutadapt demultiplexes concurrently.
-    Demultiplexing in smaller batches will yield the same result with
-    marginal speed loss, and may solve "too many files" errors related to
-    sample quantity. Set to "0" to process all samples at once.
-minimum_length : Int % Range(1, None), optional
-    Discard reads shorter than specified value. Note, the cutadapt default
-    of 0 has been overridden, because that value produces empty sequence
-    records.
-mixed_orientation : Bool, optional
-    Handle demultiplexing of mixed orientation reads (i.e. when forward and
-    reverse reads coexist in the same file).
-
-Returns
--------
-per_sample_sequences : SampleData[PairedEndSequencesWithQuality]
-    The resulting demultiplexed sequences.
-untrimmed_sequences : MultiplexedPairedEndBarcodeInSequence
-    The sequences that were unmatched to barcodes.
-  ]]></help>
-  <macros>
-    <import>qiime_citation.xml</import>
-  </macros>
-  <expand macro="qiime_citation"/>
-</tool>
\ No newline at end of file

--- a/qiime2-2020.8/qiime_cutadapt_demux-single.xml	Thu Sep 03 09:33:04 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,120 +0,0 @@
-<?xml version="1.0" ?>
-<tool id="qiime_cutadapt_demux-single" name="qiime cutadapt demux-single"
-      version="2020.8">
-  <description>Demultiplex single-end sequence data with barcodes in- sequence.</description>
-  <requirements>
-    <requirement type="package" version="2020.8">qiime2</requirement>
-  </requirements>
-  <command><![CDATA[
-qiime cutadapt demux-single
-
---i-seqs=$iseqs
-# if $input_files_mbarcodesfile:
-  # 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-barcodes-file=' + d['additional_input'].__getattr__('file_name')
-    # end for
-    # return $file_list
-  # end def
---m-barcodes-file=$list_dict_to_string($input_files_mbarcodesfile)
-# end if
-
-#if '__ob__' in str($mbarcodescolumn):
-  #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('__ob__', '[')
-  #set $mbarcodescolumn = $mbarcodescolumn_temp
-#end if
-#if '__cb__' in str($mbarcodescolumn):
-  #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('__cb__', ']')
-  #set $mbarcodescolumn = $mbarcodescolumn_temp
-#end if
-#if 'X' in str($mbarcodescolumn):
-  #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('X', '\\')
-  #set $mbarcodescolumn = $mbarcodescolumn_temp
-#end if
-#if '__sq__' in str($mbarcodescolumn):
-  #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('__sq__', "'")
-  #set $mbarcodescolumn = $mbarcodescolumn_temp
-#end if
-#if '__db__' in str($mbarcodescolumn):
-  #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('__db__', '"')
-  #set $mbarcodescolumn = $mbarcodescolumn_temp
-#end if
-
---m-barcodes-column=$mbarcodescolumn
-
-
---p-error-rate=$perrorrate
-
---p-minimum-length=$pminimumlength
-
---o-per-sample-sequences=opersamplesequences
-
---o-untrimmed-sequences=ountrimmedsequences
-
-#if str($examples) != 'None':
---examples=$examples
-#end if
-
-;
-cp ountrimmedsequences.qza $ountrimmedsequences
-
-  ]]></command>
-  <inputs>
-    <param format="qza,no_unzip.zip" label="--i-seqs: ARTIFACT MultiplexedSingleEndBarcodeInSequence The single-end sequences to be demultiplexed. [required]" name="iseqs" optional="False" type="data" />
-    <repeat name="input_files_mbarcodesfile" optional="True" title="--m-barcodes-file">
-      <param format="tabular,qza,no_unzip.zip" label="--m-barcodes-file: METADATA" name="additional_input" optional="True" type="data" />
-    </repeat>
-    <param label="--m-barcodes-column: COLUMN  MetadataColumn[Categorical] The sample metadata column listing the per-sample barcodes.                                 [required]" name="mbarcodescolumn" optional="False" type="text" />
-    <param exclude_max="False" label="--p-error-rate: PROPORTION Range(0, 1, inclusive_end=True) The level of error tolerance, specified as the maximum allowable error rate. The default value specified by cutadapt is 0.1 (=10%), which is greater than `demux emp-*`, which is 0.0 (=0%). [default: 0.1]" max="1" min="0" name="perrorrate" optional="True" type="float" value="0.1" />
-    <param label="--p-minimum-length: INTEGER Range(1, None)        Discard reads shorter than specified value. Note, the cutadapt default of 0 has been overridden, because that value produces empty sequence records. [default: 1]" min="1" name="pminimumlength" optional="True" type="integer" value="1" />
-    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
-    
-  </inputs>
-
-  <outputs>
-    <data format="qza" label="${tool.name} on ${on_string}: persamplesequences.qza" name="opersamplesequences" />
-    <data format="qza" label="${tool.name} on ${on_string}: untrimmedsequences.qza" name="ountrimmedsequences" />
-    
-  </outputs>
-
-  <help><![CDATA[
-Demultiplex single-end sequence data with barcodes in- sequence.
-###############################################################
-
-Demultiplex sequence data (i.e., map barcode reads to sample ids). Barcodes
-are expected to be located within the sequence data (versus the header, or
-a separate barcode file).
-
-Parameters
-----------
-seqs : MultiplexedSingleEndBarcodeInSequence
-    The single-end sequences to be demultiplexed.
-barcodes : MetadataColumn[Categorical]
-    The sample metadata column listing the per-sample barcodes.
-error_rate : Float % Range(0, 1, inclusive_end=True), optional
-    The level of error tolerance, specified as the maximum allowable error
-    rate. The default value specified by cutadapt is 0.1 (=10%), which is
-    greater than `demux emp-*`, which is 0.0 (=0%).
-batch_size : Int % Range(0, None), optional
-    The number of samples cutadapt demultiplexes concurrently.
-    Demultiplexing in smaller batches will yield the same result with
-    marginal speed loss, and may solve "too many files" errors related to
-    sample quantity. Set to "0" to process all samples at once.
-minimum_length : Int % Range(1, None), optional
-    Discard reads shorter than specified value. Note, the cutadapt default
-    of 0 has been overridden, because that value produces empty sequence
-    records.
-
-Returns
--------
-per_sample_sequences : SampleData[SequencesWithQuality]
-    The resulting demultiplexed sequences.
-untrimmed_sequences : MultiplexedSingleEndBarcodeInSequence
-    The sequences that were unmatched to barcodes.
-  ]]></help>
-  <macros>
-    <import>qiime_citation.xml</import>
-  </macros>
-  <expand macro="qiime_citation"/>
-</tool>
\ No newline at end of file

--- a/qiime2-2020.8/qiime_cutadapt_trim-paired.xml	Thu Sep 03 09:33:04 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,219 +0,0 @@
-<?xml version="1.0" ?>
-<tool id="qiime_cutadapt_trim-paired" name="qiime cutadapt trim-paired"
-      version="2020.8">
-  <description>Find and remove adapters in demultiplexed paired-end sequences.</description>
-  <requirements>
-    <requirement type="package" version="2020.8">qiime2</requirement>
-  </requirements>
-  <command><![CDATA[
-qiime cutadapt trim-paired
-
---i-demultiplexed-sequences=$idemultiplexedsequences
-
---p-cores=$pcores
-
-#if str($padapterf):
-  --p-adapter-f=$padapterf
-#end if
-#if str($pfrontf):
-  --p-front-f=$pfrontf
-#end if
-#if '__ob__' in str($panywheref):
-  #set $panywheref_temp = $panywheref.replace('__ob__', '[')
-  #set $panywheref = $panywheref_temp
-#end if
-#if '__cb__' in str($panywheref):
-  #set $panywheref_temp = $panywheref.replace('__cb__', ']')
-  #set $panywheref = $panywheref_temp
-#end if
-#if 'X' in str($panywheref):
-  #set $panywheref_temp = $panywheref.replace('X', '\\')
-  #set $panywheref = $panywheref_temp
-#end if
-#if '__sq__' in str($panywheref):
-  #set $panywheref_temp = $panywheref.replace('__sq__', "'")
-  #set $panywheref = $panywheref_temp
-#end if
-#if '__db__' in str($panywheref):
-  #set $panywheref_temp = $panywheref.replace('__db__', '"')
-  #set $panywheref = $panywheref_temp
-#end if
-
-#if str($panywheref):
-  --p-anywhere-f=$panywheref
-#end if
-
-#if str($padapterr):
-  --p-adapter-r=$padapterr
-#end if
-#if str($pfrontr):
-  --p-front-r=$pfrontr
-#end if
-#if '__ob__' in str($panywherer):
-  #set $panywherer_temp = $panywherer.replace('__ob__', '[')
-  #set $panywherer = $panywherer_temp
-#end if
-#if '__cb__' in str($panywherer):
-  #set $panywherer_temp = $panywherer.replace('__cb__', ']')
-  #set $panywherer = $panywherer_temp
-#end if
-#if 'X' in str($panywherer):
-  #set $panywherer_temp = $panywherer.replace('X', '\\')
-  #set $panywherer = $panywherer_temp
-#end if
-#if '__sq__' in str($panywherer):
-  #set $panywherer_temp = $panywherer.replace('__sq__', "'")
-  #set $panywherer = $panywherer_temp
-#end if
-#if '__db__' in str($panywherer):
-  #set $panywherer_temp = $panywherer.replace('__db__', '"')
-  #set $panywherer = $panywherer_temp
-#end if
-
-#if str($panywherer):
-  --p-anywhere-r=$panywherer
-#end if
-
---p-error-rate=$perrorrate
-
-#if $pnoindels:
- --p-no-indels
-#end if
-
---p-times=$ptimes
-
---p-overlap=$poverlap
-
-#if $pmatchreadwildcards:
- --p-match-read-wildcards
-#end if
-
-#if $pnomatchadapterwildcards:
- --p-no-match-adapter-wildcards
-#end if
-
---p-minimum-length=$pminimumlength
-
-#if $pdiscarduntrimmed:
- --p-discard-untrimmed
-#end if
-
---o-trimmed-sequences=otrimmedsequences
-
-#if str($examples) != 'None':
---examples=$examples
-#end if
-
-;
-cp otrimmedsequences.qza $otrimmedsequences
-
-  ]]></command>
-  <inputs>
-    <param format="qza,no_unzip.zip" label="--i-demultiplexed-sequences: ARTIFACT SampleData[PairedEndSequencesWithQuality] The paired-end sequences to be trimmed.   [required]" name="idemultiplexedsequences" optional="False" type="data" />
-    <param label="--p-adapter-f: TEXT...   Sequence of an adapter ligated to the 3\' end. The List[Str]             adapter and any subsequent bases are trimmed. If a `$` is appended, the adapter is only found if it is at the end of the read. Search in forward read. If your sequence of interest is \'framed\' by a 5\' and a 3\' adapter, use this parameter to define a \'linked\' primer - see https://cutadapt.readthedocs.io for complete details.                         [optional]" name="padapterf" optional="False" type="text" value="False" />
-    <param label="--p-front-f: TEXT...     Sequence of an adapter ligated to the 5\' end. The List[Str]             adapter and any preceding bases are trimmed. Partial matches at the 5\' end are allowed. If a `^` character is prepended, the adapter is only found if it is at the beginning of the read. Search in forward read.                             [optional]" name="pfrontf" optional="False" type="text" />
-    <param label="--p-anywhere-f: TEXT...  Sequence of an adapter that may be ligated to the List[Str]             5\' or 3\' end. Both types of matches as described under `adapter` and `front` are allowed. If the first base of the read is part of the match, the behavior is as with `front`, otherwise as with `adapter`. This option is mostly for rescuing failed library preparations - do not use if you know which end your adapter was ligated to. Search in forward read.                                     [optional]" name="panywheref" optional="False" type="text" />
-    <param label="--p-adapter-r: TEXT...   Sequence of an adapter ligated to the 3\' end. The List[Str]             adapter and any subsequent bases are trimmed. If a `$` is appended, the adapter is only found if it is at the end of the read. Search in reverse read. If your sequence of interest is \'framed\' by a 5\' and a 3\' adapter, use this parameter to define a \'linked\' primer - see https://cutadapt.readthedocs.io for complete details.                         [optional]" name="padapterr" optional="False" type="text" value="False" />
-    <param label="--p-front-r: TEXT...     Sequence of an adapter ligated to the 5\' end. The List[Str]             adapter and any preceding bases are trimmed. Partial matches at the 5\' end are allowed. If a `^` character is prepended, the adapter is only found if it is at the beginning of the read. Search in reverse read.                             [optional]" name="pfrontr" optional="False" type="text" />
-    <param label="--p-anywhere-r: TEXT...  Sequence of an adapter that may be ligated to the List[Str]             5\' or 3\' end. Both types of matches as described under `adapter` and `front` are allowed. If the first base of the read is part of the match, the behavior is as with `front`, otherwise as with `adapter`. This option is mostly for rescuing failed library preparations - do not use if you know which end your adapter was ligated to. Search in reverse read.                                     [optional]" name="panywherer" optional="False" type="text" />
-    <param exclude_max="False" label="--p-error-rate: PROPORTION Range(0, 1, inclusive_end=True) Maximum allowed error rate.           [default: 0.1]" max="1" min="0" name="perrorrate" optional="True" type="float" value="0.1" />
-    <param label="--p-no-indels: Do not allow insertions or deletions of bases when matching adapters.                   [default: True]" name="pnoindels" selected="False" type="boolean" />
-    <param label="--p-times: INTEGER       Remove multiple occurrences of an adapter if it is Range(1, None)        repeated, up to `times` times.          [default: 1]" min="1" name="ptimes" optional="True" type="integer" value="1" />
-    <param label="--p-overlap: INTEGER     Require at least `overlap` bases of overlap between Range(1, None)        read and adapter for an adapter to be found. [default: 3]" min="1" name="poverlap" optional="True" type="integer" value="3" />
-    <param label="--p-match-read-wildcards: --p-match-read-wildcards: / --p-no-match-read-wildcards Interpret IUPAC wildcards (e.g., N) in reads. [default: False]" name="pmatchreadwildcards" selected="False" type="boolean" />
-    <param label="--p-no-match-adapter-wildcards: Do not interpret IUPAC wildcards (e.g., N) in adapters. [default: True]" name="pnomatchadapterwildcards" selected="False" type="boolean" />
-    <param label="--p-minimum-length: INTEGER Range(1, None)        Discard reads shorter than specified value. Note, the cutadapt default of 0 has been overridden, because that value produces empty sequence records. [default: 1]" min="1" name="pminimumlength" optional="True" type="integer" value="1" />
-    <param label="--p-discard-untrimmed: --p-discard-untrimmed: / --p-no-discard-untrimmed Discard reads in which no adapter was found. [default: False]" name="pdiscarduntrimmed" selected="False" type="boolean" />
-    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
-    
-  </inputs>
-
-  <outputs>
-    <data format="qza" label="${tool.name} on ${on_string}: trimmedsequences.qza" name="otrimmedsequences" />
-    
-  </outputs>
-
-  <help><![CDATA[
-Find and remove adapters in demultiplexed paired-end sequences.
-###############################################################
-
-Search demultiplexed paired-end sequences for adapters and remove them. The
-parameter descriptions in this method are adapted from the official
-cutadapt docs - please see those docs at https://cutadapt.readthedocs.io
-for complete details.
-
-Parameters
-----------
-demultiplexed_sequences : SampleData[PairedEndSequencesWithQuality]
-    The paired-end sequences to be trimmed.
-cores : Int % Range(1, None), optional
-    Number of CPU cores to use.
-adapter_f : List[Str], optional
-    Sequence of an adapter ligated to the 3' end. The adapter and any
-    subsequent bases are trimmed. If a `$` is appended, the adapter is only
-    found if it is at the end of the read. Search in forward read. If your
-    sequence of interest is "framed" by a 5' and a 3' adapter, use this
-    parameter to define a "linked" primer - see
-    https://cutadapt.readthedocs.io for complete details.
-front_f : List[Str], optional
-    Sequence of an adapter ligated to the 5' end. The adapter and any
-    preceding bases are trimmed. Partial matches at the 5' end are allowed.
-    If a `^` character is prepended, the adapter is only found if it is at
-    the beginning of the read. Search in forward read.
-anywhere_f : List[Str], optional
-    Sequence of an adapter that may be ligated to the 5' or 3' end. Both
-    types of matches as described under `adapter` and `front` are allowed.
-    If the first base of the read is part of the match, the behavior is as
-    with `front`, otherwise as with `adapter`. This option is mostly for
-    rescuing failed library preparations - do not use if you know which end
-    your adapter was ligated to. Search in forward read.
-adapter_r : List[Str], optional
-    Sequence of an adapter ligated to the 3' end. The adapter and any
-    subsequent bases are trimmed. If a `$` is appended, the adapter is only
-    found if it is at the end of the read. Search in reverse read. If your
-    sequence of interest is "framed" by a 5' and a 3' adapter, use this
-    parameter to define a "linked" primer - see
-    https://cutadapt.readthedocs.io for complete details.
-front_r : List[Str], optional
-    Sequence of an adapter ligated to the 5' end. The adapter and any
-    preceding bases are trimmed. Partial matches at the 5' end are allowed.
-    If a `^` character is prepended, the adapter is only found if it is at
-    the beginning of the read. Search in reverse read.
-anywhere_r : List[Str], optional
-    Sequence of an adapter that may be ligated to the 5' or 3' end. Both
-    types of matches as described under `adapter` and `front` are allowed.
-    If the first base of the read is part of the match, the behavior is as
-    with `front`, otherwise as with `adapter`. This option is mostly for
-    rescuing failed library preparations - do not use if you know which end
-    your adapter was ligated to. Search in reverse read.
-error_rate : Float % Range(0, 1, inclusive_end=True), optional
-    Maximum allowed error rate.
-indels : Bool, optional
-    Allow insertions or deletions of bases when matching adapters.
-times : Int % Range(1, None), optional
-    Remove multiple occurrences of an adapter if it is repeated, up to
-    `times` times.
-overlap : Int % Range(1, None), optional
-    Require at least `overlap` bases of overlap between read and adapter
-    for an adapter to be found.
-match_read_wildcards : Bool, optional
-    Interpret IUPAC wildcards (e.g., N) in reads.
-match_adapter_wildcards : Bool, optional
-    Interpret IUPAC wildcards (e.g., N) in adapters.
-minimum_length : Int % Range(1, None), optional
-    Discard reads shorter than specified value. Note, the cutadapt default
-    of 0 has been overridden, because that value produces empty sequence
-    records.
-discard_untrimmed : Bool, optional
-    Discard reads in which no adapter was found.
-
-Returns
--------
-trimmed_sequences : SampleData[PairedEndSequencesWithQuality]
-    The resulting trimmed sequences.
-  ]]></help>
-  <macros>
-    <import>qiime_citation.xml</import>
-  </macros>
-  <expand macro="qiime_citation"/>
-</tool>
\ No newline at end of file

--- a/qiime2-2020.8/qiime_cutadapt_trim-single.xml	Thu Sep 03 09:33:04 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,167 +0,0 @@
-<?xml version="1.0" ?>
-<tool id="qiime_cutadapt_trim-single" name="qiime cutadapt trim-single"
-      version="2020.8">
-  <description>Find and remove adapters in demultiplexed single-end sequences.</description>
-  <requirements>
-    <requirement type="package" version="2020.8">qiime2</requirement>
-  </requirements>
-  <command><![CDATA[
-qiime cutadapt trim-single
-
---i-demultiplexed-sequences=$idemultiplexedsequences
-
---p-cores=$pcores
-
-#if $padapter:
- --p-adapter
-#end if
-
-#if str($pfront):
-  --p-front=$pfront
-#end if
-#if '__ob__' in str($panywhere):
-  #set $panywhere_temp = $panywhere.replace('__ob__', '[')
-  #set $panywhere = $panywhere_temp
-#end if
-#if '__cb__' in str($panywhere):
-  #set $panywhere_temp = $panywhere.replace('__cb__', ']')
-  #set $panywhere = $panywhere_temp
-#end if
-#if 'X' in str($panywhere):
-  #set $panywhere_temp = $panywhere.replace('X', '\\')
-  #set $panywhere = $panywhere_temp
-#end if
-#if '__sq__' in str($panywhere):
-  #set $panywhere_temp = $panywhere.replace('__sq__', "'")
-  #set $panywhere = $panywhere_temp
-#end if
-#if '__db__' in str($panywhere):
-  #set $panywhere_temp = $panywhere.replace('__db__', '"')
-  #set $panywhere = $panywhere_temp
-#end if
-
-#if str($panywhere):
-  --p-anywhere=$panywhere
-#end if
-
---p-error-rate=$perrorrate
-
-#if $pnoindels:
- --p-no-indels
-#end if
-
---p-times=$ptimes
-
---p-overlap=$poverlap
-
-#if $pmatchreadwildcards:
- --p-match-read-wildcards
-#end if
-
-#if $pnomatchadapterwildcards:
- --p-no-match-adapter-wildcards
-#end if
-
---p-minimum-length=$pminimumlength
-
-#if $pdiscarduntrimmed:
- --p-discard-untrimmed
-#end if
-
---o-trimmed-sequences=otrimmedsequences
-
-#if str($examples) != 'None':
---examples=$examples
-#end if
-
-;
-cp otrimmedsequences.qza $otrimmedsequences
-
-  ]]></command>
-  <inputs>
-    <param format="qza,no_unzip.zip" label="--i-demultiplexed-sequences: ARTIFACT SampleData[SequencesWithQuality] The single-end sequences to be trimmed.     [required]" name="idemultiplexedsequences" optional="False" type="data" />
-    <param label="--p-adapter: --p-adapter: TEXT...   Sequence of an adapter ligated to the 3\' end. The List[Str]           adapter and any subsequent bases are trimmed. If a `$` is appended, the adapter is only found if it is at the end of the read. If your sequence of interest is \'framed\' by a 5\' and a 3\' adapter, use this parameter to define a \'linked\' primer - see https://cutadapt.readthedocs.io for complete details. [optional]" name="padapter" selected="False" type="boolean" />
-    <param label="--p-front: TEXT...     Sequence of an adapter ligated to the 5\' end. The List[Str]           adapter and any preceding bases are trimmed. Partial matches at the 5\' end are allowed. If a `^` character is prepended, the adapter is only found if it is at the beginning of the read.                  [optional]" name="pfront" optional="False" type="text" />
-    <param label="--p-anywhere: TEXT...  Sequence of an adapter that may be ligated to the 5\' List[Str]           or 3\' end. Both types of matches as described under `adapter` and `front` are allowed. If the first base of the read is part of the match, the behavior is as with `front`, otherwise as with `adapter`. This option is mostly for rescuing failed library preparations - do not use if you know which end your adapter was ligated to.                                 [optional]" name="panywhere" optional="False" type="text" />
-    <param exclude_max="False" label="--p-error-rate: PROPORTION Range(0, 1, inclusive_end=True) Maximum allowed error rate.             [default: 0.1]" max="1" min="0" name="perrorrate" optional="True" type="float" value="0.1" />
-    <param label="--p-no-indels: Do not allow insertions or deletions of bases when matching adapters.                              [default: True]" name="pnoindels" selected="False" type="boolean" />
-    <param label="--p-times: INTEGER     Remove multiple occurrences of an adapter if it is Range(1, None)      repeated, up to `times` times.            [default: 1]" min="1" name="ptimes" optional="True" type="integer" value="1" />
-    <param label="--p-overlap: INTEGER   Require at least `overlap` bases of overlap between Range(1, None)      read and adapter for an adapter to be found. [default: 3]" min="1" name="poverlap" optional="True" type="integer" value="3" />
-    <param label="--p-match-read-wildcards: --p-match-read-wildcards: / --p-no-match-read-wildcards Interpret IUPAC wildcards (e.g., N) in reads. [default: False]" name="pmatchreadwildcards" selected="False" type="boolean" />
-    <param label="--p-no-match-adapter-wildcards: Do not interpret IUPAC wildcards (e.g., N) in adapters. [default: True]" name="pnomatchadapterwildcards" selected="False" type="boolean" />
-    <param label="--p-minimum-length: INTEGER Range(1, None)      Discard reads shorter than specified value. Note, the cutadapt default of 0 has been overridden, because that value produces empty sequence records. [default: 1]" min="1" name="pminimumlength" optional="True" type="integer" value="1" />
-    <param label="--p-discard-untrimmed: --p-discard-untrimmed: / --p-no-discard-untrimmed Discard reads in which no adapter was found. [default: False]" name="pdiscarduntrimmed" selected="False" type="boolean" />
-    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
-    
-  </inputs>
-
-  <outputs>
-    <data format="qza" label="${tool.name} on ${on_string}: trimmedsequences.qza" name="otrimmedsequences" />
-    
-  </outputs>
-
-  <help><![CDATA[
-Find and remove adapters in demultiplexed single-end sequences.
-###############################################################
-
-Search demultiplexed single-end sequences for adapters and remove them. The
-parameter descriptions in this method are adapted from the official
-cutadapt docs - please see those docs at https://cutadapt.readthedocs.io
-for complete details.
-
-Parameters
-----------
-demultiplexed_sequences : SampleData[SequencesWithQuality]
-    The single-end sequences to be trimmed.
-cores : Int % Range(1, None), optional
-    Number of CPU cores to use.
-adapter : List[Str], optional
-    Sequence of an adapter ligated to the 3' end. The adapter and any
-    subsequent bases are trimmed. If a `$` is appended, the adapter is only
-    found if it is at the end of the read. If your sequence of interest is
-    "framed" by a 5' and a 3' adapter, use this parameter to define a
-    "linked" primer - see https://cutadapt.readthedocs.io for complete
-    details.
-front : List[Str], optional
-    Sequence of an adapter ligated to the 5' end. The adapter and any
-    preceding bases are trimmed. Partial matches at the 5' end are allowed.
-    If a `^` character is prepended, the adapter is only found if it is at
-    the beginning of the read.
-anywhere : List[Str], optional
-    Sequence of an adapter that may be ligated to the 5' or 3' end. Both
-    types of matches as described under `adapter` and `front` are allowed.
-    If the first base of the read is part of the match, the behavior is as
-    with `front`, otherwise as with `adapter`. This option is mostly for
-    rescuing failed library preparations - do not use if you know which end
-    your adapter was ligated to.
-error_rate : Float % Range(0, 1, inclusive_end=True), optional
-    Maximum allowed error rate.
-indels : Bool, optional
-    Allow insertions or deletions of bases when matching adapters.
-times : Int % Range(1, None), optional
-    Remove multiple occurrences of an adapter if it is repeated, up to
-    `times` times.
-overlap : Int % Range(1, None), optional
-    Require at least `overlap` bases of overlap between read and adapter
-    for an adapter to be found.
-match_read_wildcards : Bool, optional
-    Interpret IUPAC wildcards (e.g., N) in reads.
-match_adapter_wildcards : Bool, optional
-    Interpret IUPAC wildcards (e.g., N) in adapters.
-minimum_length : Int % Range(1, None), optional
-    Discard reads shorter than specified value. Note, the cutadapt default
-    of 0 has been overridden, because that value produces empty sequence
-    records.
-discard_untrimmed : Bool, optional
-    Discard reads in which no adapter was found.
-
-Returns
--------
-trimmed_sequences : SampleData[SequencesWithQuality]
-    The resulting trimmed sequences.
-  ]]></help>
-  <macros>
-    <import>qiime_citation.xml</import>
-  </macros>
-  <expand macro="qiime_citation"/>
-</tool>
\ No newline at end of file

--- a/qiime2-2020.8/qiime_dada2_denoise-paired.xml	Thu Sep 03 09:33:04 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,187 +0,0 @@
-<?xml version="1.0" ?>
-<tool id="qiime_dada2_denoise-paired" name="qiime dada2 denoise-paired"
-      version="2020.8">
-  <description>Denoise and dereplicate paired-end sequences</description>
-  <requirements>
-    <requirement type="package" version="2020.8">qiime2</requirement>
-  </requirements>
-  <command><![CDATA[
-qiime dada2 denoise-paired
-
---i-demultiplexed-seqs=$idemultiplexedseqs
-
---p-trunc-len-f=$ptrunclenf
-
---p-trunc-len-r=$ptrunclenr
-
---p-trim-left-f=$ptrimleftf
-
---p-trim-left-r=$ptrimleftr
-
---p-max-ee-f=$pmaxeef
-
---p-max-ee-r=$pmaxeer
-
---p-trunc-q=$ptruncq
-
-#if str($ppoolingmethod) != 'None':
---p-pooling-method=$ppoolingmethod
-#end if
-
-#if str($pchimeramethod) != 'None':
---p-chimera-method=$pchimeramethod
-#end if
-
---p-min-fold-parent-over-abundance=$pminfoldparentoverabundance
-
---p-n-threads=$pnthreads
-
---p-n-reads-learn=$pnreadslearn
-
-#if $pnohashedfeatureids:
- --p-no-hashed-feature-ids
-#end if
-
---o-table=otable
-
---o-representative-sequences=orepresentativesequences
-
---o-denoising-stats=odenoisingstats
-
-#if str($examples) != 'None':
---examples=$examples
-#end if
-
-;
-cp odenoisingstats.qza $odenoisingstats
-
-  ]]></command>
-  <inputs>
-    <param format="qza,no_unzip.zip" label="--i-demultiplexed-seqs: ARTIFACT SampleData[PairedEndSequencesWithQuality] The paired-end demultiplexed sequences to be denoised.                                  [required]" name="idemultiplexedseqs" optional="False" type="data" />
-    <param label="--p-trunc-len-f: INTEGER Position at which forward read sequences should be truncated due to decrease in quality. This truncates the 3\' end of the of the input sequences, which will be the bases that were sequenced in the last cycles. Reads that are shorter than this value will be discarded. After this parameter is applied there must still be at least a 12 nucleotide overlap between the forward and reverse reads. If 0 is provided, no truncation or length filtering will be performed [required]" name="ptrunclenf" optional="False" type="text" />
-    <param label="--p-trunc-len-r: INTEGER Position at which reverse read sequences should be truncated due to decrease in quality. This truncates the 3\' end of the of the input sequences, which will be the bases that were sequenced in the last cycles. Reads that are shorter than this value will be discarded. After this parameter is applied there must still be at least a 12 nucleotide overlap between the forward and reverse reads. If 0 is provided, no truncation or length filtering will be performed [required]" name="ptrunclenr" optional="False" type="text" />
-    <param label="--p-trim-left-f: INTEGER Position at which forward read sequences should be trimmed due to low quality. This trims the 5\' end of the input sequences, which will be the bases that were sequenced in the first cycles.      [default: 0]" name="ptrimleftf" optional="True" type="integer" value="0" />
-    <param label="--p-trim-left-r: INTEGER Position at which reverse read sequences should be trimmed due to low quality. This trims the 5\' end of the input sequences, which will be the bases that were sequenced in the first cycles.      [default: 0]" name="ptrimleftr" optional="True" type="integer" value="0" />
-    <param label="--p-max-ee-f: NUMBER    Forward reads with number of expected errors higher than this value will be discarded.     [default: 2.0]" name="pmaxeef" optional="True" type="float" value="2.0" />
-    <param label="--p-max-ee-r: NUMBER    Reverse reads with number of expected errors higher than this value will be discarded.     [default: 2.0]" name="pmaxeer" optional="True" type="float" value="2.0" />
-    <param label="--p-trunc-q: INTEGER    Reads are truncated at the first instance of a quality score less than or equal to this value. If the resulting read is then shorter than `trunc-len-f` or `trunc-len-r` (depending on the direction of the read) it is discarded.                   [default: 2]" name="ptruncq" optional="True" type="integer" value="2" />
-    <param label="--p-pooling-method: " name="ppoolingmethod" optional="True" type="select">
-      <option selected="True" value="None">Selection is Optional</option>
-      <option value="independent">independent</option>
-      <option value="pseudo">pseudo</option>
-    </param>
-    <param label="--p-chimera-method: " name="pchimeramethod" optional="True" type="select">
-      <option selected="True" value="None">Selection is Optional</option>
-      <option value="none">none</option>
-      <option value="consensus">consensus</option>
-      <option value="pooled">pooled</option>
-    </param>
-    <param label="--p-min-fold-parent-over-abundance: NUMBER The minimum abundance of potential parents of a sequence being tested as chimeric, expressed as a fold-change versus the abundance of the sequence being tested. Values should be greater than or equal to 1 (i.e. parents should be more abundant than the sequence being tested). This parameter has no effect if chimera-method is \'none\'.           [default: 1.0]" name="pminfoldparentoverabundance" optional="True" type="float" value="1.0" />
-    <param label="--p-n-reads-learn: INTEGER The number of reads to use when training the error model. Smaller numbers will result in a shorter run time but a less reliable error model. [default: 1000000]" name="pnreadslearn" optional="True" type="integer" value="1000000" />
-    <param label="--p-no-hashed-feature-ids: Do not if true, the feature ids in the resulting table will be presented as hashes of the sequences defining each feature. The hash will always be the same for the same sequence so this allows feature tables to be merged across runs of this method. You should only merge tables if the exact same parameters are used for each run.                         [default: True]" name="pnohashedfeatureids" selected="False" type="boolean" />
-    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
-    
-  </inputs>
-
-  <outputs>
-    <data format="qza" label="${tool.name} on ${on_string}: table.qza" name="otable" />
-    <data format="qza" label="${tool.name} on ${on_string}: representativesequences.qza" name="orepresentativesequences" />
-    <data format="qza" label="${tool.name} on ${on_string}: denoisingstats.qza" name="odenoisingstats" />
-    
-  </outputs>
-
-  <help><![CDATA[
-Denoise and dereplicate paired-end sequences
-###############################################################
-
-This method denoises paired-end sequences, dereplicates them, and filters
-chimeras.
-
-Parameters
-----------
-demultiplexed_seqs : SampleData[PairedEndSequencesWithQuality]
-    The paired-end demultiplexed sequences to be denoised.
-trunc_len_f : Int
-    Position at which forward read sequences should be truncated due to
-    decrease in quality. This truncates the 3' end of the of the input
-    sequences, which will be the bases that were sequenced in the last
-    cycles. Reads that are shorter than this value will be discarded. After
-    this parameter is applied there must still be at least a 12 nucleotide
-    overlap between the forward and reverse reads. If 0 is provided, no
-    truncation or length filtering will be performed
-trunc_len_r : Int
-    Position at which reverse read sequences should be truncated due to
-    decrease in quality. This truncates the 3' end of the of the input
-    sequences, which will be the bases that were sequenced in the last
-    cycles. Reads that are shorter than this value will be discarded. After
-    this parameter is applied there must still be at least a 12 nucleotide
-    overlap between the forward and reverse reads. If 0 is provided, no
-    truncation or length filtering will be performed
-trim_left_f : Int, optional
-    Position at which forward read sequences should be trimmed due to low
-    quality. This trims the 5' end of the input sequences, which will be
-    the bases that were sequenced in the first cycles.
-trim_left_r : Int, optional
-    Position at which reverse read sequences should be trimmed due to low
-    quality. This trims the 5' end of the input sequences, which will be
-    the bases that were sequenced in the first cycles.
-max_ee_f : Float, optional
-    Forward reads with number of expected errors higher than this value
-    will be discarded.
-max_ee_r : Float, optional
-    Reverse reads with number of expected errors higher than this value
-    will be discarded.
-trunc_q : Int, optional
-    Reads are truncated at the first instance of a quality score less than
-    or equal to this value. If the resulting read is then shorter than
-    `trunc_len_f` or `trunc_len_r` (depending on the direction of the read)
-    it is discarded.
-pooling_method : Str % Choices('independent', 'pseudo'), optional
-    The method used to pool samples for denoising. "independent": Samples
-    are denoised indpendently. "pseudo": The pseudo-pooling method is used
-    to approximate pooling of samples. In short, samples are denoised
-    independently once, ASVs detected in at least 2 samples are recorded,
-    and samples are denoised independently a second time, but this time
-    with prior knowledge of the recorded ASVs and thus higher sensitivity
-    to those ASVs.
-chimera_method : Str % Choices('consensus', 'none', 'pooled'), optional
-    The method used to remove chimeras. "none": No chimera removal is
-    performed. "pooled": All reads are pooled prior to chimera detection.
-    "consensus": Chimeras are detected in samples individually, and
-    sequences found chimeric in a sufficient fraction of samples are
-    removed.
-min_fold_parent_over_abundance : Float, optional
-    The minimum abundance of potential parents of a sequence being tested
-    as chimeric, expressed as a fold-change versus the abundance of the
-    sequence being tested. Values should be greater than or equal to 1
-    (i.e. parents should be more abundant than the sequence being tested).
-    This parameter has no effect if chimera_method is "none".
-n_threads : Int, optional
-    The number of threads to use for multithreaded processing. If 0 is
-    provided, all available cores will be used.
-n_reads_learn : Int, optional
-    The number of reads to use when training the error model. Smaller
-    numbers will result in a shorter run time but a less reliable error
-    model.
-hashed_feature_ids : Bool, optional
-    If true, the feature ids in the resulting table will be presented as
-    hashes of the sequences defining each feature. The hash will always be
-    the same for the same sequence so this allows feature tables to be
-    merged across runs of this method. You should only merge tables if the
-    exact same parameters are used for each run.
-
-Returns
--------
-table : FeatureTable[Frequency]
-    The resulting feature table.
-representative_sequences : FeatureData[Sequence]
-    The resulting feature sequences. Each feature in the feature table will
-    be represented by exactly one sequence, and these sequences will be the
-    joined paired-end sequences.
-denoising_stats : SampleData[DADA2Stats]
-  ]]></help>
-  <macros>
-    <import>qiime_citation.xml</import>
-  </macros>
-  <expand macro="qiime_citation"/>
-</tool>
\ No newline at end of file

--- a/qiime2-2020.8/qiime_dada2_denoise-pyro.xml	Thu Sep 03 09:33:04 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,166 +0,0 @@
-<?xml version="1.0" ?>
-<tool id="qiime_dada2_denoise-pyro" name="qiime dada2 denoise-pyro"
-      version="2020.8">
-  <description>Denoise and dereplicate single-end pyrosequences</description>
-  <requirements>
-    <requirement type="package" version="2020.8">qiime2</requirement>
-  </requirements>
-  <command><![CDATA[
-qiime dada2 denoise-pyro
-
---i-demultiplexed-seqs=$idemultiplexedseqs
-
---p-trunc-len=$ptrunclen
-
---p-trim-left=$ptrimleft
-
---p-max-ee=$pmaxee
-
---p-trunc-q=$ptruncq
-
---p-max-len=$pmaxlen
-
-#if str($ppoolingmethod) != 'None':
---p-pooling-method=$ppoolingmethod
-#end if
-
-#if str($pchimeramethod) != 'None':
---p-chimera-method=$pchimeramethod
-#end if
-
---p-min-fold-parent-over-abundance=$pminfoldparentoverabundance
-
---p-n-threads=$pnthreads
-
---p-n-reads-learn=$pnreadslearn
-
-#if $pnohashedfeatureids:
- --p-no-hashed-feature-ids
-#end if
-
---o-table=otable
-
---o-representative-sequences=orepresentativesequences
-
---o-denoising-stats=odenoisingstats
-
-#if str($examples) != 'None':
---examples=$examples
-#end if
-
-;
-cp odenoisingstats.qza $odenoisingstats
-
-  ]]></command>
-  <inputs>
-    <param format="qza,no_unzip.zip" label="--i-demultiplexed-seqs: ARTIFACT SampleData[SequencesWithQuality] The single-end demultiplexed pyrosequencing sequences (e.g. 454, IonTorrent) to be denoised. [required]" name="idemultiplexedseqs" optional="False" type="data" />
-    <param label="--p-trunc-len: INTEGER  Position at which sequences should be truncated due to decrease in quality. This truncates the 3\' end of the of the input sequences, which will be the bases that were sequenced in the last cycles. Reads that are shorter than this value will be discarded. If 0 is provided, no truncation or length filtering will be performed                               [required]" name="ptrunclen" optional="False" type="text" />
-    <param label="--p-trim-left: INTEGER  Position at which sequences should be trimmed due to low quality. This trims the 5\' end of the of the input sequences, which will be the bases that were sequenced in the first cycles.           [default: 0]" name="ptrimleft" optional="True" type="integer" value="0" />
-    <param label="--p-max-ee: NUMBER      Reads with number of expected errors higher than this value will be discarded.          [default: 2.0]" name="pmaxee" optional="True" type="float" value="2.0" />
-    <param label="--p-trunc-q: INTEGER    Reads are truncated at the first instance of a quality score less than or equal to this value. If the resulting read is then shorter than `trunc-len`, it is discarded.                         [default: 2]" name="ptruncq" optional="True" type="integer" value="2" />
-    <param label="--p-max-len: INTEGER    Remove reads prior to trimming or truncation which are longer than this value. If 0 is provided no reads will be removed based on length.         [default: 0]" name="pmaxlen" optional="True" type="integer" value="0" />
-    <param label="--p-pooling-method: " name="ppoolingmethod" optional="True" type="select">
-      <option selected="True" value="None">Selection is Optional</option>
-      <option value="independent">independent</option>
-      <option value="pseudo">pseudo</option>
-    </param>
-    <param label="--p-chimera-method: " name="pchimeramethod" optional="True" type="select">
-      <option selected="True" value="None">Selection is Optional</option>
-      <option value="none">none</option>
-      <option value="consensus">consensus</option>
-      <option value="pooled">pooled</option>
-    </param>
-    <param label="--p-min-fold-parent-over-abundance: NUMBER The minimum abundance of potential parents of a sequence being tested as chimeric, expressed as a fold-change versus the abundance of the sequence being tested. Values should be greater than or equal to 1 (i.e. parents should be more abundant than the sequence being tested). This parameter has no effect if chimera-method is \'none\'.           [default: 1.0]" name="pminfoldparentoverabundance" optional="True" type="float" value="1.0" />
-    <param label="--p-n-reads-learn: INTEGER The number of reads to use when training the error model. Smaller numbers will result in a shorter run time but a less reliable error model. [default: 250000]" name="pnreadslearn" optional="True" type="integer" value="250000" />
-    <param label="--p-no-hashed-feature-ids: Do not if true, the feature ids in the resulting table will be presented as hashes of the sequences defining each feature. The hash will always be the same for the same sequence so this allows feature tables to be merged across runs of this method. You should only merge tables if the exact same parameters are used for each run.                         [default: True]" name="pnohashedfeatureids" selected="False" type="boolean" />
-    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
-    
-  </inputs>
-
-  <outputs>
-    <data format="qza" label="${tool.name} on ${on_string}: table.qza" name="otable" />
-    <data format="qza" label="${tool.name} on ${on_string}: representativesequences.qza" name="orepresentativesequences" />
-    <data format="qza" label="${tool.name} on ${on_string}: denoisingstats.qza" name="odenoisingstats" />
-    
-  </outputs>
-
-  <help><![CDATA[
-Denoise and dereplicate single-end pyrosequences
-###############################################################
-
-This method denoises single-end pyrosequencing sequences, dereplicates
-them, and filters chimeras.
-
-Parameters
-----------
-demultiplexed_seqs : SampleData[SequencesWithQuality]
-    The single-end demultiplexed pyrosequencing sequences (e.g. 454,
-    IonTorrent) to be denoised.
-trunc_len : Int
-    Position at which sequences should be truncated due to decrease in
-    quality. This truncates the 3' end of the of the input sequences, which
-    will be the bases that were sequenced in the last cycles. Reads that
-    are shorter than this value will be discarded. If 0 is provided, no
-    truncation or length filtering will be performed
-trim_left : Int, optional
-    Position at which sequences should be trimmed due to low quality. This
-    trims the 5' end of the of the input sequences, which will be the bases
-    that were sequenced in the first cycles.
-max_ee : Float, optional
-    Reads with number of expected errors higher than this value will be
-    discarded.
-trunc_q : Int, optional
-    Reads are truncated at the first instance of a quality score less than
-    or equal to this value. If the resulting read is then shorter than
-    `trunc_len`, it is discarded.
-max_len : Int, optional
-    Remove reads prior to trimming or truncation which are longer than this
-    value. If 0 is provided no reads will be removed based on length.
-pooling_method : Str % Choices('independent', 'pseudo'), optional
-    The method used to pool samples for denoising. "independent": Samples
-    are denoised indpendently. "pseudo": The pseudo-pooling method is used
-    to approximate pooling of samples. In short, samples are denoised
-    independently once, ASVs detected in at least 2 samples are recorded,
-    and samples are denoised independently a second time, but this time
-    with prior knowledge of the recorded ASVs and thus higher sensitivity
-    to those ASVs.
-chimera_method : Str % Choices('consensus', 'none', 'pooled'), optional
-    The method used to remove chimeras. "none": No chimera removal is
-    performed. "pooled": All reads are pooled prior to chimera detection.
-    "consensus": Chimeras are detected in samples individually, and
-    sequences found chimeric in a sufficient fraction of samples are
-    removed.
-min_fold_parent_over_abundance : Float, optional
-    The minimum abundance of potential parents of a sequence being tested
-    as chimeric, expressed as a fold-change versus the abundance of the
-    sequence being tested. Values should be greater than or equal to 1
-    (i.e. parents should be more abundant than the sequence being tested).
-    This parameter has no effect if chimera_method is "none".
-n_threads : Int, optional
-    The number of threads to use for multithreaded processing. If 0 is
-    provided, all available cores will be used.
-n_reads_learn : Int, optional
-    The number of reads to use when training the error model. Smaller
-    numbers will result in a shorter run time but a less reliable error
-    model.
-hashed_feature_ids : Bool, optional
-    If true, the feature ids in the resulting table will be presented as
-    hashes of the sequences defining each feature. The hash will always be
-    the same for the same sequence so this allows feature tables to be
-    merged across runs of this method. You should only merge tables if the
-    exact same parameters are used for each run.
-
-Returns
--------
-table : FeatureTable[Frequency]
-    The resulting feature table.
-representative_sequences : FeatureData[Sequence]
-    The resulting feature sequences. Each feature in the feature table will
-    be represented by exactly one sequence.
-denoising_stats : SampleData[DADA2Stats]
-  ]]></help>
-  <macros>
-    <import>qiime_citation.xml</import>
-  </macros>
-  <expand macro="qiime_citation"/>
-</tool>
\ No newline at end of file

--- a/qiime2-2020.8/qiime_dada2_denoise-single.xml	Thu Sep 03 09:33:04 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,159 +0,0 @@
-<?xml version="1.0" ?>
-<tool id="qiime_dada2_denoise-single" name="qiime dada2 denoise-single"
-      version="2020.8">
-  <description>Denoise and dereplicate single-end sequences</description>
-  <requirements>
-    <requirement type="package" version="2020.8">qiime2</requirement>
-  </requirements>
-  <command><![CDATA[
-qiime dada2 denoise-single
-
---i-demultiplexed-seqs=$idemultiplexedseqs
-
---p-trunc-len=$ptrunclen
-
---p-trim-left=$ptrimleft
-
---p-max-ee=$pmaxee
-
---p-trunc-q=$ptruncq
-
-#if str($ppoolingmethod) != 'None':
---p-pooling-method=$ppoolingmethod
-#end if
-
-#if str($pchimeramethod) != 'None':
---p-chimera-method=$pchimeramethod
-#end if
-
---p-min-fold-parent-over-abundance=$pminfoldparentoverabundance
-
---p-n-threads=$pnthreads
-
---p-n-reads-learn=$pnreadslearn
-
-#if $pnohashedfeatureids:
- --p-no-hashed-feature-ids
-#end if
-
---o-table=otable
-
---o-representative-sequences=orepresentativesequences
-
---o-denoising-stats=odenoisingstats
-
-#if str($examples) != 'None':
---examples=$examples
-#end if
-
-;
-cp odenoisingstats.qza $odenoisingstats
-
-  ]]></command>
-  <inputs>
-    <param format="qza,no_unzip.zip" label="--i-demultiplexed-seqs: ARTIFACT SampleData[SequencesWithQuality | PairedEndSequencesWithQuality] The single-end demultiplexed sequences to be denoised.                                  [required]" name="idemultiplexedseqs" optional="False" type="data" />
-    <param label="--p-trunc-len: INTEGER  Position at which sequences should be truncated due to decrease in quality. This truncates the 3\' end of the of the input sequences, which will be the bases that were sequenced in the last cycles. Reads that are shorter than this value will be discarded. If 0 is provided, no truncation or length filtering will be performed                               [required]" name="ptrunclen" optional="False" type="text" />
-    <param label="--p-trim-left: INTEGER  Position at which sequences should be trimmed due to low quality. This trims the 5\' end of the of the input sequences, which will be the bases that were sequenced in the first cycles.           [default: 0]" name="ptrimleft" optional="True" type="integer" value="0" />
-    <param label="--p-max-ee: NUMBER      Reads with number of expected errors higher than this value will be discarded.          [default: 2.0]" name="pmaxee" optional="True" type="float" value="2.0" />
-    <param label="--p-trunc-q: INTEGER    Reads are truncated at the first instance of a quality score less than or equal to this value. If the resulting read is then shorter than `trunc-len`, it is discarded.                         [default: 2]" name="ptruncq" optional="True" type="integer" value="2" />
-    <param label="--p-pooling-method: " name="ppoolingmethod" optional="True" type="select">
-      <option selected="True" value="None">Selection is Optional</option>
-      <option value="independent">independent</option>
-      <option value="pseudo">pseudo</option>
-    </param>
-    <param label="--p-chimera-method: " name="pchimeramethod" optional="True" type="select">
-      <option selected="True" value="None">Selection is Optional</option>
-      <option value="none">none</option>
-      <option value="consensus">consensus</option>
-      <option value="pooled">pooled</option>
-    </param>
-    <param label="--p-min-fold-parent-over-abundance: NUMBER The minimum abundance of potential parents of a sequence being tested as chimeric, expressed as a fold-change versus the abundance of the sequence being tested. Values should be greater than or equal to 1 (i.e. parents should be more abundant than the sequence being tested). This parameter has no effect if chimera-method is \'none\'.           [default: 1.0]" name="pminfoldparentoverabundance" optional="True" type="float" value="1.0" />
-    <param label="--p-n-reads-learn: INTEGER The number of reads to use when training the error model. Smaller numbers will result in a shorter run time but a less reliable error model. [default: 1000000]" name="pnreadslearn" optional="True" type="integer" value="1000000" />
-    <param label="--p-no-hashed-feature-ids: Do not if true, the feature ids in the resulting table will be presented as hashes of the sequences defining each feature. The hash will always be the same for the same sequence so this allows feature tables to be merged across runs of this method. You should only merge tables if the exact same parameters are used for each run.                         [default: True]" name="pnohashedfeatureids" selected="False" type="boolean" />
-    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
-    
-  </inputs>
-
-  <outputs>
-    <data format="qza" label="${tool.name} on ${on_string}: table.qza" name="otable" />
-    <data format="qza" label="${tool.name} on ${on_string}: representativesequences.qza" name="orepresentativesequences" />
-    <data format="qza" label="${tool.name} on ${on_string}: denoisingstats.qza" name="odenoisingstats" />
-    
-  </outputs>
-
-  <help><![CDATA[
-Denoise and dereplicate single-end sequences
-###############################################################
-
-This method denoises single-end sequences, dereplicates them, and filters
-chimeras.
-
-Parameters
-----------
-demultiplexed_seqs : SampleData[SequencesWithQuality | PairedEndSequencesWithQuality]
-    The single-end demultiplexed sequences to be denoised.
-trunc_len : Int
-    Position at which sequences should be truncated due to decrease in
-    quality. This truncates the 3' end of the of the input sequences, which
-    will be the bases that were sequenced in the last cycles. Reads that
-    are shorter than this value will be discarded. If 0 is provided, no
-    truncation or length filtering will be performed
-trim_left : Int, optional
-    Position at which sequences should be trimmed due to low quality. This
-    trims the 5' end of the of the input sequences, which will be the bases
-    that were sequenced in the first cycles.
-max_ee : Float, optional
-    Reads with number of expected errors higher than this value will be
-    discarded.
-trunc_q : Int, optional
-    Reads are truncated at the first instance of a quality score less than
-    or equal to this value. If the resulting read is then shorter than
-    `trunc_len`, it is discarded.
-pooling_method : Str % Choices('independent', 'pseudo'), optional
-    The method used to pool samples for denoising. "independent": Samples
-    are denoised independently. "pseudo": The pseudo-pooling method is used
-    to approximate pooling of samples. In short, samples are denoised
-    independently once, ASVs detected in at least 2 samples are recorded,
-    and samples are denoised independently a second time, but this time
-    with prior knowledge of the recorded ASVs and thus higher sensitivity
-    to those ASVs.
-chimera_method : Str % Choices('consensus', 'none', 'pooled'), optional
-    The method used to remove chimeras. "none": No chimera removal is
-    performed. "pooled": All reads are pooled prior to chimera detection.
-    "consensus": Chimeras are detected in samples individually, and
-    sequences found chimeric in a sufficient fraction of samples are
-    removed.
-min_fold_parent_over_abundance : Float, optional
-    The minimum abundance of potential parents of a sequence being tested
-    as chimeric, expressed as a fold-change versus the abundance of the
-    sequence being tested. Values should be greater than or equal to 1
-    (i.e. parents should be more abundant than the sequence being tested).
-    This parameter has no effect if chimera_method is "none".
-n_threads : Int, optional
-    The number of threads to use for multithreaded processing. If 0 is
-    provided, all available cores will be used.
-n_reads_learn : Int, optional
-    The number of reads to use when training the error model. Smaller
-    numbers will result in a shorter run time but a less reliable error
-    model.
-hashed_feature_ids : Bool, optional
-    If true, the feature ids in the resulting table will be presented as
-    hashes of the sequences defining each feature. The hash will always be
-    the same for the same sequence so this allows feature tables to be
-    merged across runs of this method. You should only merge tables if the
-    exact same parameters are used for each run.
-
-Returns
--------
-table : FeatureTable[Frequency]
-    The resulting feature table.
-representative_sequences : FeatureData[Sequence]
-    The resulting feature sequences. Each feature in the feature table will
-    be represented by exactly one sequence.
-denoising_stats : SampleData[DADA2Stats]
-  ]]></help>
-  <macros>
-    <import>qiime_citation.xml</import>
-  </macros>
-  <expand macro="qiime_citation"/>
-</tool>
\ No newline at end of file

--- a/qiime2-2020.8/qiime_deblur_denoise-16S.xml	Thu Sep 03 09:33:04 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,126 +0,0 @@
-<?xml version="1.0" ?>
-<tool id="qiime_deblur_denoise-16S" name="qiime deblur denoise-16S"
-      version="2020.8">
-  <description>Deblur sequences using a 16S positive filter.</description>
-  <requirements>
-    <requirement type="package" version="2020.8">qiime2</requirement>
-  </requirements>
-  <command><![CDATA[
-qiime deblur denoise-16S
-
---i-demultiplexed-seqs=$idemultiplexedseqs
-
---p-trim-length=$ptrimlength
-
---p-left-trim-len=$plefttrimlen
-
-#if $psamplestats:
- --p-sample-stats
-#end if
-
---p-mean-error=$pmeanerror
-
---p-indel-prob=$pindelprob
-
---p-indel-max=$pindelmax
-
---p-min-reads=$pminreads
-
---p-min-size=$pminsize
-
---p-jobs-to-start=$pjobstostart
-
-#if $pnohashedfeatureids:
- --p-no-hashed-feature-ids
-#end if
-
---o-table=otable
-
---o-representative-sequences=orepresentativesequences
-
---o-stats=ostats
-
-#if str($examples) != 'None':
---examples=$examples
-#end if
-
-;
-cp ostats.qza $ostats
-
-  ]]></command>
-  <inputs>
-    <param format="qza,no_unzip.zip" label="--i-demultiplexed-seqs: ARTIFACT SampleData[SequencesWithQuality | PairedEndSequencesWithQuality | JoinedSequencesWithQuality] The demultiplexed sequences to be denoised. [required]" name="idemultiplexedseqs" optional="False" type="data" />
-    <param label="--p-trim-length: INTEGER Sequence trim length, specify -1 to disable trimming.                                  [required]" name="ptrimlength" optional="False" type="text" />
-    <param label="--p-left-trim-len: INTEGER Range(0, None)       Sequence trimming from the 5\' end. A value of 0 will disable this trim.                       [default: 0]" min="0" name="plefttrimlen" optional="True" type="integer" value="0" />
-    <param label="--p-sample-stats: --p-sample-stats: / --p-no-sample-stats If true, gather stats per sample.    [default: False]" name="psamplestats" selected="False" type="boolean" />
-    <param label="--p-mean-error: NUMBER  The mean per nucleotide error, used for original sequence estimate.                   [default: 0.005]" name="pmeanerror" optional="True" type="float" value="0.005" />
-    <param label="--p-indel-prob: NUMBER  Insertion/deletion (indel) probability (same for N indels).                              [default: 0.01]" name="pindelprob" optional="True" type="float" value="0.01" />
-    <param label="--p-indel-max: INTEGER  Maximum number of insertion/deletions.   [default: 3]" name="pindelmax" optional="True" type="integer" value="3" />
-    <param label="--p-min-reads: INTEGER  Retain only features appearing at least min-reads times across all samples in the resulting feature table.                                  [default: 10]" name="pminreads" optional="True" type="integer" value="10" />
-    <param label="--p-min-size: INTEGER   In each sample, discard all features with an abundance less than min-size.            [default: 2]" name="pminsize" optional="True" type="integer" value="2" />
-    <param label="--p-no-hashed-feature-ids: Do not if true, hash the feature IDs.        [default: True]" name="pnohashedfeatureids" selected="False" type="boolean" />
-    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
-    
-  </inputs>
-
-  <outputs>
-    <data format="qza" label="${tool.name} on ${on_string}: table.qza" name="otable" />
-    <data format="qza" label="${tool.name} on ${on_string}: representativesequences.qza" name="orepresentativesequences" />
-    <data format="qza" label="${tool.name} on ${on_string}: stats.qza" name="ostats" />
-    
-  </outputs>
-
-  <help><![CDATA[
-Deblur sequences using a 16S positive filter.
-###############################################################
-
-Perform sequence quality control for Illumina data using the Deblur
-workflow with a 16S reference as a positive filter. Only forward reads are
-supported at this time. The specific reference used is the 88% OTUs from
-Greengenes 13_8. This mode of operation should only be used when data were
-generated from a 16S amplicon protocol on an Illumina platform. The
-reference is only used to assess whether each sequence is likely to be 16S
-by a local alignment using SortMeRNA with a permissive e-value; the
-reference is not used to characterize the sequences.
-
-Parameters
-----------
-demultiplexed_seqs : SampleData[SequencesWithQuality | PairedEndSequencesWithQuality | JoinedSequencesWithQuality]
-    The demultiplexed sequences to be denoised.
-trim_length : Int
-    Sequence trim length, specify -1 to disable trimming.
-left_trim_len : Int % Range(0, None), optional
-    Sequence trimming from the 5' end. A value of 0 will disable this trim.
-sample_stats : Bool, optional
-    If true, gather stats per sample.
-mean_error : Float, optional
-    The mean per nucleotide error, used for original sequence estimate.
-indel_prob : Float, optional
-    Insertion/deletion (indel) probability (same for N indels).
-indel_max : Int, optional
-    Maximum number of insertion/deletions.
-min_reads : Int, optional
-    Retain only features appearing at least min_reads times across all
-    samples in the resulting feature table.
-min_size : Int, optional
-    In each sample, discard all features with an abundance less than
-    min_size.
-jobs_to_start : Int, optional
-    Number of jobs to start (if to run in parallel).
-hashed_feature_ids : Bool, optional
-    If true, hash the feature IDs.
-
-Returns
--------
-table : FeatureTable[Frequency]
-    The resulting denoised feature table.
-representative_sequences : FeatureData[Sequence]
-    The resulting feature sequences.
-stats : DeblurStats
-    Per-sample stats if requested.
-  ]]></help>
-  <macros>
-    <import>qiime_citation.xml</import>
-  </macros>
-  <expand macro="qiime_citation"/>
-</tool>
\ No newline at end of file

--- a/qiime2-2020.8/qiime_deblur_denoise-other.xml	Thu Sep 03 09:33:04 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,132 +0,0 @@
-<?xml version="1.0" ?>
-<tool id="qiime_deblur_denoise-other" name="qiime deblur denoise-other"
-      version="2020.8">
-  <description>Deblur sequences using a user-specified positive filter.</description>
-  <requirements>
-    <requirement type="package" version="2020.8">qiime2</requirement>
-  </requirements>
-  <command><![CDATA[
-qiime deblur denoise-other
-
---i-demultiplexed-seqs=$idemultiplexedseqs
-
---i-reference-seqs=$ireferenceseqs
-
---p-trim-length=$ptrimlength
-
---p-left-trim-len=$plefttrimlen
-
-#if $psamplestats:
- --p-sample-stats
-#end if
-
---p-mean-error=$pmeanerror
-
---p-indel-prob=$pindelprob
-
---p-indel-max=$pindelmax
-
---p-min-reads=$pminreads
-
---p-min-size=$pminsize
-
---p-jobs-to-start=$pjobstostart
-
-#if $pnohashedfeatureids:
- --p-no-hashed-feature-ids
-#end if
-
---o-table=otable
-
---o-representative-sequences=orepresentativesequences
-
---o-stats=ostats
-
-#if str($examples) != 'None':
---examples=$examples
-#end if
-
-;
-cp ostats.qza $ostats
-
-  ]]></command>
-  <inputs>
-    <param format="qza,no_unzip.zip" label="--i-demultiplexed-seqs: ARTIFACT SampleData[SequencesWithQuality | PairedEndSequencesWithQuality | JoinedSequencesWithQuality] The demultiplexed sequences to be denoised. [required]" name="idemultiplexedseqs" optional="False" type="data" />
-    <param format="qza,no_unzip.zip" label="--i-reference-seqs: ARTIFACT FeatureData[Sequence] Positive filtering database. Keep all sequences aligning to these sequences.               [required]" name="ireferenceseqs" optional="False" type="data" />
-    <param label="--p-trim-length: INTEGER Sequence trim length, specify -1 to disable trimming.                                  [required]" name="ptrimlength" optional="False" type="text" />
-    <param label="--p-left-trim-len: INTEGER Range(0, None)       Sequence trimming from the 5\' end. A value of 0 will disable this trim.                       [default: 0]" min="0" name="plefttrimlen" optional="True" type="integer" value="0" />
-    <param label="--p-sample-stats: --p-sample-stats: / --p-no-sample-stats If true, gather stats per sample.    [default: False]" name="psamplestats" selected="False" type="boolean" />
-    <param label="--p-mean-error: NUMBER  The mean per nucleotide error, used for original sequence estimate.                   [default: 0.005]" name="pmeanerror" optional="True" type="float" value="0.005" />
-    <param label="--p-indel-prob: NUMBER  Insertion/deletion (indel) probability (same for N indels).                              [default: 0.01]" name="pindelprob" optional="True" type="float" value="0.01" />
-    <param label="--p-indel-max: INTEGER  Maximum number of insertion/deletions.   [default: 3]" name="pindelmax" optional="True" type="integer" value="3" />
-    <param label="--p-min-reads: INTEGER  Retain only features appearing at least min-reads times across all samples in the resulting feature table.                                  [default: 10]" name="pminreads" optional="True" type="integer" value="10" />
-    <param label="--p-min-size: INTEGER   In each sample, discard all features with an abundance less than min-size.            [default: 2]" name="pminsize" optional="True" type="integer" value="2" />
-    <param label="--p-no-hashed-feature-ids: Do not if true, hash the feature IDs.        [default: True]" name="pnohashedfeatureids" selected="False" type="boolean" />
-    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
-    
-  </inputs>
-
-  <outputs>
-    <data format="qza" label="${tool.name} on ${on_string}: table.qza" name="otable" />
-    <data format="qza" label="${tool.name} on ${on_string}: representativesequences.qza" name="orepresentativesequences" />
-    <data format="qza" label="${tool.name} on ${on_string}: stats.qza" name="ostats" />
-    
-  </outputs>
-
-  <help><![CDATA[
-Deblur sequences using a user-specified positive filter.
-###############################################################
-
-Perform sequence quality control for Illumina data using the Deblur
-workflow, including positive alignment-based filtering. Only forward reads
-are supported at this time. This mode of execution is particularly useful
-when operating on non-16S data. For example, to apply Deblur to 18S data,
-you would want to specify a reference composed of 18S sequences in order to
-filter out sequences which do not appear to be 18S. The assessment is
-performed by local alignment using SortMeRNA with a permissive e-value
-threshold.
-
-Parameters
-----------
-demultiplexed_seqs : SampleData[SequencesWithQuality | PairedEndSequencesWithQuality | JoinedSequencesWithQuality]
-    The demultiplexed sequences to be denoised.
-reference_seqs : FeatureData[Sequence]
-    Positive filtering database. Keep all sequences aligning to these
-    sequences.
-trim_length : Int
-    Sequence trim length, specify -1 to disable trimming.
-left_trim_len : Int % Range(0, None), optional
-    Sequence trimming from the 5' end. A value of 0 will disable this trim.
-sample_stats : Bool, optional
-    If true, gather stats per sample.
-mean_error : Float, optional
-    The mean per nucleotide error, used for original sequence estimate.
-indel_prob : Float, optional
-    Insertion/deletion (indel) probability (same for N indels).
-indel_max : Int, optional
-    Maximum number of insertion/deletions.
-min_reads : Int, optional
-    Retain only features appearing at least min_reads times across all
-    samples in the resulting feature table.
-min_size : Int, optional
-    In each sample, discard all features with an abundance less than
-    min_size.
-jobs_to_start : Int, optional
-    Number of jobs to start (if to run in parallel).
-hashed_feature_ids : Bool, optional
-    If true, hash the feature IDs.
-
-Returns
--------
-table : FeatureTable[Frequency]
-    The resulting denoised feature table.
-representative_sequences : FeatureData[Sequence]
-    The resulting feature sequences.
-stats : DeblurStats
-    Per-sample stats if requested.
-  ]]></help>
-  <macros>
-    <import>qiime_citation.xml</import>
-  </macros>
-  <expand macro="qiime_citation"/>
-</tool>
\ No newline at end of file

--- a/qiime2-2020.8/qiime_deblur_visualize-stats.xml	Thu Sep 03 09:33:04 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,59 +0,0 @@
-<?xml version="1.0" ?>
-<tool id="qiime_deblur_visualize-stats" name="qiime deblur visualize-stats"
-      version="2020.8">
-  <description>Visualize Deblur stats per sample.</description>
-  <requirements>
-    <requirement type="package" version="2020.8">qiime2</requirement>
-  </requirements>
-  <command><![CDATA[
-qiime deblur visualize-stats
-
---i-deblur-stats=$ideblurstats
-
---o-visualization=ovisualization
-
-#if str($examples) != 'None':
---examples=$examples
-#end if
-
-;
-cp ostats.qza $ostats
-
-;
-qiime tools export  ovisualization.qzv --output-path out
-&& mkdir -p '$ovisualization.files_path'
-&& cp -r out/* '$ovisualization.files_path'
-&& mv '$ovisualization.files_path/index.html' '$ovisualization'
-
-  ]]></command>
-  <inputs>
-    <param format="qza,no_unzip.zip" label="--i-deblur-stats: ARTIFACT DeblurStats        Summary statistics of the Deblur process.    [required]" name="ideblurstats" optional="False" type="data" />
-    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
-    
-  </inputs>
-
-  <outputs>
-    <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
-    
-  </outputs>
-
-  <help><![CDATA[
-Visualize Deblur stats per sample.
-###############################################################
-
-Display Deblur statistics per sample
-
-Parameters
-----------
-deblur_stats : DeblurStats
-    Summary statistics of the Deblur process.
-
-Returns
--------
-visualization : Visualization
-  ]]></help>
-  <macros>
-    <import>qiime_citation.xml</import>
-  </macros>
-  <expand macro="qiime_citation"/>
-</tool>
\ No newline at end of file

--- a/qiime2-2020.8/qiime_demux_emp-paired.xml	Thu Sep 03 09:33:04 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,125 +0,0 @@
-<?xml version="1.0" ?>
-<tool id="qiime_demux_emp-paired" name="qiime demux emp-paired"
-      version="2020.8">
-  <description>Demultiplex paired-end sequence data generated with the EMP protocol.</description>
-  <requirements>
-    <requirement type="package" version="2020.8">qiime2</requirement>
-  </requirements>
-  <command><![CDATA[
-qiime demux emp-paired
-
---i-seqs=$iseqs
-# if $input_files_mbarcodesfile:
-  # 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-barcodes-file=' + d['additional_input'].__getattr__('file_name')
-    # end for
-    # return $file_list
-  # end def
---m-barcodes-file=$list_dict_to_string($input_files_mbarcodesfile)
-# end if
-
-#if '__ob__' in str($mbarcodescolumn):
-  #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('__ob__', '[')
-  #set $mbarcodescolumn = $mbarcodescolumn_temp
-#end if
-#if '__cb__' in str($mbarcodescolumn):
-  #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('__cb__', ']')
-  #set $mbarcodescolumn = $mbarcodescolumn_temp
-#end if
-#if 'X' in str($mbarcodescolumn):
-  #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('X', '\\')
-  #set $mbarcodescolumn = $mbarcodescolumn_temp
-#end if
-#if '__sq__' in str($mbarcodescolumn):
-  #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('__sq__', "'")
-  #set $mbarcodescolumn = $mbarcodescolumn_temp
-#end if
-#if '__db__' in str($mbarcodescolumn):
-  #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('__db__', '"')
-  #set $mbarcodescolumn = $mbarcodescolumn_temp
-#end if
-
---m-barcodes-column=$mbarcodescolumn
-
-
-#if $pnogolayerrorcorrection:
- --p-no-golay-error-correction
-#end if
-
-#if $prevcompbarcodes:
- --p-rev-comp-barcodes
-#end if
-
-#if $prevcompmappingbarcodes:
- --p-rev-comp-mapping-barcodes
-#end if
-
---o-per-sample-sequences=opersamplesequences
-
---o-error-correction-details=oerrorcorrectiondetails
-
-#if str($examples) != 'None':
---examples=$examples
-#end if
-
-;
-cp oerrorcorrectiondetails.qza $oerrorcorrectiondetails
-
-  ]]></command>
-  <inputs>
-    <param format="qza,no_unzip.zip" label="--i-seqs: ARTIFACT EMPPairedEndSequences The paired-end sequences to be demultiplexed. [required]" name="iseqs" optional="False" type="data" />
-    <repeat name="input_files_mbarcodesfile" optional="True" title="--m-barcodes-file">
-      <param format="tabular,qza,no_unzip.zip" label="--m-barcodes-file: METADATA" name="additional_input" optional="True" type="data" />
-    </repeat>
-    <param label="--m-barcodes-column: COLUMN  MetadataColumn[Categorical] The sample metadata column containing the per-sample barcodes.                                    [required]" name="mbarcodescolumn" optional="False" type="text" />
-    <param label="--p-no-golay-error-correction: Do not perform 12nt Golay error correction on the barcode reads.                                  [default: True]" name="pnogolayerrorcorrection" selected="False" type="boolean" />
-    <param format="tabular,qza,no_unzip.zip" label="--p-rev-comp-barcodes: --p-rev-comp-barcodes: / --p-no-rev-comp-barcodes If provided, the barcode sequence reads will be reverse complemented prior to demultiplexing. [default: False]" name="prevcompbarcodes" selected="False" type="boolean" />
-    <param format="tabular,qza,no_unzip.zip" label="--p-rev-comp-mapping-barcodes: --p-rev-comp-mapping-barcodes: / --p-no-rev-comp-mapping-barcodes If provided, the barcode sequences in the sample metadata will be reverse complemented prior to demultiplexing.                        [default: False]" name="prevcompmappingbarcodes" selected="False" type="boolean" />
-    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
-    
-  </inputs>
-
-  <outputs>
-    <data format="qza" label="${tool.name} on ${on_string}: persamplesequences.qza" name="opersamplesequences" />
-    <data format="qza" label="${tool.name} on ${on_string}: errorcorrectiondetails.qza" name="oerrorcorrectiondetails" />
-    
-  </outputs>
-
-  <help><![CDATA[
-Demultiplex paired-end sequence data generated with the EMP protocol.
-###############################################################
-
-Demultiplex paired-end sequence data (i.e., map barcode reads to sample
-ids) for data generated with the Earth Microbiome Project (EMP) amplicon
-sequencing protocol. Details about this protocol can be found at
-http://www.earthmicrobiome.org/protocols-and-standards/
-
-Parameters
-----------
-seqs : EMPPairedEndSequences
-    The paired-end sequences to be demultiplexed.
-barcodes : MetadataColumn[Categorical]
-    The sample metadata column containing the per-sample barcodes.
-golay_error_correction : Bool, optional
-    Perform 12nt Golay error correction on the barcode reads.
-rev_comp_barcodes : Bool, optional
-    If provided, the barcode sequence reads will be reverse complemented
-    prior to demultiplexing.
-rev_comp_mapping_barcodes : Bool, optional
-    If provided, the barcode sequences in the sample metadata will be
-    reverse complemented prior to demultiplexing.
-
-Returns
--------
-per_sample_sequences : SampleData[PairedEndSequencesWithQuality]
-    The resulting demultiplexed sequences.
-error_correction_details : ErrorCorrectionDetails
-    Detail about the barcode error corrections.
-  ]]></help>
-  <macros>
-    <import>qiime_citation.xml</import>
-  </macros>
-  <expand macro="qiime_citation"/>
-</tool>
\ No newline at end of file

--- a/qiime2-2020.8/qiime_demux_emp-single.xml	Thu Sep 03 09:33:04 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,125 +0,0 @@
-<?xml version="1.0" ?>
-<tool id="qiime_demux_emp-single" name="qiime demux emp-single"
-      version="2020.8">
-  <description>Demultiplex sequence data generated with the EMP protocol.</description>
-  <requirements>
-    <requirement type="package" version="2020.8">qiime2</requirement>
-  </requirements>
-  <command><![CDATA[
-qiime demux emp-single
-
---i-seqs=$iseqs
-# if $input_files_mbarcodesfile:
-  # 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-barcodes-file=' + d['additional_input'].__getattr__('file_name')
-    # end for
-    # return $file_list
-  # end def
---m-barcodes-file=$list_dict_to_string($input_files_mbarcodesfile)
-# end if
-
-#if '__ob__' in str($mbarcodescolumn):
-  #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('__ob__', '[')
-  #set $mbarcodescolumn = $mbarcodescolumn_temp
-#end if
-#if '__cb__' in str($mbarcodescolumn):
-  #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('__cb__', ']')
-  #set $mbarcodescolumn = $mbarcodescolumn_temp
-#end if
-#if 'X' in str($mbarcodescolumn):
-  #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('X', '\\')
-  #set $mbarcodescolumn = $mbarcodescolumn_temp
-#end if
-#if '__sq__' in str($mbarcodescolumn):
-  #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('__sq__', "'")
-  #set $mbarcodescolumn = $mbarcodescolumn_temp
-#end if
-#if '__db__' in str($mbarcodescolumn):
-  #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('__db__', '"')
-  #set $mbarcodescolumn = $mbarcodescolumn_temp
-#end if
-
---m-barcodes-column=$mbarcodescolumn
-
-
-#if $pnogolayerrorcorrection:
- --p-no-golay-error-correction
-#end if
-
-#if $prevcompbarcodes:
- --p-rev-comp-barcodes
-#end if
-
-#if $prevcompmappingbarcodes:
- --p-rev-comp-mapping-barcodes
-#end if
-
---o-per-sample-sequences=opersamplesequences
-
---o-error-correction-details=oerrorcorrectiondetails
-
-#if str($examples) != 'None':
---examples=$examples
-#end if
-
-;
-cp oerrorcorrectiondetails.qza $oerrorcorrectiondetails
-
-  ]]></command>
-  <inputs>
-    <param format="qza,no_unzip.zip" label="--i-seqs: ARTIFACT RawSequences | EMPSingleEndSequences | EMPPairedEndSequences The single-end sequences to be demultiplexed. [required]" name="iseqs" optional="False" type="data" />
-    <repeat name="input_files_mbarcodesfile" optional="True" title="--m-barcodes-file">
-      <param format="tabular,qza,no_unzip.zip" label="--m-barcodes-file: METADATA" name="additional_input" optional="True" type="data" />
-    </repeat>
-    <param label="--m-barcodes-column: COLUMN  MetadataColumn[Categorical] The sample metadata column containing the per-sample barcodes.                                    [required]" name="mbarcodescolumn" optional="False" type="text" />
-    <param label="--p-no-golay-error-correction: Do not perform 12nt Golay error correction on the barcode reads.                                  [default: True]" name="pnogolayerrorcorrection" selected="False" type="boolean" />
-    <param format="tabular,qza,no_unzip.zip" label="--p-rev-comp-barcodes: --p-rev-comp-barcodes: / --p-no-rev-comp-barcodes If provided, the barcode sequence reads will be reverse complemented prior to demultiplexing. [default: False]" name="prevcompbarcodes" selected="False" type="boolean" />
-    <param format="tabular,qza,no_unzip.zip" label="--p-rev-comp-mapping-barcodes: --p-rev-comp-mapping-barcodes: / --p-no-rev-comp-mapping-barcodes If provided, the barcode sequences in the sample metadata will be reverse complemented prior to demultiplexing.                        [default: False]" name="prevcompmappingbarcodes" selected="False" type="boolean" />
-    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
-    
-  </inputs>
-
-  <outputs>
-    <data format="qza" label="${tool.name} on ${on_string}: persamplesequences.qza" name="opersamplesequences" />
-    <data format="qza" label="${tool.name} on ${on_string}: errorcorrectiondetails.qza" name="oerrorcorrectiondetails" />
-    
-  </outputs>
-
-  <help><![CDATA[
-Demultiplex sequence data generated with the EMP protocol.
-###############################################################
-
-Demultiplex sequence data (i.e., map barcode reads to sample ids) for data
-generated with the Earth Microbiome Project (EMP) amplicon sequencing
-protocol. Details about this protocol can be found at
-http://www.earthmicrobiome.org/protocols-and-standards/
-
-Parameters
-----------
-seqs : RawSequences | EMPSingleEndSequences | EMPPairedEndSequences
-    The single-end sequences to be demultiplexed.
-barcodes : MetadataColumn[Categorical]
-    The sample metadata column containing the per-sample barcodes.
-golay_error_correction : Bool, optional
-    Perform 12nt Golay error correction on the barcode reads.
-rev_comp_barcodes : Bool, optional
-    If provided, the barcode sequence reads will be reverse complemented
-    prior to demultiplexing.
-rev_comp_mapping_barcodes : Bool, optional
-    If provided, the barcode sequences in the sample metadata will be
-    reverse complemented prior to demultiplexing.
-
-Returns
--------
-per_sample_sequences : SampleData[SequencesWithQuality]
-    The resulting demultiplexed sequences.
-error_correction_details : ErrorCorrectionDetails
-    Detail about the barcode error corrections.
-  ]]></help>
-  <macros>
-    <import>qiime_citation.xml</import>
-  </macros>
-  <expand macro="qiime_citation"/>
-</tool>
\ No newline at end of file

--- a/qiime2-2020.8/qiime_demux_filter-samples.xml	Thu Sep 03 09:33:04 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,113 +0,0 @@
-<?xml version="1.0" ?>
-<tool id="qiime_demux_filter-samples" name="qiime demux filter-samples"
-      version="2020.8">
-  <description>Filter samples out of demultiplexed data.</description>
-  <requirements>
-    <requirement type="package" version="2020.8">qiime2</requirement>
-  </requirements>
-  <command><![CDATA[
-qiime demux filter-samples
-
---i-demux=$idemux
-# 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
-#end if
-
-#if $pexcludeids:
- --p-exclude-ids
-#end if
-
---o-filtered-demux=ofiltereddemux
-
-#if str($examples) != 'None':
---examples=$examples
-#end if
-
-;
-cp ofiltereddemux.qza $ofiltereddemux
-
-  ]]></command>
-  <inputs>
-    <param format="qza,no_unzip.zip" label="--i-demux: ARTIFACT SampleData[SequencesWithQuality¹ | PairedEndSequencesWithQuality² | JoinedSequencesWithQuality³] The demultiplexed data from which samples should be filtered.                                    [required]" name="idemux" optional="False" type="data" />
-    <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
-      <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA... (multiple          Sample metadata indicating which sample ids to filter. arguments will    The optional `where` parameter may be used to filter be merged)        ids based on specified conditions in the metadata. The optional `exclude-ids` parameter may be used to exclude the ids specified in the metadata from the filter. [required]" name="additional_input" optional="False" type="data" />
-    </repeat>
-    <param label="--p-where: TEXT       Optional SQLite WHERE clause specifying sample metadata criteria that must be met to be included in the filtered data. If not provided, all samples in `metadata` that are also in the demultiplexed data will be retained.                                 [optional]" name="pwhere" optional="False" type="text" />
-    <param label="--p-exclude-ids: --p-exclude-ids: / --p-no-exclude-ids Defaults to False. If True, the samples selected by the `metadata` and optional `where` parameter will be excluded from the filtered data.       [default: False]" name="pexcludeids" selected="False" type="boolean" />
-    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
-    
-  </inputs>
-
-  <outputs>
-    <data format="qza" label="${tool.name} on ${on_string}: filtereddemux.qza" name="ofiltereddemux" />
-    
-  </outputs>
-
-  <help><![CDATA[
-Filter samples out of demultiplexed data.
-###############################################################
-
-Filter samples indicated in given metadata out of demultiplexed data.
-Specific samples can be further selected with the WHERE clause, and the
-`exclude_ids` parameter allows for filtering of all samples not specified.
-
-Parameters
-----------
-demux : SampleData[SequencesWithQuality¹ | PairedEndSequencesWithQuality² | JoinedSequencesWithQuality³]
-    The demultiplexed data from which samples should be filtered.
-metadata : Metadata
-    Sample metadata indicating which sample ids to filter. The optional
-    `where` parameter may be used to filter ids based on specified
-    conditions in the metadata. The optional `exclude_ids` parameter may be
-    used to exclude the ids specified in the metadata from the filter.
-where : Str, optional
-    Optional SQLite WHERE clause specifying sample metadata criteria that
-    must be met to be included in the filtered data. If not provided, all
-    samples in `metadata` that are also in the demultiplexed data will be
-    retained.
-exclude_ids : Bool, optional
-    Defaults to False. If True, the samples selected by the `metadata` and
-    optional `where` parameter will be excluded from the filtered data.
-
-Returns
--------
-filtered_demux : SampleData[SequencesWithQuality¹ | PairedEndSequencesWithQuality² | JoinedSequencesWithQuality³]
-    Filtered demultiplexed data.
-  ]]></help>
-  <macros>
-    <import>qiime_citation.xml</import>
-  </macros>
-  <expand macro="qiime_citation"/>
-</tool>
\ No newline at end of file

--- a/qiime2-2020.8/qiime_demux_subsample-paired.xml	Thu Sep 03 09:33:04 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,63 +0,0 @@
-<?xml version="1.0" ?>
-<tool id="qiime_demux_subsample-paired" name="qiime demux subsample-paired"
-      version="2020.8">
-  <description>Subsample paired-end sequences without replacement.</description>
-  <requirements>
-    <requirement type="package" version="2020.8">qiime2</requirement>
-  </requirements>
-  <command><![CDATA[
-qiime demux subsample-paired
-
---i-sequences=$isequences
-
---p-fraction=$pfraction
-
---o-subsampled-sequences=osubsampledsequences
-
-#if str($examples) != 'None':
---examples=$examples
-#end if
-
-;
-cp osubsampledsequences.qza $osubsampledsequences
-
-  ]]></command>
-  <inputs>
-    <param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT SampleData[PairedEndSequencesWithQuality] The demultiplexed sequences to be subsampled. [required]" name="isequences" optional="False" type="data" />
-    <param label="--p-fraction: PROPORTION Range(0, 1, inclusive_start=False) The fraction of sequences to retain in subsample. [required]" name="pfraction" optional="False" type="text" />
-    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
-    
-  </inputs>
-
-  <outputs>
-    <data format="qza" label="${tool.name} on ${on_string}: subsampledsequences.qza" name="osubsampledsequences" />
-    
-  </outputs>
-
-  <help><![CDATA[
-Subsample paired-end sequences without replacement.
-###############################################################
-
-Generate a random subsample of paired-end sequences containing
-approximately the fraction of input sequences specified by the fraction
-parameter. The number of output samples will always be equal to the number
-of input samples, even if some of those samples contain no sequences after
-subsampling.
-
-Parameters
-----------
-sequences : SampleData[PairedEndSequencesWithQuality]
-    The demultiplexed sequences to be subsampled.
-fraction : Float % Range(0, 1, inclusive_start=False)
-    The fraction of sequences to retain in subsample.
-
-Returns
--------
-subsampled_sequences : SampleData[PairedEndSequencesWithQuality]
-    The subsampled sequences.
-  ]]></help>
-  <macros>
-    <import>qiime_citation.xml</import>
-  </macros>
-  <expand macro="qiime_citation"/>
-</tool>
\ No newline at end of file

--- a/qiime2-2020.8/qiime_demux_subsample-single.xml	Thu Sep 03 09:33:04 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,63 +0,0 @@
-<?xml version="1.0" ?>
-<tool id="qiime_demux_subsample-single" name="qiime demux subsample-single"
-      version="2020.8">
-  <description>Subsample single-end sequences without replacement.</description>
-  <requirements>
-    <requirement type="package" version="2020.8">qiime2</requirement>
-  </requirements>
-  <command><![CDATA[
-qiime demux subsample-single
-
---i-sequences=$isequences
-
---p-fraction=$pfraction
-
---o-subsampled-sequences=osubsampledsequences
-
-#if str($examples) != 'None':
---examples=$examples
-#end if
-
-;
-cp osubsampledsequences.qza $osubsampledsequences
-
-  ]]></command>
-  <inputs>
-    <param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT SampleData[SequencesWithQuality | PairedEndSequencesWithQuality] The demultiplexed sequences to be subsampled. [required]" name="isequences" optional="False" type="data" />
-    <param label="--p-fraction: PROPORTION Range(0, 1, inclusive_start=False) The fraction of sequences to retain in subsample. [required]" name="pfraction" optional="False" type="text" />
-    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
-    
-  </inputs>
-
-  <outputs>
-    <data format="qza" label="${tool.name} on ${on_string}: subsampledsequences.qza" name="osubsampledsequences" />
-    
-  </outputs>
-
-  <help><![CDATA[
-Subsample single-end sequences without replacement.
-###############################################################
-
-Generate a random subsample of single-end sequences containing
-approximately the fraction of input sequences specified by the fraction
-parameter. The number of output samples will always be equal to the number
-of input samples, even if some of those samples contain no sequences after
-subsampling.
-
-Parameters
-----------
-sequences : SampleData[SequencesWithQuality | PairedEndSequencesWithQuality]
-    The demultiplexed sequences to be subsampled.
-fraction : Float % Range(0, 1, inclusive_start=False)
-    The fraction of sequences to retain in subsample.
-
-Returns
--------
-subsampled_sequences : SampleData[SequencesWithQuality]
-    The subsampled sequences.
-  ]]></help>
-  <macros>
-    <import>qiime_citation.xml</import>
-  </macros>
-  <expand macro="qiime_citation"/>
-</tool>
\ No newline at end of file

--- a/qiime2-2020.8/qiime_demux_summarize.xml	Thu Sep 03 09:33:04 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,79 +0,0 @@
-<?xml version="1.0" ?>
-<tool id="qiime_demux_summarize" name="qiime demux summarize"
-      version="2020.8">
-  <description>Summarize counts per sample.</description>
-  <requirements>
-    <requirement type="package" version="2020.8">qiime2</requirement>
-  </requirements>
-  <command><![CDATA[
-qiime demux summarize
-# if $input_files_idata:
-  # 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 + ' --i-data=' + d['additional_input'].__getattr__('file_name')
-    # end for
-    # return $file_list
-  # end def
---i-data=$list_dict_to_string($input_files_idata)
-# end if
-
---p-n=$pn
-
---o-visualization=ovisualization
-
-#if str($examples) != 'None':
---examples=$examples
-#end if
-
-;
-cp osubsampledsequences.qza $osubsampledsequences
-
-;
-qiime tools export  ovisualization.qzv --output-path out
-&& mkdir -p '$ovisualization.files_path'
-&& cp -r out/* '$ovisualization.files_path'
-&& mv '$ovisualization.files_path/index.html' '$ovisualization'
-
-  ]]></command>
-  <inputs>
-    <repeat name="input_files_idata" optional="False" title="--i-data">
-      <param format="qza,no_unzip.zip" label="--i-data: ARTIFACT SampleData[SequencesWithQuality | PairedEndSequencesWithQuality | JoinedSequencesWithQuality] The demultiplexed sequences to be summarized. [required]" name="additional_input" optional="False" type="data" />
-    </repeat>
-    <param label="--p-n: INTEGER        The number of sequences that should be selected at random for quality score plots. The quality plots will present the average positional qualities across all of the sequences selected. If input sequences are paired end, plots will be generated for both forward and reverse reads for the same `n` sequences. [default: 10000]" name="pn" optional="True" type="integer" value="10000" />
-    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
-    
-  </inputs>
-
-  <outputs>
-    <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
-    
-  </outputs>
-
-  <help><![CDATA[
-Summarize counts per sample.
-###############################################################
-
-Summarize counts per sample for all samples, and generate interactive
-positional quality plots based on `n` randomly selected sequences.
-
-Parameters
-----------
-data : SampleData[SequencesWithQuality | PairedEndSequencesWithQuality | JoinedSequencesWithQuality]
-    The demultiplexed sequences to be summarized.
-n : Int, optional
-    The number of sequences that should be selected at random for quality
-    score plots. The quality plots will present the average positional
-    qualities across all of the sequences selected. If input sequences are
-    paired end, plots will be generated for both forward and reverse reads
-    for the same `n` sequences.
-
-Returns
--------
-visualization : Visualization
-  ]]></help>
-  <macros>
-    <import>qiime_citation.xml</import>
-  </macros>
-  <expand macro="qiime_citation"/>
-</tool>
\ No newline at end of file

--- a/qiime2-2020.8/qiime_diversity-lib_alpha-passthrough.xml	Thu Sep 03 09:33:04 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,88 +0,0 @@
-<?xml version="1.0" ?>
-<tool id="qiime_diversity-lib_alpha-passthrough" name="qiime diversity-lib alpha-passthrough"
-      version="2020.8">
-  <description>Alpha Passthrough (non-phylogenetic)</description>
-  <requirements>
-    <requirement type="package" version="2020.8">qiime2</requirement>
-  </requirements>
-  <command><![CDATA[
-qiime diversity-lib alpha-passthrough
-
---i-table=$itable
-
---p-metric=$pmetric
-
---o-vector=ovector
-
-#if str($examples) != 'None':
---examples=$examples
-#end if
-
-;
-cp ovector.qza $ovector
-
-  ]]></command>
-  <inputs>
-    <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table containing the samples for which a selected metric should be computed.          [required]" name="itable" optional="False" type="data" />
-    <param label="--p-metric: " name="pmetric" optional="False" type="select">
-      <option value="gini_index">gini_index</option>
-      <option value="simpson_e">simpson_e</option>
-      <option value="osd">osd</option>
-      <option value="mcintosh_e">mcintosh_e</option>
-      <option value="esty_ci">esty_ci</option>
-      <option value="berger_parker_d">berger_parker_d</option>
-      <option value="robbins">robbins</option>
-      <option value="doubles">doubles</option>
-      <option value="michaelis_menten_fit">michaelis_menten_fit</option>
-      <option value="singles">singles</option>
-      <option value="kempton_taylor_q">kempton_taylor_q</option>
-      <option value="fisher_alpha">fisher_alpha</option>
-      <option value="strong">strong</option>
-      <option value="heip_e">heip_e</option>
-      <option value="dominance">dominance</option>
-      <option value="goods_coverage">goods_coverage</option>
-      <option value="ace">ace</option>
-      <option value="enspie">enspie</option>
-      <option value="mcintosh_d">mcintosh_d</option>
-      <option value="chao1_ci">chao1_ci</option>
-      <option value="lladser_pe">lladser_pe</option>
-      <option value="brillouin_d">brillouin_d</option>
-      <option value="menhinick">menhinick</option>
-      <option value="simpson">simpson</option>
-      <option value="margalef">margalef</option>
-      <option value="chao1">chao1</option>
-    </param>
-    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
-    
-  </inputs>
-
-  <outputs>
-    <data format="qza" label="${tool.name} on ${on_string}: vector.qza" name="ovector" />
-    
-  </outputs>
-
-  <help><![CDATA[
-Alpha Passthrough (non-phylogenetic)
-###############################################################
-
-Computes a vector of values (one value for each samples in a feature table)
-using the scikit-bio implementation of the selected alpha diversity metric.
-
-Parameters
-----------
-table : FeatureTable[Frequency]
-    The feature table containing the samples for which a selected metric
-    should be computed.
-metric : Str % Choices('ace', 'berger_parker_d', 'simpson_e', 'doubles', 'gini_index', 'michaelis_menten_fit', 'chao1_ci', 'dominance', 'robbins', 'lladser_pe', 'brillouin_d', 'goods_coverage', 'mcintosh_e', 'esty_ci', 'chao1', 'margalef', 'heip_e', 'enspie', 'menhinick', 'simpson', 'strong', 'fisher_alpha', 'osd', 'singles', 'kempton_taylor_q', 'mcintosh_d')
-    The alpha diversity metric to be computed.
-
-Returns
--------
-vector : SampleData[AlphaDiversity]
-    Vector containing per-sample values for the chosen metric.
-  ]]></help>
-  <macros>
-    <import>qiime_citation.xml</import>
-  </macros>
-  <expand macro="qiime_citation"/>
-</tool>
\ No newline at end of file

--- a/qiime2-2020.8/qiime_diversity-lib_beta-passthrough.xml	Thu Sep 03 09:33:04 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,103 +0,0 @@
-<?xml version="1.0" ?>
-<tool id="qiime_diversity-lib_beta-passthrough" name="qiime diversity-lib beta-passthrough"
-      version="2020.8">
-  <description>Beta Passthrough (non-phylogenetic)</description>
-  <requirements>
-    <requirement type="package" version="2020.8">qiime2</requirement>
-  </requirements>
-  <command><![CDATA[
-qiime diversity-lib beta-passthrough
-
---i-table=$itable
-
---p-metric=$pmetric
-
---p-pseudocount=$ppseudocount
-
-#if str($pnjobs) != 'None':
---p-n-jobs=$pnjobs
-#end if
-
---o-distance-matrix=odistancematrix
-
-#if str($examples) != 'None':
---examples=$examples
-#end if
-
-;
-cp odistancematrix.qza $odistancematrix
-
-  ]]></command>
-  <inputs>
-    <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table containing the samples over which beta diversity should be computed.           [required]" name="itable" optional="False" type="data" />
-    <param label="--p-metric: " name="pmetric" optional="False" type="select">
-      <option value="euclidean">euclidean</option>
-      <option value="cityblock">cityblock</option>
-      <option value="matching">matching</option>
-      <option value="russellrao">russellrao</option>
-      <option value="sokalmichener">sokalmichener</option>
-      <option value="kulsinski">kulsinski</option>
-      <option value="hamming">hamming</option>
-      <option value="chebyshev">chebyshev</option>
-      <option value="yule">yule</option>
-      <option value="dice">dice</option>
-      <option value="canberra_adkins">canberra_adkins</option>
-      <option value="rogerstanimoto">rogerstanimoto</option>
-      <option value="cosine">cosine</option>
-      <option value="minkowski">minkowski</option>
-      <option value="correlation">correlation</option>
-      <option value="sokalsneath">sokalsneath</option>
-      <option value="seuclidean">seuclidean</option>
-      <option value="canberra">canberra</option>
-      <option value="jensenshannon">jensenshannon</option>
-      <option value="sqeuclidean">sqeuclidean</option>
-      <option value="aitchison">aitchison</option>
-    </param>
-    <param label="--p-pseudocount: INTEGER Range(1, None)     A pseudocount to handle zeros for compositional metrics. This is ignored for non-compositional metrics. [default: 1]" min="1" name="ppseudocount" optional="True" type="integer" value="1" />
-    <param label="--p-n-jobs: " name="pnjobs" optional="True" type="select">
-      <option selected="True" value="None">Selection is Optional</option>
-      <option value="Int % Range(1">Int % Range(1</option>
-      <option value="None">None</option>
-    </param>
-    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
-    
-  </inputs>
-
-  <outputs>
-    <data format="qza" label="${tool.name} on ${on_string}: distancematrix.qza" name="odistancematrix" />
-    
-  </outputs>
-
-  <help><![CDATA[
-Beta Passthrough (non-phylogenetic)
-###############################################################
-
-Computes a distance matrix for all pairs of samples in a feature table
-using the scikit-bio implementation of the selected beta diversity metric.
-
-Parameters
-----------
-table : FeatureTable[Frequency]
-    The feature table containing the samples over which beta diversity
-    should be computed.
-metric : Str % Choices('yule', 'seuclidean', 'sokalmichener', 'aitchison', 'canberra_adkins', 'sokalsneath', 'hamming', 'canberra', 'jensenshannon', 'cityblock', 'russellrao', 'minkowski', 'euclidean', 'kulsinski', 'cosine', 'sqeuclidean', 'correlation', 'dice', 'rogerstanimoto', 'chebyshev', 'matching')
-    The beta diversity metric to be computed.
-pseudocount : Int % Range(1, None), optional
-    A pseudocount to handle zeros for compositional metrics. This is
-    ignored for non-compositional metrics.
-n_jobs : Int % Range(1, None) | Str % Choices('auto'), optional
-    The number of concurrent jobs to use in performing this calculation.
-    May not exceed the number of available physical cores. If n_jobs =
-    'auto', one job will be launched for each identified CPU core on the
-    host.
-
-Returns
--------
-distance_matrix : DistanceMatrix
-    The resulting distance matrix.
-  ]]></help>
-  <macros>
-    <import>qiime_citation.xml</import>
-  </macros>
-  <expand macro="qiime_citation"/>
-</tool>
\ No newline at end of file

--- a/qiime2-2020.8/qiime_diversity-lib_beta-phylogenetic-passthrough.xml	Thu Sep 03 09:33:04 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,117 +0,0 @@
-<?xml version="1.0" ?>
-<tool id="qiime_diversity-lib_beta-phylogenetic-passthrough" name="qiime diversity-lib beta-phylogenetic-passthrough"
-      version="2020.8">
-  <description>Beta Phylogenetic Passthrough</description>
-  <requirements>
-    <requirement type="package" version="2020.8">qiime2</requirement>
-  </requirements>
-  <command><![CDATA[
-qiime diversity-lib beta-phylogenetic-passthrough
-
---i-table=$itable
-
---i-phylogeny=$iphylogeny
-
---p-metric=$pmetric
-
-#if str($pthreads) != 'None':
---p-threads=$pthreads
-#end if
-
-#if $pvarianceadjusted:
- --p-variance-adjusted
-#end if
-
-#if str($palpha):
-  --p-alpha=$palpha
-#end if
-#if $pbypasstips:
- --p-bypass-tips
-#end if
-
---o-distance-matrix=odistancematrix
-
-#if str($examples) != 'None':
---examples=$examples
-#end if
-
-;
-cp odistancematrix.qza $odistancematrix
-
-  ]]></command>
-  <inputs>
-    <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table containing the samples over which beta diversity should be computed.        [required]" name="itable" optional="False" type="data" />
-    <param format="qza,no_unzip.zip" label="--i-phylogeny: ARTIFACT  Phylogenetic tree containing tip identifiers that Phylogeny[Rooted]     correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree.                  [required]" name="iphylogeny" optional="False" type="data" />
-    <param label="--p-metric: " name="pmetric" optional="False" type="select">
-      <option value="weighted_unifrac">weighted_unifrac</option>
-      <option value="unweighted_unifrac">unweighted_unifrac</option>
-      <option value="weighted_normalized_unifrac">weighted_normalized_unifrac</option>
-      <option value="generalized_unifrac">generalized_unifrac</option>
-    </param>
-    <param label="--p-threads: " name="pthreads" optional="True" type="select">
-      <option selected="True" value="None">Selection is Optional</option>
-      <option value="Int % Range(1">Int % Range(1</option>
-      <option value="None">None</option>
-    </param>
-    <param label="--p-variance-adjusted: --p-variance-adjusted: / --p-no-variance-adjusted Perform variance adjustment based on Chang et al. BMC Bioinformatics 2011. Weights distances based on the proportion of the relative abundance represented between the samples at a given node under evaluation.                         [default: False]" name="pvarianceadjusted" selected="False" type="boolean" />
-    <param label="--p-alpha: PROPORTION Range(0, 1, inclusive_end=True) This parameter is only used when the choice of metric is generalized_unifrac. The value of alpha controls importance of sample proportions. 1.0 is weighted normalized UniFrac. 0.0 is close to unweighted UniFrac, but only if the sample proportions are dichotomized.             [optional]" name="palpha" optional="False" type="text" />
-    <param label="--p-bypass-tips: --p-bypass-tips: / --p-no-bypass-tips In a bifurcating tree, the tips make up about 50% of the nodes in a tree. By ignoring them, specificity can be traded for reduced compute time. This has the effect of collapsing the phylogeny, and is analogous (in concept) to moving from 99% to 97% OTUs                                [default: False]" name="pbypasstips" selected="False" type="boolean" />
-    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
-    
-  </inputs>
-
-  <outputs>
-    <data format="qza" label="${tool.name} on ${on_string}: distancematrix.qza" name="odistancematrix" />
-    
-  </outputs>
-
-  <help><![CDATA[
-Beta Phylogenetic Passthrough
-###############################################################
-
-Computes a distance matrix for all pairs of samples in a feature table
-using the unifrac implementation of the selected beta diversity metric.
-
-Parameters
-----------
-table : FeatureTable[Frequency]
-    The feature table containing the samples over which beta diversity
-    should be computed.
-phylogeny : Phylogeny[Rooted]
-    Phylogenetic tree containing tip identifiers that correspond to the
-    feature identifiers in the table. This tree can contain tip ids that
-    are not present in the table, but all feature ids in the table must be
-    present in this tree.
-metric : Str % Choices('unweighted_unifrac', 'generalized_unifrac', 'weighted_normalized_unifrac', 'weighted_unifrac')
-    The beta diversity metric to be computed.
-threads : Int % Range(1, None) | Str % Choices('auto'), optional
-    The number of CPU threads to use in performing this calculation. May
-    not exceed the number of available physical cores. If threads = 'auto',
-    one thread will be created for each identified CPU core on the host.
-variance_adjusted : Bool, optional
-    Perform variance adjustment based on Chang et al. BMC Bioinformatics
-    2011. Weights distances based on the proportion of the relative
-    abundance represented between the samples at a given node under
-    evaluation.
-alpha : Float % Range(0, 1, inclusive_end=True), optional
-    This parameter is only used when the choice of metric is
-    generalized_unifrac. The value of alpha controls importance of sample
-    proportions. 1.0 is weighted normalized UniFrac. 0.0 is close to
-    unweighted UniFrac, but only if the sample proportions are
-    dichotomized.
-bypass_tips : Bool, optional
-    In a bifurcating tree, the tips make up about 50% of the nodes in a
-    tree. By ignoring them, specificity can be traded for reduced compute
-    time. This has the effect of collapsing the phylogeny, and is analogous
-    (in concept) to moving from 99% to 97% OTUs
-
-Returns
--------
-distance_matrix : DistanceMatrix
-    The resulting distance matrix.
-  ]]></help>
-  <macros>
-    <import>qiime_citation.xml</import>
-  </macros>
-  <expand macro="qiime_citation"/>
-</tool>
\ No newline at end of file

--- a/qiime2-2020.8/qiime_diversity-lib_bray-curtis.xml	Thu Sep 03 09:33:04 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,73 +0,0 @@
-<?xml version="1.0" ?>
-<tool id="qiime_diversity-lib_bray-curtis" name="qiime diversity-lib bray-curtis"
-      version="2020.8">
-  <description>Bray-Curtis Dissimilarity</description>
-  <requirements>
-    <requirement type="package" version="2020.8">qiime2</requirement>
-  </requirements>
-  <command><![CDATA[
-qiime diversity-lib bray-curtis
-
---i-table=$itable
-
-#if str($pnjobs) != 'None':
---p-n-jobs=$pnjobs
-#end if
-
---o-distance-matrix=odistancematrix
-
-#if str($examples) != 'None':
---examples=$examples
-#end if
-
-;
-cp odistancematrix.qza $odistancematrix
-
-  ]]></command>
-  <inputs>
-    <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table containing the samples for which Bray-Curtis dissimilarity should be computed. [required]" name="itable" optional="False" type="data" />
-    <param label="--p-n-jobs: " name="pnjobs" optional="True" type="select">
-      <option selected="True" value="None">Selection is Optional</option>
-      <option value="Int % Range(1">Int % Range(1</option>
-      <option value="None">None</option>
-    </param>
-    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
-    
-  </inputs>
-
-  <outputs>
-    <data format="qza" label="${tool.name} on ${on_string}: distancematrix.qza" name="odistancematrix" />
-    
-  </outputs>
-
-  <help><![CDATA[
-Bray-Curtis Dissimilarity
-###############################################################
-
-Compute Bray-Curtis dissimilarity for each sample in a feature table. Note:
-Frequency and relative frequency data produce different results unless
-overall sample sizes are identical. Please consider the impact on your
-results if you use Bray-Curtis with count data that has not been adjusted
-(normalized).
-
-Parameters
-----------
-table : FeatureTable[Frequency]
-    The feature table containing the samples for which Bray-Curtis
-    dissimilarity should be computed.
-n_jobs : Int % Range(1, None) | Str % Choices('auto'), optional
-    The number of concurrent jobs to use in performing this calculation.
-    May not exceed the number of available physical cores. If n_jobs =
-    'auto', one job will be launched for each identified CPU core on the
-    host.
-
-Returns
--------
-distance_matrix : DistanceMatrix
-    Distance matrix for Bray-Curtis dissimilarity
-  ]]></help>
-  <macros>
-    <import>qiime_citation.xml</import>
-  </macros>
-  <expand macro="qiime_citation"/>
-</tool>
\ No newline at end of file

--- a/qiime2-2020.8/qiime_diversity-lib_faith-pd.xml	Thu Sep 03 09:33:04 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,66 +0,0 @@
-<?xml version="1.0" ?>
-<tool id="qiime_diversity-lib_faith-pd" name="qiime diversity-lib faith-pd"
-      version="2020.8">
-  <description>Faith\'s Phylogenetic Diversity</description>
-  <requirements>
-    <requirement type="package" version="2020.8">qiime2</requirement>
-  </requirements>
-  <command><![CDATA[
-qiime diversity-lib faith-pd
-
-#if $itable:
- --i-table
-#end if
-
---i-phylogeny=$iphylogeny
-
---o-vector=ovector
-
-#if str($examples) != 'None':
---examples=$examples
-#end if
-
-;
-cp ovector.qza $ovector
-
-  ]]></command>
-  <inputs>
-    <param format="qza,no_unzip.zip" label="--i-table: --i-table: ARTIFACT FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]      The feature table containing the samples for which Faith\'s phylogenetic diversity should be computed. Table values will be converted to presence/absence. [required]" name="itable" selected="False" type="boolean" />
-    <param format="qza,no_unzip.zip" label="--i-phylogeny: ARTIFACT  Phylogenetic tree containing tip identifiers that Phylogeny[Rooted]     correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree.                  [required]" name="iphylogeny" optional="False" type="data" />
-    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
-    
-  </inputs>
-
-  <outputs>
-    <data format="qza" label="${tool.name} on ${on_string}: vector.qza" name="ovector" />
-    
-  </outputs>
-
-  <help><![CDATA[
-Faith\'s Phylogenetic Diversity
-###############################################################
-
-Computes Faith's Phylogenetic Diversity for all samples in a feature table.
-
-Parameters
-----------
-table : FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]
-    The feature table containing the samples for which Faith's phylogenetic
-    diversity should be computed. Table values will be converted to
-    presence/absence.
-phylogeny : Phylogeny[Rooted]
-    Phylogenetic tree containing tip identifiers that correspond to the
-    feature identifiers in the table. This tree can contain tip ids that
-    are not present in the table, but all feature ids in the table must be
-    present in this tree.
-
-Returns
--------
-vector : SampleData[AlphaDiversity]
-    Vector containing per-sample values for Faith's Phylogenetic Diversity.
-  ]]></help>
-  <macros>
-    <import>qiime_citation.xml</import>
-  </macros>
-  <expand macro="qiime_citation"/>
-</tool>
\ No newline at end of file

--- a/qiime2-2020.8/qiime_diversity-lib_jaccard.xml	Thu Sep 03 09:33:04 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,71 +0,0 @@
-<?xml version="1.0" ?>
-<tool id="qiime_diversity-lib_jaccard" name="qiime diversity-lib jaccard"
-      version="2020.8">
-  <description>Jaccard Distance</description>
-  <requirements>
-    <requirement type="package" version="2020.8">qiime2</requirement>
-  </requirements>
-  <command><![CDATA[
-qiime diversity-lib jaccard
-
---i-table=$itable
-
-#if str($pnjobs) != 'None':
---p-n-jobs=$pnjobs
-#end if
-
---o-distance-matrix=odistancematrix
-
-#if str($examples) != 'None':
---examples=$examples
-#end if
-
-;
-cp odistancematrix.qza $odistancematrix
-
-  ]]></command>
-  <inputs>
-    <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]   The feature table containing the samples for which Jaccard distance should be computed.         [required]" name="itable" optional="False" type="data" />
-    <param label="--p-n-jobs: " name="pnjobs" optional="True" type="select">
-      <option selected="True" value="None">Selection is Optional</option>
-      <option value="Int % Range(1">Int % Range(1</option>
-      <option value="None">None</option>
-    </param>
-    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
-    
-  </inputs>
-
-  <outputs>
-    <data format="qza" label="${tool.name} on ${on_string}: distancematrix.qza" name="odistancematrix" />
-    
-  </outputs>
-
-  <help><![CDATA[
-Jaccard Distance
-###############################################################
-
-Compute Jaccard distance for each sample in a feature table. Jaccard is
-calculated usingpresence/absence data. Data of type FeatureTable[Frequency
-| Relative Frequency] is reducedto presence/absence prior to calculation.
-
-Parameters
-----------
-table : FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]
-    The feature table containing the samples for which Jaccard distance
-    should be computed.
-n_jobs : Int % Range(1, None) | Str % Choices('auto'), optional
-    The number of concurrent jobs to use in performing this calculation.
-    May not exceed the number of available physical cores. If n_jobs =
-    'auto', one job will be launched for each identified CPU core on the
-    host.
-
-Returns
--------
-distance_matrix : DistanceMatrix
-    Distance matrix for Jaccard index
-  ]]></help>
-  <macros>
-    <import>qiime_citation.xml</import>
-  </macros>
-  <expand macro="qiime_citation"/>
-</tool>
\ No newline at end of file

--- a/qiime2-2020.8/qiime_diversity-lib_observed-features.xml	Thu Sep 03 09:33:04 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,58 +0,0 @@
-<?xml version="1.0" ?>
-<tool id="qiime_diversity-lib_observed-features" name="qiime diversity-lib observed-features"
-      version="2020.8">
-  <description>Observed Features</description>
-  <requirements>
-    <requirement type="package" version="2020.8">qiime2</requirement>
-  </requirements>
-  <command><![CDATA[
-qiime diversity-lib observed-features
-
-#if $itable:
- --i-table
-#end if
-
---o-vector=ovector
-
-#if str($examples) != 'None':
---examples=$examples
-#end if
-
-;
-cp ovector.qza $ovector
-
-  ]]></command>
-  <inputs>
-    <param format="qza,no_unzip.zip" label="--i-table: --i-table: ARTIFACT FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]   The feature table containing the samples for which the number of observed features should be calculated. Table values will be converted to presence/absence. [required]" name="itable" selected="False" type="boolean" />
-    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
-    
-  </inputs>
-
-  <outputs>
-    <data format="qza" label="${tool.name} on ${on_string}: vector.qza" name="ovector" />
-    
-  </outputs>
-
-  <help><![CDATA[
-Observed Features
-###############################################################
-
-Compute the number of observed features for each sample in a feature table
-
-Parameters
-----------
-table : FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]
-    The feature table containing the samples for which the number of
-    observed features should be calculated. Table values will be converted
-    to presence/absence.
-
-Returns
--------
-vector : SampleData[AlphaDiversity]
-    Vector containing per-sample counts of observed features.
-  ]]></help>
-  <macros>
-    <import>qiime_citation.xml</import>
-  </macros>
-  <expand macro="qiime_citation"/>
-</tool>
\ No newline at end of file

--- a/qiime2-2020.8/qiime_diversity-lib_pielou-evenness.xml	Thu Sep 03 09:33:04 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,63 +0,0 @@
-<?xml version="1.0" ?>
-<tool id="qiime_diversity-lib_pielou-evenness" name="qiime diversity-lib pielou-evenness"
-      version="2020.8">
-  <description>Pielou\'s Evenness</description>
-  <requirements>
-    <requirement type="package" version="2020.8">qiime2</requirement>
-  </requirements>
-  <command><![CDATA[
-qiime diversity-lib pielou-evenness
-
---i-table=$itable
-
-#if $pdropundefinedsamples:
- --p-drop-undefined-samples
-#end if
-
---o-vector=ovector
-
-#if str($examples) != 'None':
---examples=$examples
-#end if
-
-;
-cp ovector.qza $ovector
-
-  ]]></command>
-  <inputs>
-    <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency | RelativeFrequency] The feature table containing the samples for which Pielou\'s evenness should be computed.        [required]" name="itable" optional="False" type="data" />
-    <param label="--p-drop-undefined-samples: --p-drop-undefined-samples: / --p-no-drop-undefined-samples Samples with fewer than two observed features produce undefined (NaN) values. If true, these samples are dropped from the output vector.        [default: False]" name="pdropundefinedsamples" selected="False" type="boolean" />
-    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
-    
-  </inputs>
-
-  <outputs>
-    <data format="qza" label="${tool.name} on ${on_string}: vector.qza" name="ovector" />
-    
-  </outputs>
-
-  <help><![CDATA[
-Pielou\'s Evenness
-###############################################################
-
-Compute Pielou's Evenness for each sample in a feature table
-
-Parameters
-----------
-table : FeatureTable[Frequency | RelativeFrequency]
-    The feature table containing the samples for which Pielou's evenness
-    should be computed.
-drop_undefined_samples : Bool, optional
-    Samples with fewer than two observed features produce undefined (NaN)
-    values. If true, these samples are dropped from the output vector.
-
-Returns
--------
-vector : SampleData[AlphaDiversity]
-    Vector containing per-sample values for Pielou's Evenness.
-  ]]></help>
-  <macros>
-    <import>qiime_citation.xml</import>
-  </macros>
-  <expand macro="qiime_citation"/>
-</tool>
\ No newline at end of file

--- a/qiime2-2020.8/qiime_diversity-lib_shannon-entropy.xml	Thu Sep 03 09:33:04 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,63 +0,0 @@
-<?xml version="1.0" ?>
-<tool id="qiime_diversity-lib_shannon-entropy" name="qiime diversity-lib shannon-entropy"
-      version="2020.8">
-  <description>Shannon\'s Entropy</description>
-  <requirements>
-    <requirement type="package" version="2020.8">qiime2</requirement>
-  </requirements>
-  <command><![CDATA[
-qiime diversity-lib shannon-entropy
-
---i-table=$itable
-
-#if $pdropundefinedsamples:
- --p-drop-undefined-samples
-#end if
-
---o-vector=ovector
-
-#if str($examples) != 'None':
---examples=$examples
-#end if
-
-;
-cp ovector.qza $ovector
-
-  ]]></command>
-  <inputs>
-    <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency | RelativeFrequency] The feature table containing the samples for which Shannon\'s Entropy should be computed.        [required]" name="itable" optional="False" type="data" />
-    <param label="--p-drop-undefined-samples: --p-drop-undefined-samples: / --p-no-drop-undefined-samples Samples with no observed features produce undefined (NaN) values. If true, these samples are dropped from the output vector.                     [default: False]" name="pdropundefinedsamples" selected="False" type="boolean" />
-    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
-    
-  </inputs>
-
-  <outputs>
-    <data format="qza" label="${tool.name} on ${on_string}: vector.qza" name="ovector" />
-    
-  </outputs>
-
-  <help><![CDATA[
-Shannon\'s Entropy
-###############################################################
-
-Compute Shannon's Entropy for each sample in a feature table
-
-Parameters
-----------
-table : FeatureTable[Frequency | RelativeFrequency]
-    The feature table containing the samples for which Shannon's Entropy
-    should be computed.
-drop_undefined_samples : Bool, optional
-    Samples with no observed features produce undefined (NaN) values. If
-    true, these samples are dropped from the output vector.
-
-Returns
--------
-vector : SampleData[AlphaDiversity]
-    Vector containing per-sample values for Shannon's Entropy.
-  ]]></help>
-  <macros>
-    <import>qiime_citation.xml</import>
-  </macros>
-  <expand macro="qiime_citation"/>
-</tool>
\ No newline at end of file

--- a/qiime2-2020.8/qiime_diversity-lib_unweighted-unifrac.xml	Thu Sep 03 09:33:04 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,86 +0,0 @@
-<?xml version="1.0" ?>
-<tool id="qiime_diversity-lib_unweighted-unifrac" name="qiime diversity-lib unweighted-unifrac"
-      version="2020.8">
-  <description>Unweighted Unifrac</description>
-  <requirements>
-    <requirement type="package" version="2020.8">qiime2</requirement>
-  </requirements>
-  <command><![CDATA[
-qiime diversity-lib unweighted-unifrac
-
---i-table=$itable
-
---i-phylogeny=$iphylogeny
-
-#if str($pthreads) != 'None':
---p-threads=$pthreads
-#end if
-
-#if $pbypasstips:
- --p-bypass-tips
-#end if
-
---o-distance-matrix=odistancematrix
-
-#if str($examples) != 'None':
---examples=$examples
-#end if
-
-;
-cp odistancematrix.qza $odistancematrix
-
-  ]]></command>
-  <inputs>
-    <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]      The feature table containing the samples for which Unweighted Unifrac should be computed.    [required]" name="itable" optional="False" type="data" />
-    <param format="qza,no_unzip.zip" label="--i-phylogeny: ARTIFACT  Phylogenetic tree containing tip identifiers that Phylogeny[Rooted]     correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree.                  [required]" name="iphylogeny" optional="False" type="data" />
-    <param label="--p-threads: " name="pthreads" optional="True" type="select">
-      <option selected="True" value="None">Selection is Optional</option>
-      <option value="Int % Range(1">Int % Range(1</option>
-      <option value="None">None</option>
-    </param>
-    <param label="--p-bypass-tips: --p-bypass-tips: / --p-no-bypass-tips In a bifurcating tree, the tips make up about 50% of the nodes in a tree. By ignoring them, specificity can be traded for reduced compute time. This has the effect of collapsing the phylogeny, and is analogous (in concept) to moving from 99% to 97% OTUs                                [default: False]" name="pbypasstips" selected="False" type="boolean" />
-    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
-    
-  </inputs>
-
-  <outputs>
-    <data format="qza" label="${tool.name} on ${on_string}: distancematrix.qza" name="odistancematrix" />
-    
-  </outputs>
-
-  <help><![CDATA[
-Unweighted Unifrac
-###############################################################
-
-Compute Unweighted Unifrac for each sample in a feature table
-
-Parameters
-----------
-table : FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]
-    The feature table containing the samples for which Unweighted Unifrac
-    should be computed.
-phylogeny : Phylogeny[Rooted]
-    Phylogenetic tree containing tip identifiers that correspond to the
-    feature identifiers in the table. This tree can contain tip ids that
-    are not present in the table, but all feature ids in the table must be
-    present in this tree.
-threads : Int % Range(1, None) | Str % Choices('auto'), optional
-    The number of CPU threads to use in performing this calculation. May
-    not exceed the number of available physical cores. If threads = 'auto',
-    one thread will be created for each identified CPU core on the host.
-bypass_tips : Bool, optional
-    In a bifurcating tree, the tips make up about 50% of the nodes in a
-    tree. By ignoring them, specificity can be traded for reduced compute
-    time. This has the effect of collapsing the phylogeny, and is analogous
-    (in concept) to moving from 99% to 97% OTUs
-
-Returns
--------
-distance_matrix : DistanceMatrix
-    Distance matrix for Unweighted Unifrac.
-  ]]></help>
-  <macros>
-    <import>qiime_citation.xml</import>
-  </macros>
-  <expand macro="qiime_citation"/>
-</tool>
\ No newline at end of file

--- a/qiime2-2020.8/qiime_diversity-lib_weighted-unifrac.xml	Thu Sep 03 09:33:04 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,86 +0,0 @@
-<?xml version="1.0" ?>
-<tool id="qiime_diversity-lib_weighted-unifrac" name="qiime diversity-lib weighted-unifrac"
-      version="2020.8">
-  <description>Weighted Unifrac</description>
-  <requirements>
-    <requirement type="package" version="2020.8">qiime2</requirement>
-  </requirements>
-  <command><![CDATA[
-qiime diversity-lib weighted-unifrac
-
---i-table=$itable
-
---i-phylogeny=$iphylogeny
-
-#if str($pthreads) != 'None':
---p-threads=$pthreads
-#end if
-
-#if $pbypasstips:
- --p-bypass-tips
-#end if
-
---o-distance-matrix=odistancematrix
-
-#if str($examples) != 'None':
---examples=$examples
-#end if
-
-;
-cp odistancematrix.qza $odistancematrix
-
-  ]]></command>
-  <inputs>
-    <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency | RelativeFrequency] The feature table containing the samples for which Weighted Unifrac should be computed.      [required]" name="itable" optional="False" type="data" />
-    <param format="qza,no_unzip.zip" label="--i-phylogeny: ARTIFACT  Phylogenetic tree containing tip identifiers that Phylogeny[Rooted]     correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree.                  [required]" name="iphylogeny" optional="False" type="data" />
-    <param label="--p-threads: " name="pthreads" optional="True" type="select">
-      <option selected="True" value="None">Selection is Optional</option>
-      <option value="Int % Range(1">Int % Range(1</option>
-      <option value="None">None</option>
-    </param>
-    <param label="--p-bypass-tips: --p-bypass-tips: / --p-no-bypass-tips In a bifurcating tree, the tips make up about 50% of the nodes in a tree. By ignoring them, specificity can be traded for reduced compute time. This has the effect of collapsing the phylogeny, and is analogous (in concept) to moving from 99% to 97% OTUs                                [default: False]" name="pbypasstips" selected="False" type="boolean" />
-    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
-    
-  </inputs>
-
-  <outputs>
-    <data format="qza" label="${tool.name} on ${on_string}: distancematrix.qza" name="odistancematrix" />
-    
-  </outputs>
-
-  <help><![CDATA[
-Weighted Unifrac
-###############################################################
-
-Compute Weighted Unifrac for each sample in a feature table
-
-Parameters
-----------
-table : FeatureTable[Frequency | RelativeFrequency]
-    The feature table containing the samples for which Weighted Unifrac
-    should be computed.
-phylogeny : Phylogeny[Rooted]
-    Phylogenetic tree containing tip identifiers that correspond to the
-    feature identifiers in the table. This tree can contain tip ids that
-    are not present in the table, but all feature ids in the table must be
-    present in this tree.
-threads : Int % Range(1, None) | Str % Choices('auto'), optional
-    The number of CPU threads to use in performing this calculation. May
-    not exceed the number of available physical cores. If threads = 'auto',
-    one thread will be created for each identified CPU core on the host.
-bypass_tips : Bool, optional
-    In a bifurcating tree, the tips make up about 50% of the nodes in a
-    tree. By ignoring them, specificity can be traded for reduced compute
-    time. This has the effect of collapsing the phylogeny, and is analogous
-    (in concept) to moving from 99% to 97% OTUs
-
-Returns
--------
-distance_matrix : DistanceMatrix
-    Distance matrix for Unweighted Unifrac.
-  ]]></help>
-  <macros>
-    <import>qiime_citation.xml</import>
-  </macros>
-  <expand macro="qiime_citation"/>
-</tool>
\ No newline at end of file