# HG changeset patch
# User florianbegusch
# Date 1564556760 14400
# Node ID 914fa4daf16a72aaddeb74199130c63c14de5b1e
# Parent  5586454168418579ce7178e086da758f5a822591
Fixes

diff -r 558645416841 -r 914fa4daf16a qiime2/merge_feature_table_and_taxonomy.xml
--- a/qiime2/merge_feature_table_and_taxonomy.xml	Sun Jul 21 02:21:34 2019 -0400
+++ b/qiime2/merge_feature_table_and_taxonomy.xml	Wed Jul 31 03:06:00 2019 -0400
@@ -7,8 +7,8 @@
 	<command>
 mkdir out;
 
-qiime tools export --input-path --output-path out $taxonomy_qza;
-qiime tools export --input-path --output-path out $biom_qza;
+qiime tools export --input-path $taxonomy_qza --output-path out;
+qiime tools export --input-path $biom_qza --output-path out;
 
 sed -i '1s;^;#;' out/*.tsv;
 sed -i 's/Confidence/confidence/g' out/*.tsv;
diff -r 558645416841 -r 914fa4daf16a qiime2/qiime_alignment_mask.xml
--- a/qiime2/qiime_alignment_mask.xml	Sun Jul 21 02:21:34 2019 -0400
+++ b/qiime2/qiime_alignment_mask.xml	Wed Jul 31 03:06:00 2019 -0400
@@ -19,6 +19,7 @@
  --p-min-conservation=$pminconservation
 #end if
 
+;
 cp omaskedalignment.qza $omaskedalignment
 	]]></command>
 	<inputs>
diff -r 558645416841 -r 914fa4daf16a qiime2/qiime_cutadapt_demux-paired.xml
--- a/qiime2/qiime_cutadapt_demux-paired.xml	Sun Jul 21 02:21:34 2019 -0400
+++ b/qiime2/qiime_cutadapt_demux-paired.xml	Wed Jul 31 03:06:00 2019 -0400
@@ -9,33 +9,70 @@
 --i-seqs=$iseqs
 
 
-#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 + ',' + d['additional_input'].__getattr__('file_name')
-  #end for
-  #return $file_list
+#if $input_files_mforwardbarcodesfile:
+#def list_dict_to_string_forward(list_dict):
+	#set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
+	#for d in list_dict[1:]:
+		#set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
+	#end for
+	#return $file_list
 #end def
-
-#if $input_files_mforwardbarcodesfile:
---m-forward-barcodes-file=$list_dict_to_string("$input_files_mforwardbarcodesfile")
+--m-forward-barcodes-file=$list_dict_to_string_forward($input_files_mforwardbarcodesfile)
 #end if
 
 #if $input_files_mreversebarcodesfile:
---m-reverse-barcodes-file=$list_dict_to_string("$input_files_mreversebarcodesfile")
+#def list_dict_to_string_reverse(list_dict):
+	#set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
+	#for d in list_dict[1:]:
+		#set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
+	#end for
+	#return $file_list
+#end def
+--m-reverse-barcodes-file=$list_dict_to_string_reverse($input_files_mreversebarcodesfile)
+#end if
+
+
+
+
+#if '__sq__' in str($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 = $mforwardbarcodescolumn_temp
+#end if
+
+#if str($mforwardbarcodescolumn):
 --m-forward-barcodes-column="$mforwardbarcodescolumn"
+#end if
+
+
+
+
+#if '__sq__' in str($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
 
+
+
 #if $perrorrate:
  --p-error-rate=$perrorrate
 #end if
 
 
+
 --o-per-sample-sequences=opersamplesequences
 --o-untrimmed-sequences=ountrimmedsequences
 ;
diff -r 558645416841 -r 914fa4daf16a qiime2/qiime_cutadapt_demux-single.xml
--- a/qiime2/qiime_cutadapt_demux-single.xml	Sun Jul 21 02:21:34 2019 -0400
+++ b/qiime2/qiime_cutadapt_demux-single.xml	Wed Jul 31 03:06:00 2019 -0400
@@ -8,22 +8,37 @@
 qiime cutadapt demux-single
 
 --i-seqs=$iseqs
+
+
+
+#if '__sq__' in str($mbarcodescolumn):
+  #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('__sq__', "'")
+  #set $mbarcodescolumn = $mbarcodescolumn_temp
+#end if
+
 --m-barcodes-column="$mbarcodescolumn"
+
+
 --o-per-sample-sequences=opersamplesequences
 --o-untrimmed-sequences=ountrimmedsequences
 
 
+
+
+
+
 #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 + ',' + d['additional_input'].__getattr__('file_name')
-  #end for
-  #return $file_list
+#set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
+#for d in list_dict[1:]:
+	#set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
+#end for
+#return $file_list
 #end def
---m-barcodes-file=$list_dict_to_string("$input_files_mbarcodesfile")
+--m-barcodes-file=$list_dict_to_string($input_files_mbarcodesfile)
 #end if
 
+
 #if $perrorrate:
  --p-error-rate=$perrorrate
 #end if
@@ -35,7 +50,7 @@
 	]]></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="$input_files_mbarcodesfile" optional="False" title="--m-barcodes-file">
+		<repeat name="input_files_mbarcodesfile" optional="False" title="--m-barcodes-file">
 			<param label="--m-barcodes-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
 		</repeat>
 		<param label="--m-barcodes-column: COLUMN  MetadataColumn[Categorical] The sample metadata column listing the per-sample barcodes.                                 [required]" name="mbarcodescolumn" optional="False" type="text"/>
diff -r 558645416841 -r 914fa4daf16a qiime2/qiime_cutadapt_trim-paired.xml
--- a/qiime2/qiime_cutadapt_trim-paired.xml	Sun Jul 21 02:21:34 2019 -0400
+++ b/qiime2/qiime_cutadapt_trim-paired.xml	Wed Jul 31 03:06:00 2019 -0400
@@ -14,14 +14,37 @@
 --p-cores=$pcores
 #end if
 
+
+
+#if '__sq__' in str($padapterf):
+  #set $padapterf_temp = $padapterf.replace('__sq__', "'")
+  #set $padapterf = $padapterf_temp
+#end if
+
+#if 'X' in str($padapterf):
+  #set $padapterf_temp = $padapterf.replace('X', "$")
+  #set $padapterf = $padapterf_temp
+#end if
+
 #if str($padapterf):
  --p-adapter-f="$padapterf"
 #end if
 
+
+
+
+#if '__sq__' in str($pfrontf):
+  #set $pfrontf_temp = $pfrontf.replace('__sq__', "'")
+  #set $pfrontf = $pfrontf_temp
+#end if
+
 #if str($pfrontf):
  --p-front-f="$pfrontf"
 #end if
 
+
+
+
 #if '__sq__' in str($panywheref):
   #set $panywheref_temp = $panywheref.replace('__sq__', "'")
   #set $panywheref = $panywheref_temp
@@ -32,14 +55,36 @@
 #end if
 
 
+
+
+
+#if '__sq__' in str($padapterr):
+  #set $padapterr_temp = $padapterr.replace('__sq__', "'")
+  #set $padapterr = $padapterr_temp
+#end if
+
+#if 'X' in str($padapterr):
+  #set $padapterr_temp = $padapterr.replace('X', "$")
+  #set $padapterr = $padapterr_temp
+#end if
+
 #if str($padapterr):
  --p-adapter-r="$padapterr"
 #end if
 
+
+
+#if '__sq__' in str($pfrontr):
+  #set $pfrontr_temp = $pfrontr.replace('__sq__', "'")
+  #set $pfrontr = $pfrontr_temp
+#end if
+
 #if str($pfrontr):
  --p-front-r="$pfrontr"
 #end if
 
+
+
 #if '__sq__' in str($panywherer):
   #set $panywherer_temp = $panywherer.replace('__sq__', "'")
   #set $panywherer = $panywherer_temp
@@ -49,6 +94,8 @@
  --p-anywhere-r="$panywherer"
 #end if
 
+
+
 #if $perrorrate:
  --p-error-rate=$perrorrate
 #end if
diff -r 558645416841 -r 914fa4daf16a qiime2/qiime_cutadapt_trim-single.xml
--- a/qiime2/qiime_cutadapt_trim-single.xml	Sun Jul 21 02:21:34 2019 -0400
+++ b/qiime2/qiime_cutadapt_trim-single.xml	Wed Jul 31 03:06:00 2019 -0400
@@ -13,14 +13,38 @@
 --p-cores=$pcores
 #end if
 
+
+#if '__sq__' in str($padapter):
+  #set $padapter_temp = $padapter.replace('__sq__', "'")
+  #set $padapter = $padapter_temp
+#end if
+
+#if 'X' in str($padapter):
+  #set $padapter_temp = $padapter.replace('X', "$")
+  #set $padapter = $padapter_temp
+#end if
+
 #if str($padapter):
  --p-adapter="$padapter"
 #end if
 
+
+
+
+
+#if '__sq__' in str($pfront):
+  #set $pfront_temp = $pfront.replace('__sq__', "'")
+  #set $pfront = $pfront_temp
+#end if
+
 #if str($pfront):
  --p-front="$pfront"
 #end if
 
+
+
+
+
 #if '__sq__' in str($panywhere):
   #set $panywhere_temp = $panywhere.replace('__sq__', "'")
   #set $panywhere = $panywhere_temp
@@ -31,6 +55,8 @@
 #end if
 
 
+
+
 #if $perrorrate:
  --p-error-rate=$perrorrate
 #end if
diff -r 558645416841 -r 914fa4daf16a qiime2/qiime_dada2_denoise-pyro.xml
--- a/qiime2/qiime_dada2_denoise-pyro.xml	Sun Jul 21 02:21:34 2019 -0400
+++ b/qiime2/qiime_dada2_denoise-pyro.xml	Wed Jul 31 03:06:00 2019 -0400
@@ -141,6 +141,7 @@
     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>
diff -r 558645416841 -r 914fa4daf16a qiime2/qiime_dada2_denoise-single.xml
--- a/qiime2/qiime_dada2_denoise-single.xml	Sun Jul 21 02:21:34 2019 -0400
+++ b/qiime2/qiime_dada2_denoise-single.xml	Wed Jul 31 03:06:00 2019 -0400
@@ -66,7 +66,7 @@
 		</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: If false, 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: Fales]" name="pnohashedfeatureids" selected="False" type="boolean"/>
+		<param label="--p-no-hashed-feature-ids: If false, 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: False]" name="pnohashedfeatureids" selected="False" type="boolean"/>
 	</inputs>
 	<outputs>
 		<data format="qza" label="${tool.name} on ${on_string}: table.qza" name="otable"/>
diff -r 558645416841 -r 914fa4daf16a qiime2/qiime_demux_emp-single.xml
--- a/qiime2/qiime_demux_emp-single.xml	Sun Jul 21 02:21:34 2019 -0400
+++ b/qiime2/qiime_demux_emp-single.xml	Wed Jul 31 03:06:00 2019 -0400
@@ -42,8 +42,8 @@
 cp oerrorcorrectiondetails.qza $oerrorcorrectiondetails
 	]]></command>
 	<inputs>
-		<repeat name="input_files_mbarcodesfile" optional="False" title="--m-barcodes-file">
-			<param label="--m-barcodes-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip"/>
+		<repeat name="input_files_mbarcodesfile" optional="True" title="--m-barcodes-file [optional]">
+			<param label="--m-barcodes-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip"/>
 		</repeat>
 
 		<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"/>
diff -r 558645416841 -r 914fa4daf16a qiime2/qiime_diversity_adonis.xml
--- a/qiime2/qiime_diversity_adonis.xml	Sun Jul 21 02:21:34 2019 -0400
+++ b/qiime2/qiime_diversity_adonis.xml	Wed Jul 31 03:06:00 2019 -0400
@@ -14,16 +14,24 @@
 #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 + ',' + d['additional_input'].__getattr__('file_name')
+	  #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("$input_files_mmetadatafile")
+--m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
 #end if
 
 
+
+#if '__sq__' in str($pformula):
+  #set $pformula_temp = $pformula.replace('__sq__', "'")
+  #set $pformula = $pformula_temp
+#end if
+
 --p-formula="$pformula"
 
+
+
 #if $ppermutations:
  --p-permutations=$ppermutations
 #end if
@@ -44,7 +52,7 @@
 		<param label="--p-formula: TEXT     Model formula containing only independent terms contained in the sample metadata. These can be continuous variables or factors, and they can have interactions as in a typical R formula. E.g., the formula 'treatment+block' would test whether the input distance matrix partitions based on 'treatment' and 'block' sample metadata. The formula 'treatment*block' would test both of those effects as well as their interaction. Enclose formulae in quotes to avoid unpleasant surprises.                        [required]" name="pformula" optional="False" type="text"/>
 		<param label="--p-permutations: INTEGER Range(1, None)     The number of permutations to be run when computing p-values.                                [default: 999]" name="ppermutations" optional="True" min="1" type="integer" value="999"/>
 
-		<repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
+		<repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file  [required]">
 			<param format="tabular" label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [required]" name="additional_input" type="data"/>
 		</repeat>
 	</inputs>
diff -r 558645416841 -r 914fa4daf16a qiime2/qiime_diversity_alpha-correlation.xml
--- a/qiime2/qiime_diversity_alpha-correlation.xml	Sun Jul 21 02:21:34 2019 -0400
+++ b/qiime2/qiime_diversity_alpha-correlation.xml	Wed Jul 31 03:06:00 2019 -0400
@@ -38,12 +38,11 @@
 			<option value="pearson">pearson</option>
 		</param>
 
-		<repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
+		<repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file  [required]">
 			<param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
 		</repeat>
 	</inputs>
 	<outputs>
-		<data format="qza" label="${tool.name} on ${on_string}: metadatafile.qza" name="mmetadatafile"/>
 		<data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
 	</outputs>
 	<help><![CDATA[
diff -r 558645416841 -r 914fa4daf16a qiime2/qiime_diversity_alpha-group-significance.xml
--- a/qiime2/qiime_diversity_alpha-group-significance.xml	Sun Jul 21 02:21:34 2019 -0400
+++ b/qiime2/qiime_diversity_alpha-group-significance.xml	Wed Jul 31 03:06:00 2019 -0400
@@ -31,7 +31,7 @@
 	<inputs>
 		<param format="qza,no_unzip.zip" label="--i-alpha-diversity: ARTIFACT SampleData[AlphaDiversity] Vector of alpha diversity values by sample.  [required]" name="ialphadiversity" optional="False" type="data"/>
 
-		<repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
+		<repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file  [required]">
 			<param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
 		</repeat>
 	</inputs>
diff -r 558645416841 -r 914fa4daf16a qiime2/qiime_diversity_beta-correlation.xml
--- a/qiime2/qiime_diversity_beta-correlation.xml	Sun Jul 21 02:21:34 2019 -0400
+++ b/qiime2/qiime_diversity_beta-correlation.xml	Wed Jul 31 03:06:00 2019 -0400
@@ -8,8 +8,18 @@
 qiime diversity beta-correlation
 
 --i-distance-matrix=$idistancematrix
+
+
+
+#if '__sq__' in str($mmetadatacolumn):
+  #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__sq__', "'")
+  #set $mmetadatacolumn = $mmetadatacolumn_temp
+#end if
+
 --m-metadata-column="$mmetadatacolumn"
 
+
+
 #if str($pmethod) != 'None':
  --p-method=$pmethod
 #end if
@@ -22,14 +32,31 @@
  --p-intersect-ids
 #end if
 
+
+
+
+#if '__sq__' in str($plabel1):
+  #set $plabel1_temp = $plabel1.replace('__sq__', "'")
+  #set $plabel1 = $plabel1_temp
+#end if
+
 #if str($plabel1):
  --p-label1="$plabel1"
 #end if
 
+
+
+#if '__sq__' in str($plabel2):
+  #set $plabel2_temp = $plabel2.replace('__sq__', "'")
+  #set $plabel2 = $plabel2_temp
+#end if
+
 #if str($plabel2):
  --p-label2="$plabel2"
 #end if
 
+
+
 #if $input_files_mmetadatafile:
 #def list_dict_to_string(list_dict):
 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
@@ -59,9 +86,9 @@
 		</param>
 		<param label="--p-permutations: INTEGER Range(0, None)     The number of permutations to be run when computing p-values. Supplying a value of zero will disable permutation testing and p-values will not be calculated (this results in *much* quicker execution time if p-values are not desired).               [default: 999]" name="ppermutations" optional="True" type="integer" min="0" value="999"/>
 		<param label="--p-intersect-ids: --p-no-intersect-ids If supplied, IDs that are not found in both distance matrices will be discarded before applying the Mantel test. Default behavior is to error on any mismatched IDs.                                   [default: False]" name="pintersectids" selected="False" type="boolean"/>
-		<param label="--p-label1: TEXT      Label for `distance-matrix` in the output visualization.                    [default: 'Metadata']" name="plabel1" optional="True" type="text" value="'Metadata'"/>
-		<param label="--p-label2: TEXT      Label for `metadata-distance-matrix` in the output visualization.             [default: 'Distance Matrix']" name="plabel2" optional="True" type="text" value="'Distance Matrix'"/>
-		<repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
+		<param label="--p-label1: TEXT      Label for `distance-matrix` in the output visualization.                    [default: 'Metadata']" name="plabel1" optional="True" type="text" value="Metadata"/>
+		<param label="--p-label2: TEXT      Label for `metadata-distance-matrix` in the output visualization.             [default: 'Distance Matrix']" name="plabel2" optional="True" type="text" value="Distance Matrix"/>
+		<repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file  [required]">
 			<param label="--m-metadata-file" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
 		</repeat>
 	</inputs>
diff -r 558645416841 -r 914fa4daf16a qiime2/qiime_diversity_beta-group-significance.xml
--- a/qiime2/qiime_diversity_beta-group-significance.xml	Sun Jul 21 02:21:34 2019 -0400
+++ b/qiime2/qiime_diversity_beta-group-significance.xml	Wed Jul 31 03:06:00 2019 -0400
@@ -55,7 +55,7 @@
 		<param label="--p-pairwise: --p-no-pairwise Perform pairwise tests between all pairs of groups in addition to the test across all groups. This can be very slow if there are a lot of groups in the metadata column.                                [default: False]" name="ppairwise" selected="False" type="boolean"/>
 		<param label="--p-permutations: INTEGER The number of permutations to be run when computing p-values.                                [default: 999]" name="ppermutations" optional="True" type="integer" value="999"/>
 
-		<repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
+		<repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file [required]">
 			<param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
 		</repeat>
 	</inputs>
diff -r 558645416841 -r 914fa4daf16a qiime2/qiime_diversity_beta-phylogenetic-alt.xml
--- a/qiime2/qiime_diversity_beta-phylogenetic-alt.xml	Sun Jul 21 02:21:34 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,112 +0,0 @@
-<?xml version="1.0" ?>
-<tool id="qiime_diversity_beta-phylogenetic-alt" name="qiime diversity beta-phylogenetic-alt" version="2019.4">
-	<description> - Beta diversity (phylogenetic) - High Performance Computation</description>
-	<requirements>
-		<requirement type="package" version="2019.4">qiime2</requirement>
-	</requirements>
-	<command><![CDATA[
-  
-  qiime diversity beta-phylogenetic-alt --i-table=$itable --i-phylogeny=$iphylogeny --p-metric=$pmetric
-  
-  #if str($cmdconfig) != 'None':
-   --cmd-config=$cmdconfig
-  #end if
-  
-  #if $pbypasstips:
-   --p-bypass-tips
-  #else
-    --p-no-bypass-tips
-  #end if
-  
-  #set $pnjobs = '${GALAXY_SLOTS:-4}'
-  
-  #if str($pnjobs):
-   --p-n-jobs="$pnjobs"
-  #end if
-  
-   --o-distance-matrix=odistancematrix
-   
-  #if $pvarianceadjusted:
-   --p-variance-adjusted
-  #else
-    --p-no-variance-adjusted
-  #end if
-  
-  #if str($palpha):
-   --p-alpha="$palpha"
-  #end if
-  ;
-  cp odistancematrix.qza $odistancematrix;
-  ]]></command>
-	<inputs>
-		<param format="qza,no_unzip.zip" label="--i-table: 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: 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.  [required]" name="iphylogeny" optional="False" type="data"/>
-		<param label="--p-metric: The beta diversity metric to be computed.
-                                  [required]" name="pmetric" optional="False" type="select">
-			<option selected="True" value="generalized_unifrac">generalized_unifrac</option>
-			<option value="weighted_unifrac">weighted_unifrac</option>
-			<option value="weighted_normalized_unifrac">weighted_normalized_unifrac</option>
-			<option value="unweighted_unifrac">unweighted_unifrac</option>
-		</param>
-		<param label="--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" checked="False" type="boolean"/>
-		<param label="--p-alpha: 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="True" type="text"/>
-		<param label="--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" checked="False" type="boolean"/>
-		<param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
-	</inputs>
-	<outputs>
-		<data format="qza" label="${tool.name} on ${on_string}: distance-matrix.qza" name="odistancematrix"/>
-	</outputs>
-	<help>
- <![CDATA[
-Beta diversity (phylogenetic) - High Performance Computation
--------------------------------------------------------------
-
-Computes a user-specified phylogenetic beta diversity metric for all pairs
-of samples in a feature table. This implementation is recommended for large
-datasets, otherwise the results are identical to beta_phylogenetic.  This
-method is an implementation of the Strided State UniFrac algorithm.
-Multiple variants of the UniFrac metric are available, including
-Generalized UniFrac (Chen et al. 2012), Variance Adjusted UniFrac (Chang et
-al. 2011), as well as Weighted normalized and unnormalized UniFrac
-(Lozupone et al. 2007) and unweighted UniFrac (Lozupone et al. 2005)
-
-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({'generalized_unifrac', 'unweighted_unifrac', 'weighted_normalized_unifrac', 'weighted_unifrac'})
-    The beta diversity metric to be computed.
-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 % Properties(['phylogenetic'])
-    The resulting distance matrix.
-    ]]>
-	</help>
-<macros>
-	<import>qiime_citation.xml</import>
-</macros>
-<expand macro="qiime_citation" />
-</tool>
diff -r 558645416841 -r 914fa4daf16a qiime2/qiime_diversity_beta-rarefaction.xml
--- a/qiime2/qiime_diversity_beta-rarefaction.xml	Sun Jul 21 02:21:34 2019 -0400
+++ b/qiime2/qiime_diversity_beta-rarefaction.xml	Wed Jul 31 03:06:00 2019 -0400
@@ -32,7 +32,7 @@
 #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 + ',' + d['additional_input'].__getattr__('file_name')
+	#set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
 #end for
 #return $file_list
 #end def
@@ -41,7 +41,6 @@
 
 --o-visualization=ovisualization
 ;
-cp mmetadatafile.qza $mmetadatafile;
 qiime tools export --input-path ovisualization.qzv --output-path out   && mkdir -p '$ovisualization.files_path'
 && cp -r out/* '$ovisualization.files_path'
 && mv '$ovisualization.files_path/index.html' '$ovisualization';
@@ -109,7 +108,7 @@
 			<option value="RdYlGn_r">RdYlGn_r</option>
 		</param>
 
-		<repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
+		<repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file  [required]">
 			<param label="--m-metadata-file: METADATA... (multiple arguments will be merged) The sample metadata used for the Emperor jackknifed PCoA plot. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
 		</repeat>
 
diff -r 558645416841 -r 914fa4daf16a qiime2/qiime_diversity_bioenv.xml
--- a/qiime2/qiime_diversity_bioenv.xml	Sun Jul 21 02:21:34 2019 -0400
+++ b/qiime2/qiime_diversity_bioenv.xml	Wed Jul 31 03:06:00 2019 -0400
@@ -24,7 +24,6 @@
 
 --o-visualization=ovisualization
 ;
-cp mmetadatafile.qza $mmetadatafile;
 qiime tools export --input-path ovisualization.qzv --output-path out   && mkdir -p '$ovisualization.files_path'
 && cp -r out/* '$ovisualization.files_path'
 && mv '$ovisualization.files_path/index.html' '$ovisualization';
@@ -32,7 +31,7 @@
 	<inputs>
 		<param format="qza,no_unzip.zip" label="--i-distance-matrix: ARTIFACT DistanceMatrix     Matrix of distances between pairs of samples. [required]" name="idistancematrix" optional="False" type="data"/>
 
-		<repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
+		<repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file  [required]">
 			<param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
 		</repeat>
 
diff -r 558645416841 -r 914fa4daf16a qiime2/qiime_diversity_core-metrics-phylogenetic.xml
--- a/qiime2/qiime_diversity_core-metrics-phylogenetic.xml	Sun Jul 21 02:21:34 2019 -0400
+++ b/qiime2/qiime_diversity_core-metrics-phylogenetic.xml	Wed Jul 31 03:06:00 2019 -0400
@@ -79,8 +79,8 @@
 		<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-sampling-depth: INTEGER Range(1, None)        The total frequency that each sample should be rarefied to prior to computing diversity metrics. [required]" name="psamplingdepth" optional="False" min="1" value="" type="integer"/>
 
-		<repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
-			<param label="--m-metadata-file:  (multiple arguments will be merged) The sample metadata to use in the emperor plots. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
+		<repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file [required]">
+			<param label="--m-metadata-file:  (multiple arguments will be merged) The sample metadata to use in the emperor plots. [required]" name="additional_input" optional="False" type="data" format="tabular,qza,no_unzip.zip" />
 		</repeat>
 
 	</inputs>
diff -r 558645416841 -r 914fa4daf16a qiime2/qiime_diversity_core-metrics.xml
--- a/qiime2/qiime_diversity_core-metrics.xml	Sun Jul 21 02:21:34 2019 -0400
+++ b/qiime2/qiime_diversity_core-metrics.xml	Wed Jul 31 03:06:00 2019 -0400
@@ -19,11 +19,10 @@
 #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 + ',' + d['additional_input'].__getattr__('file_name')
+	#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
 
@@ -57,7 +56,7 @@
 		<param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table containing the samples over which diversity metrics should be computed.        [required]" name="itable" optional="False" type="data"/>
 		<param label="--p-sampling-depth: INTEGER Range(1, None)     The total frequency that each sample should be rarefied to prior to computing diversity metrics. [required]" name="psamplingdepth" optional="False" min="1" value="" type="integer"/>
 
-		<repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
+		<repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file  [required]">
 			<param label="--m-metadata-file: METADATA... (multiple arguments will be merged) The sample metadata to use in the emperor plots. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
 		</repeat>
 
diff -r 558645416841 -r 914fa4daf16a qiime2/qiime_diversity_filter-distance-matrix.xml
--- a/qiime2/qiime_diversity_filter-distance-matrix.xml	Sun Jul 21 02:21:34 2019 -0400
+++ b/qiime2/qiime_diversity_filter-distance-matrix.xml	Wed Jul 31 03:06:00 2019 -0400
@@ -45,7 +45,7 @@
 		<param label="--p-where: TEXT       SQLite WHERE clause specifying sample metadata criteria that must be met to be included in the filtered distance matrix. If not provided, all samples in `metadata` that are also in the input distance matrix will be retained.                     [optional]" name="pwhere" optional="True" type="text"/>
 		<param label="--p-exclude-ids: --p-no-exclude-ids If `True`, the samples selected by `metadata` or `where` parameters will be excluded from the filtered distance matrix instead of being retained. [default: False]" name="pexcludeids" selected="False" type="boolean"/>
 
-		<repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
+		<repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file  [required]">
 			<param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
 		</repeat>
 
diff -r 558645416841 -r 914fa4daf16a qiime2/qiime_diversity_mantel.xml
--- a/qiime2/qiime_diversity_mantel.xml	Sun Jul 21 02:21:34 2019 -0400
+++ b/qiime2/qiime_diversity_mantel.xml	Wed Jul 31 03:06:00 2019 -0400
@@ -14,7 +14,7 @@
  --p-method=$pmethod
 #end if
 
-#if $ppermutations:
+#if str($ppermutations):
  --p-permutations=$ppermutations
 #end if
 
@@ -22,14 +22,30 @@
  --p-intersect-ids
 #end if
 
+
+
+#if '__sq__' in str($plabel1):
+  #set $plabel1_temp = $plabel1.replace('__sq__', "'")
+  #set $plabel1 = $plabel1_temp
+#end if
+
 #if str($plabel1):
  --p-label1="$plabel1"
 #end if
 
+
+
+#if '__sq__' in str($plabel2):
+  #set $plabel2_temp = $plabel2.replace('__sq__', "'")
+  #set $plabel2 = $plabel2_temp
+#end if
+
 #if str($plabel2):
  --p-label2="$plabel2"
 #end if
 
+
+
 --o-visualization=ovisualization
 ;
 qiime tools export --input-path ovisualization.qzv --output-path out   && mkdir -p '$ovisualization.files_path'
@@ -46,8 +62,8 @@
 		</param>
 		<param label="--p-permutations: INTEGER Range(0, None)     The number of permutations to be run when computing p-values. Supplying a value of zero will disable permutation testing and p-values will not be calculated (this results in *much* quicker execution time if p-values are not desired).               [default: 999]" name="ppermutations" optional="True" type="integer" min="0" value="999"/>
 		<param label="--p-intersect-ids: --p-no-intersect-ids If supplied, IDs that are not found in both distance matrices will be discarded before applying the Mantel test. Default behavior is to error on any mismatched IDs.                                   [default: False]" name="pintersectids" selected="False" type="boolean"/>
-		<param label="--p-label1: TEXT      Label for `dm1` in the output visualization. [default: 'Distance Matrix 1']" name="plabel1" optional="True" type="text" value="'Distance Matrix 1'"/>
-		<param label="--p-label2: TEXT      Label for `dm2` in the output visualization. [default: 'Distance Matrix 2']" name="plabel2" optional="True" type="text" value="'Distance Matrix 2'"/>
+		<param label="--p-label1: TEXT      Label for `dm1` in the output visualization. [default: 'Distance Matrix 1']" name="plabel1" optional="True" type="text" value="Distance Matrix 1"/>
+		<param label="--p-label2: TEXT      Label for `dm2` in the output visualization. [default: 'Distance Matrix 2']" name="plabel2" optional="True" type="text" value="Distance Matrix 2"/>
 	</inputs>
 	<outputs>
 		<data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
diff -r 558645416841 -r 914fa4daf16a qiime2/qiime_emperor_biplot.xml
--- a/qiime2/qiime_emperor_biplot.xml	Sun Jul 21 02:21:34 2019 -0400
+++ b/qiime2/qiime_emperor_biplot.xml	Wed Jul 31 03:06:00 2019 -0400
@@ -10,23 +10,32 @@
 --i-biplot=$ibiplot
 
 
-#def list_dict_to_string(list_dict):
+#if $m_sample_metadatafile:
+#def list_dict_to_string_sample_mdata(list_dict):
 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
 #for d in list_dict[1:]:
-	#set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
+	#set $file_list = $file_list + ' --m-sample-metadata-file=' + d['additional_input'].__getattr__('file_name')
 #end for
 #return $file_list
 #end def
-
-#if $m_sample_metadatafile:
---m-sample-metadata-file=$list_dict_to_string($m_sample_metadatafile)
+--m-sample-metadata-file=$list_dict_to_string_sample_mdata($m_sample_metadatafile)
 #end if
 
-if $m_feature_metadatafile:
---m-feature-metadata-file=$list_dict_to_string($m_feature_metadatafile)
+
+
+#if $m_feature_metadatafile:
+#def list_dict_to_string_feature_mdata(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-feature-metadata-file=' + d['additional_input'].__getattr__('file_name')
+#end for
+#return $file_list
+#end def
+--m-feature-metadata-file=$list_dict_to_string_feature_mdata($m_feature_metadatafile)
 #end if
 
 
+
 #if $pignoremissingsamples:
  --p-ignore-missing-samples
 #end if
@@ -46,11 +55,11 @@
 		<param label="--p-ignore-missing-samples: --p-no-ignore-missing-samples This will suppress the error raised when the coordinates matrix contains samples that are not present in the metadata. Samples without metadata are included by setting all metadata values to: 'This sample has no metadata'. This flag is only applied if at least one sample is present in both the coordinates matrix and the metadata.               [default: False]" name="pignoremissingsamples" selected="False" type="boolean"/>
 		<param label="--p-number-of-features: INTEGER Range(1, None)     The number of most important features (arrows) to display in the ordination.                 [default: 5]" name="pnumberoffeatures" optional="True" type="integer" min="1" value="5"/>
 
-		<repeat name="m_sample_metadatafile" optional="False" title="--m-metadata-file">
+		<repeat name="m_sample_metadatafile" optional="False" title="--m-sample-metadata-file  [required]">
 			<param label="--m-sample-metadata-file: (multiple arguments will be merged)  The sample metadata. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
 		</repeat>
 
-		<repeat name="m_feature_metadatafile" optional="True" title="--m-metadata-file">
+		<repeat name="m_feature_metadatafile" optional="True" title="--m-feature-metadata-file">
 			<param label="--m-feature-metadata-file: (multiple arguments will be merged)  The feature metadata (useful to manipulate the arrows in the plot).  [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
 		</repeat>
 
diff -r 558645416841 -r 914fa4daf16a qiime2/qiime_emperor_plot.xml
--- a/qiime2/qiime_emperor_plot.xml	Sun Jul 21 02:21:34 2019 -0400
+++ b/qiime2/qiime_emperor_plot.xml	Wed Jul 31 03:06:00 2019 -0400
@@ -41,7 +41,7 @@
 		<param label="--p-custom-axes: TEXT... List[Str]          Numeric sample metadata columns that should be included as axes in the Emperor plot.        [optional]" name="pcustomaxes" optional="True" type="text"/>
 		<param label="--p-ignore-missing-samples: --p-no-ignore-missing-samples This will suppress the error raised when the coordinates matrix contains samples that are not present in the metadata. Samples without metadata are included by setting all metadata values to: 'This sample has no metadata'. This flag is only applied if at least one sample is present in both the coordinates matrix and the metadata.               [default: False]" name="pignoremissingsamples" selected="False" type="boolean"/>
 
-		<repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
+		<repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file [required]">
 			<param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
 		</repeat>
 
diff -r 558645416841 -r 914fa4daf16a qiime2/qiime_emperor_procrustes-plot.xml
--- a/qiime2/qiime_emperor_procrustes-plot.xml	Sun Jul 21 02:21:34 2019 -0400
+++ b/qiime2/qiime_emperor_procrustes-plot.xml	Wed Jul 31 03:06:00 2019 -0400
@@ -8,6 +8,7 @@
 qiime emperor procrustes-plot
 
 --i-reference-pcoa=$ireferencepcoa
+
 --i-other-pcoa=$iotherpcoa
 
 
@@ -24,10 +25,23 @@
 
 
 
+#if '__sq__' in str($pcustomaxes):
+  #set $pcustomaxes_temp = $pcustomaxes.replace('__sq__', "'")
+  #set $pcustomaxes = $pcustomaxes_temp
+#end if
+
+#if '__cb__' in str($pcustomaxes):
+  #set $pcustomaxes_temp = $pcustomaxes.replace('__cb__', "]")
+  #set $pcustomaxes = $pcustomaxes_temp
+#end if
+
 #if str($pcustomaxes):
  --p-custom-axes="$pcustomaxes"
 #end if
 
+
+
+
 #if $pignoremissingsamples:
  --p-ignore-missing-samples
 #end if
@@ -44,7 +58,7 @@
 		<param label="--p-custom-axes: TEXT... List[Str]          Numeric sample metadata columns that should be included as axes in the Emperor plot.        [optional]" name="pcustomaxes" optional="True" type="text"/>
 		<param label="--p-ignore-missing-samples: --p-no-ignore-missing-samples This will suppress the error raised when the coordinates matrix contains samples that are not present in the metadata. Samples without metadata are included by setting all metadata values to: 'This sample has no metadata'. This flag is only applied if at least one sample is present in both the coordinates matrix and the metadata.               [default: False]" name="pignoremissingsamples" selected="False" type="boolean"/>
 
-		<repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
+		<repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file  [required]">
 			<param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
 		</repeat>
 
diff -r 558645416841 -r 914fa4daf16a qiime2/qiime_feature-classifier_classify-consensus-blast.xml
--- a/qiime2/qiime_feature-classifier_classify-consensus-blast.xml	Sun Jul 21 02:21:34 2019 -0400
+++ b/qiime2/qiime_feature-classifier_classify-consensus-blast.xml	Wed Jul 31 03:06:00 2019 -0400
@@ -43,10 +43,21 @@
  --p-min-consensus=$pminconsensus
 #end if
 
+
+
+
+
+#if '__sq__' in str($punassignablelabel):
+  #set $punassignablelabel_temp = $punassignablelabel.replace('__sq__', "'")
+  #set $punassignablelabel = $punassignablelabel_temp
+#end if
+
 #if str($punassignablelabel):
  --p-unassignable-label="$punassignablelabel"
 #end if
 
+
+
 --o-classification=oclassification
 ;
 cp oclassification.qza $oclassification
@@ -81,7 +92,7 @@
 		</param>
 		<param label="--p-evalue: NUMBER       BLAST expectation value (E) threshold for saving hits.                               [default: 0.001]" name="pevalue" optional="True" type="float" value="0.001"/>
 		<param label="--p-min-consensus: NUMBER Range(0.5, 1.0, inclusive_start=False, inclusive_end=True)   Minimum fraction of assignments must match top hit to be accepted as consensus assignment. Must be in range (0.5, 1.0].                    [default: 0.51]" name="pminconsensus" optional="True" type="float" min="0.5" max="1" exclude_min="True" exclude_max="False" value="0.51"/>
-		<param label="--p-unassignable-label: TEXT [default: 'Unassigned']" name="punassignablelabel" optional="True" type="text" value="'Unassigned'"/>
+		<param label="--p-unassignable-label: TEXT [default: 'Unassigned']" name="punassignablelabel" optional="True" type="text" value="Unassigned"/>
 	</inputs>
 	<outputs>
 		<data format="qza" label="${tool.name} on ${on_string}: classification.qza" name="oclassification"/>
diff -r 558645416841 -r 914fa4daf16a qiime2/qiime_feature-classifier_classify-consensus-vsearch.xml
--- a/qiime2/qiime_feature-classifier_classify-consensus-vsearch.xml	Sun Jul 21 02:21:34 2019 -0400
+++ b/qiime2/qiime_feature-classifier_classify-consensus-vsearch.xml	Wed Jul 31 03:06:00 2019 -0400
@@ -20,6 +20,7 @@
 #end if
 
 
+
 #if $pmaxaccepts:
  --p-maxaccepts=$pmaxaccepts
 #end if
@@ -40,10 +41,22 @@
  --p-min-consensus=$pminconsensus
 #end if
 
+
+
+
+
+#if '__sq__' in str($punassignablelabel):
+  #set $punassignablelabel_temp = $punassignablelabel.replace('__sq__', "'")
+  #set $punassignablelabel = $punassignablelabel_temp
+#end if
+
 #if str($punassignablelabel):
  --p-unassignable-label="$punassignablelabel"
 #end if
 
+
+
+
 #set $pthreads = '${GALAXY_SLOTS:-4}'
 #if str($pthreads):
  --p-threads="$pthreads"
@@ -81,7 +94,7 @@
 			<option value="plus">plus</option>
 		</param>
 		<param label="--p-min-consensus: NUMBER Range(0.5, 1.0, inclusive_start=False, inclusive_end=True)   Minimum fraction of assignments must match top hit to be accepted as consensus assignment. Must be in range (0.5, 1.0].                    [default: 0.51]" name="pminconsensus" optional="True" type="float" min="0.5" max="1" exclude_min="True" exclude_max="False" value="0.51"/>
-		<param label="--p-unassignable-label: TEXT [default: 'Unassigned']" name="punassignablelabel" optional="True" type="text" value="'Unassigned'"/>
+		<param label="--p-unassignable-label: TEXT [default: 'Unassigned']" name="punassignablelabel" optional="True" type="text" value="Unassigned"/>
 	</inputs>
 	<outputs>
 		<data format="qza" label="${tool.name} on ${on_string}: classification.qza" name="oclassification"/>
diff -r 558645416841 -r 914fa4daf16a qiime2/qiime_feature-classifier_extract-reads.xml
--- a/qiime2/qiime_feature-classifier_extract-reads.xml	Sun Jul 21 02:21:34 2019 -0400
+++ b/qiime2/qiime_feature-classifier_extract-reads.xml	Wed Jul 31 03:06:00 2019 -0400
@@ -11,23 +11,23 @@
 --p-f-primer="$pfprimer"
 --p-r-primer="$prprimer"
 
-#if $ptrunclen:
+#if str($ptrunclen):
  --p-trunc-len=$ptrunclen
 #end if
 
-#if $ptrimleft:
+#if str($ptrimleft):
  --p-trim-left=$ptrimleft
 #end if
 
-#if $pidentity:
+#if str($pidentity):
  --p-identity=$pidentity
 #end if
 
-#if $pminlength:
+#if str($pminlength):
  --p-min-length=$pminlength
 #end if
 
-#if $pmaxlength:
+#if str($pmaxlength):
  --p-max-length=$pmaxlength
 #end if
 
diff -r 558645416841 -r 914fa4daf16a qiime2/qiime_feature-classifier_fit-classifier-naive-bayes.xml
--- a/qiime2/qiime_feature-classifier_fit-classifier-naive-bayes.xml	Sun Jul 21 02:21:34 2019 -0400
+++ b/qiime2/qiime_feature-classifier_fit-classifier-naive-bayes.xml	Wed Jul 31 03:06:00 2019 -0400
@@ -31,10 +31,21 @@
  --p-classify--chunk-size=$pclassifychunksize
 #end if
 
+
+
+
+#if '__sq__' in str($pclassifyclassprior):
+  #set $pclassifyclassprior_temp = $pclassifyclassprior.replace('__sq__', "'")
+  #set $pclassifyclassprior = $pclassifyclassprior_temp
+#end if
+
 #if str($pclassifyclassprior):
  --p-classify--class-prior="$pclassifyclassprior"
 #end if
 
+
+
+
 #if $pclassifyfitprior:
  --p-classify--fit-prior
 #end if
@@ -43,26 +54,67 @@
  --p-feat-ext--alternate-sign
 #end if
 
+
+
+
+
+#if '__sq__' in str($pfeatextanalyzer):
+  #set $pfeatextanalyzer_temp = $pfeatextanalyzer.replace('__sq__', "'")
+  #set $pfeatextanalyzer = $pfeatextanalyzer_temp
+#end if
+
 #if str($pfeatextanalyzer):
  --p-feat-ext--analyzer="$pfeatextanalyzer"
 #end if
 
+
+
+
+
 #if $pfeatextbinary:
  --p-feat-ext--binary
 #end if
 
+
+
+#if '__sq__' in str($pfeatextdecodeerror):
+  #set $pfeatextdecodeerror_temp = $pfeatextdecodeerror.replace('__sq__', "'")
+  #set $pfeatextdecodeerror = $pfeatextdecodeerror_temp
+#end if
+
 #if str($pfeatextdecodeerror):
  --p-feat-ext--decode-error="$pfeatextdecodeerror"
 #end if
 
+
+
+
+
+#if '__sq__' in str($pfeatextencoding):
+  #set $pfeatextencoding_temp = $pfeatextencoding.replace('__sq__', "'")
+  #set $pfeatextencoding = $pfeatextencoding_temp
+#end if
+
 #if str($pfeatextencoding):
  --p-feat-ext--encoding="$pfeatextencoding"
 #end if
 
+
+
+
+
+#if '__sq__' in str($pfeatextinput):
+  #set $pfeatextinput_temp = $pfeatextinput.replace('__sq__', "'")
+  #set $pfeatextinput = $pfeatextinput_temp
+#end if
+
 #if str($pfeatextinput):
  --p-feat-ext--input="$pfeatextinput"
 #end if
 
+
+
+
 #if $pnofeatextlowercase:
  --p-no-feat-ext--lowercase
 #end if
@@ -71,6 +123,14 @@
  --p-feat-ext--n-features=$pfeatextnfeatures
 #end if
 
+
+
+
+#if '__sq__' in str($pfeatextngramrange):
+  #set $pfeatextngramrange_temp = $pfeatextngramrange.replace('__sq__', "'")
+  #set $pfeatextngramrange = $pfeatextngramrange_temp
+#end if
+
 #if '__ob__' in str($pfeatextngramrange):
   #set $pfeatextngramrange_temp = $pfeatextngramrange.replace('__ob__', '[')
   #set $pfeatextngramrange = $pfeatextngramrange_temp
@@ -85,30 +145,75 @@
 #end if
 
 
+
+
+
 #if $pfeatextnonnegative:
  --p-feat-ext--non-negative
 #end if
 
+
+#if '__sq__' in str($pfeatextnorm):
+  #set $pfeatextnorm_temp = $pfeatextnorm.replace('__sq__', "'")
+  #set $pfeatextnorm = $pfeatextnorm_temp
+#end if
+
 #if str($pfeatextnorm):
  --p-feat-ext--norm="$pfeatextnorm"
 #end if
 
+
+
+
+#if '__sq__' in str($pfeatextpreprocessor):
+  #set $pfeatextpreprocessor_temp = $pfeatextpreprocessor.replace('__sq__', "'")
+  #set $pfeatextpreprocessor = $pfeatextpreprocessor_temp
+#end if
+
 #if str($pfeatextpreprocessor):
  --p-feat-ext--preprocessor="$pfeatextpreprocessor"
 #end if
 
+
+
+
+#if '__sq__' in str($pfeatextstopwords):
+  #set $pfeatextstopwords_temp = $pfeatextstopwords.replace('__sq__', "'")
+  #set $pfeatextstopwords = $pfeatextstopwords_temp
+#end if
+
 #if str($pfeatextstopwords):
  --p-feat-ext--stop-words="$pfeatextstopwords"
 #end if
 
+
+
+
+
+#if '__sq__' in str($pfeatextstripaccents):
+  #set $pfeatextstripaccents_temp = $pfeatextstripaccents.replace('__sq__', "'")
+  #set $pfeatextstripaccents = $pfeatextstripaccents_temp
+#end if
+
 #if str($pfeatextstripaccents):
  --p-feat-ext--strip-accents="$pfeatextstripaccents"
 #end if
 
+
+
+
+
+
+#if '__sq__' in str($pfeatexttokenpattern):
+  #set $pfeatexttokenpattern_temp = $pfeatexttokenpattern.replace('__sq__', "'")
+  #set $pfeatexttokenpattern = $pfeatexttokenpattern_temp
+#end if
+
 #if '__ob__' in str($pfeatexttokenpattern):
   #set $pfeatexttokenpattern_temp = $pfeatexttokenpattern.replace('__ob__', '[')
   #set $pfeatexttokenpattern = $pfeatexttokenpattern_temp
 #end if
+
 #if 'X' in str($pfeatexttokenpattern):
   #set $pfeatexttokenpattern_temp = $pfeatexttokenpattern.replace('X', '\\')
   #set $pfeatexttokenpattern = $pfeatexttokenpattern_temp
@@ -119,6 +224,14 @@
 #end if
 
 
+
+
+
+#if '__sq__' in str($pfeatexttokenizer):
+  #set $pfeatexttokenizer_temp = $pfeatexttokenizer.replace('__sq__', "'")
+  #set $pfeatexttokenizer = $pfeatexttokenizer_temp
+#end if
+
 #if str($pfeatexttokenizer):
  --p-feat-ext--tokenizer="$pfeatexttokenizer"
 #end if
@@ -148,24 +261,24 @@
 
 		<param label="--p-classify--alpha: NUMBER [default: 0.001]" name="pclassifyalpha" optional="True" type="float" value="0.001"/>
 		<param label="--p-classify--chunk-size: INTEGER [default: 20000]" name="pclassifychunksize" optional="True" type="integer" value="20000"/>
-		<param label="--p-classify--class-prior: TEXT [default: 'null']" name="pclassifyclassprior" optional="True" type="text" value="'null'"/>
+		<param label="--p-classify--class-prior: TEXT [default: 'null']" name="pclassifyclassprior" optional="True" type="text" value="null"/>
 		<param label="--p-classify--fit-prior: --p-no-classify--fit-prior [default: False]" name="pclassifyfitprior" selected="False" type="boolean"/>
 		<param label="--p-feat-ext--alternate-sign: --p-no-feat-ext--alternate-sign [default: False]" name="pfeatextalternatesign" selected="False" type="boolean"/>
-		<param label="--p-feat-ext--analyzer: TEXT [default: 'char_wb']" name="pfeatextanalyzer" optional="True" type="text" value="'char_wb'"/>
+		<param label="--p-feat-ext--analyzer: TEXT [default: 'char_wb']" name="pfeatextanalyzer" optional="True" type="text" value="char_wb"/>
 		<param label="--p-feat-ext--binary: --p-no-feat-ext--binary [default: False]" name="pfeatextbinary" selected="False" type="boolean"/>
-		<param label="--p-feat-ext--decode-error: TEXT [default: 'strict']" name="pfeatextdecodeerror" optional="True" type="text" value="'strict'"/>
-		<param label="--p-feat-ext--encoding: TEXT [default: 'utf-8']" name="pfeatextencoding" optional="True" type="text" value="'utf-8'"/>
-		<param label="--p-feat-ext--input: TEXT [default: 'content']" name="pfeatextinput" optional="True" type="text" value="'content'"/>
+		<param label="--p-feat-ext--decode-error: TEXT [default: 'strict']" name="pfeatextdecodeerror" optional="True" type="text" value="strict"/>
+		<param label="--p-feat-ext--encoding: TEXT [default: 'utf-8']" name="pfeatextencoding" optional="True" type="text" value="utf-8"/>
+		<param label="--p-feat-ext--input: TEXT [default: 'content']" name="pfeatextinput" optional="True" type="text" value="content"/>
 		<param label="--p-no-feat-ext--lowercase:  [default: False]" name="pnofeatextlowercase" selected="False" type="boolean"/>
 		<param label="--p-feat-ext--n-features: INTEGER [default: 8192]" name="pfeatextnfeatures" optional="True" type="integer" value="8192"/>
-		<param label="--p-feat-ext--ngram-range: TEXT [default: '[7, 7]']" name="pfeatextngramrange" optional="True" type="text" value="'[7, 7]"/>
+		<param label="--p-feat-ext--ngram-range: TEXT [default: '[7, 7]']" name="pfeatextngramrange" optional="True" type="text" value="[7, 7]"/>
 		<param label="--p-feat-ext--non-negative: --p-no-feat-ext--non-negative [default: False]" name="pfeatextnonnegative" selected="False" type="boolean"/>
-		<param label="--p-feat-ext--norm: TEXT [default: 'l2']" name="pfeatextnorm" optional="True" type="text" value="'l2'"/>
-		<param label="--p-feat-ext--preprocessor: TEXT [default: 'null']" name="pfeatextpreprocessor" optional="True" type="text" value="'null'"/>
-		<param label="--p-feat-ext--stop-words: TEXT [default: 'null']" name="pfeatextstopwords" optional="True" type="text" value="'null'"/>
-		<param label="--p-feat-ext--strip-accents: TEXT [default: 'null']" name="pfeatextstripaccents" optional="True" type="text" value="'null'"/>
-		<param label="--p-feat-ext--token-pattern: TEXT [default: '(?u)\\b\\w\\w+\\b']" name="pfeatexttokenpattern" optional="True" type="text" value="'(?u)\\b\\w\\w+\\b'"/>
-		<param label="--p-feat-ext--tokenizer: TEXT [default: 'null']" name="pfeatexttokenizer" optional="True" type="text" value="'null'"/>
+		<param label="--p-feat-ext--norm: TEXT [default: 'l2']" name="pfeatextnorm" optional="True" type="text" value="l2"/>
+		<param label="--p-feat-ext--preprocessor: TEXT [default: 'null']" name="pfeatextpreprocessor" optional="True" type="text" value="null"/>
+		<param label="--p-feat-ext--stop-words: TEXT [default: 'null']" name="pfeatextstopwords" optional="True" type="text" value="null"/>
+		<param label="--p-feat-ext--strip-accents: TEXT [default: 'null']" name="pfeatextstripaccents" optional="True" type="text" value="null"/>
+		<param label="--p-feat-ext--token-pattern: TEXT [default: '(?u)\\b\\w\\w+\\b']" name="pfeatexttokenpattern" optional="True" type="text" value="(?u)\\b\\w\\w+\\b"/>
+		<param label="--p-feat-ext--tokenizer: TEXT [default: 'null']" name="pfeatexttokenizer" optional="True" type="text" value="null"/>
 	</inputs>
 	<outputs>
 		<data format="qza" label="${tool.name} on ${on_string}: classifier.qza" name="oclassifier"/>
diff -r 558645416841 -r 914fa4daf16a qiime2/qiime_feature-table_core-features.xml
--- a/qiime2/qiime_feature-table_core-features.xml	Sun Jul 21 02:21:34 2019 -0400
+++ b/qiime2/qiime_feature-table_core-features.xml	Wed Jul 31 03:06:00 2019 -0400
@@ -9,15 +9,15 @@
 
 --i-table=$itable
 
-#if $pminfraction:
+#if str($pminfraction):
  --p-min-fraction=$pminfraction
 #end if
 
-#if $pmaxfraction:
+#if str($pmaxfraction):
  --p-max-fraction=$pmaxfraction
 #end if
 
-#if $psteps:
+#if str($psteps):
  --p-steps=$psteps
 #end if
 
diff -r 558645416841 -r 914fa4daf16a qiime2/qiime_feature-table_filter-features.xml
--- a/qiime2/qiime_feature-table_filter-features.xml	Sun Jul 21 02:21:34 2019 -0400
+++ b/qiime2/qiime_feature-table_filter-features.xml	Wed Jul 31 03:06:00 2019 -0400
@@ -22,7 +22,7 @@
 #end if
 
 
-#if $pminfrequency:
+#if str($pminfrequency):
  --p-min-frequency=$pminfrequency
 #end if
 
@@ -30,7 +30,7 @@
  --p-max-frequency="$pmaxfrequency"
 #end if
 
-#if $pminsamples:
+#if str($pminsamples):
  --p-min-samples=$pminsamples
 #end if
 
@@ -47,7 +47,7 @@
  --p-where="$pwhere"
 #end if
 
-#if $pexcludeids:
+#if str($pexcludeids):
  --p-exclude-ids
 #end if
 
diff -r 558645416841 -r 914fa4daf16a qiime2/qiime_feature-table_group.xml
--- a/qiime2/qiime_feature-table_group.xml	Sun Jul 21 02:21:34 2019 -0400
+++ b/qiime2/qiime_feature-table_group.xml	Wed Jul 31 03:06:00 2019 -0400
@@ -13,17 +13,7 @@
 --p-mode=$pmode
 
 
-#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($input_files_mmetadatafile)
-#end if
-
+--m-metadata-file=$mmedatafile
 
 --o-grouped-table=ogroupedtable
 ;
@@ -42,9 +32,7 @@
 			<option value="sum">sum</option>
 		</param>
 
-		<repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
-			<param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
-		</repeat>
+		<param label="--m-metadata-file  [required]" name="mmedatafile" type="data" format="tabular,qza,no_unzip.zip" />
 
 	</inputs>
 	<outputs>
diff -r 558645416841 -r 914fa4daf16a qiime2/qiime_feature-table_heatmap.xml
--- a/qiime2/qiime_feature-table_heatmap.xml	Sun Jul 21 02:21:34 2019 -0400
+++ b/qiime2/qiime_feature-table_heatmap.xml	Wed Jul 31 03:06:00 2019 -0400
@@ -10,16 +10,7 @@
 --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($input_files_mmetadatafile)
-#end if
+--m-metadata-file=$mmedatafile
 
 
 #if str($mmetadatacolumn):
@@ -282,9 +273,8 @@
 			<option value="PRGn">PRGn</option>
 		</param>
 
-		<repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
-			<param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
-		</repeat>
+		<param label="--m-metadata-file" name="mmedatafile" optional="True" type="data" format="tabular,qza,no_unzip.zip" />
+
 	</inputs>
 	<outputs>
 		<data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
diff -r 558645416841 -r 914fa4daf16a qiime2/qiime_fragment-insertion_sepp.xml
--- a/qiime2/qiime_fragment-insertion_sepp.xml	Sun Jul 21 02:21:34 2019 -0400
+++ b/qiime2/qiime_fragment-insertion_sepp.xml	Wed Jul 31 03:06:00 2019 -0400
@@ -23,7 +23,7 @@
 #end if
 
 
-#if $palignmentsubsetsize:
+#if str($palignmentsubsetsize):
  --p-alignment-subset-size=$palignmentsubsetsize
 #end if
 
@@ -31,10 +31,6 @@
  --p-placement-subset-size="$pplacementsubsetsize"
 #end if
 
-#if $pdebug:
- --p-debug
-#end if
-
 --o-tree=otree
 --o-placements=oplacements
 ;
@@ -47,7 +43,6 @@
 		<param format="qza,no_unzip.zip" label="--i-reference-phylogeny: ARTIFACT Phylogeny[Rooted]  The rooted reference phylogeny. Must be in sync with reference-alignment, i.e. each tip name must have exactly one corresponding record.            [optional]" name="ireferencephylogeny" optional="True" type="data"/>
 		<param label="--p-alignment-subset-size: INTEGER Each placement subset is further broken into subsets of at most these many sequences and a separate HMM is trained on each subset. The default alignment subset size is set to balance the exhaustiveness of the alignment step with the running time.   [default: 1000]" name="palignmentsubsetsize" optional="True" type="integer" value="1000"/>
 		<param label="--p-placement-subset-size: INTEGER The tree is divided into subsets such that each subset includes at most these many subsets. The placement step places the fragment on only one subset, determined based on alignment scores. The default placement subset is set to make sure the memory requirement of the pplacer step does not become prohibitively large." name="pplacementsubsetsize" optional="True" type="integer"/>
-		<param label="--p-debug: --p-no-debug Print additional run information to STDOUT for debugging. Run together with --verbose to actually see the information on STDOUT. Temporary directories will not be removed if run fails.           [default: False]" name="pdebug" selected="False" type="boolean"/>
 	</inputs>
 	<outputs>
 		<data format="qza" label="${tool.name} on ${on_string}: tree.qza" name="otree"/>
diff -r 558645416841 -r 914fa4daf16a qiime2/qiime_gneiss_add-pseudocount.xml
--- a/qiime2/qiime_gneiss_add-pseudocount.xml	Sun Jul 21 02:21:34 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,55 +0,0 @@
-<?xml version="1.0" ?>
-<tool id="qiime_gneiss_add-pseudocount" name="qiime gneiss add-pseudocount" version="2019.4">
-	<description> - Add pseudocount to table</description>
-	<requirements>
-		<requirement type="package" version="2019.4">qiime2</requirement>
-	</requirements>
-	<command>
-	<![CDATA[
-	qiime gneiss add-pseudocount --i-table=$itable
-
-	#if $ppseudocount:
-	 --p-pseudocount=$ppseudocount
-	#end if
-
-	#if str($cmdconfig) != 'None':
-	 --cmd-config=$cmdconfig
-	#end if
-	 --o-composition-table=ocompositiontable;
-
- cp ocompositiontable.qza $ocompositiontable
-	]]>
-	</command>
-	<inputs>
-		<param format="qza,no_unzip.zip" label="--i-table: FeatureTable[Frequency] The feature table to which pseudocounts should be added.  [required]" name="itable" optional="False" type="data"/>
-		<param label="--p-pseudocount: The value to add to all counts in the feature table.  [default: 1]" name="ppseudocount" optional="True" type="integer" value="1"/>
-		<param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
-	</inputs>
-	<outputs>
-		<data format="qza" label="${tool.name} on ${on_string}: composition-table.qza" name="ocompositiontable"/>
-	</outputs>
-	<help>
-		<![CDATA[
-Add pseudocount to table
--------------------------
-
-Increment all counts in table by pseudocount.
-
-Parameters
-----------
-table : FeatureTable[Frequency]
-    The feature table to which pseudocounts should be added.
-pseudocount : Int, optional
-    The value to add to all counts in the feature table.
-
-Returns
--------
-composition_table : FeatureTable[Composition]
-    The resulting feature table.
-		]]>
-	</help>
-<macros>
-	<import>qiime_citation.xml</import>
-</macros>
-<expand macro="qiime_citation" />
-</tool>
diff -r 558645416841 -r 914fa4daf16a qiime2/qiime_gneiss_ilr-hierarchical.xml
--- a/qiime2/qiime_gneiss_ilr-hierarchical.xml	Sun Jul 21 02:21:34 2019 -0400
+++ b/qiime2/qiime_gneiss_ilr-hierarchical.xml	Wed Jul 31 03:06:00 2019 -0400
@@ -10,7 +10,7 @@
 --i-table=$itable
 --i-tree=$itree
 
-#if $ppseudocount:
+#if str($ppseudocount):
  --p-pseudocount=$ppseudocount
 #end if
 
diff -r 558645416841 -r 914fa4daf16a qiime2/qiime_gneiss_ilr-phylogenetic.xml
--- a/qiime2/qiime_gneiss_ilr-phylogenetic.xml	Sun Jul 21 02:21:34 2019 -0400
+++ b/qiime2/qiime_gneiss_ilr-phylogenetic.xml	Wed Jul 31 03:06:00 2019 -0400
@@ -10,7 +10,7 @@
 --i-table=$itable
 --i-tree=$itree
 
-#if $ppseudocount:
+#if str($ppseudocount):
  --p-pseudocount=$ppseudocount
 #end if
 
diff -r 558645416841 -r 914fa4daf16a qiime2/qiime_gneiss_ilr-transform.xml
--- a/qiime2/qiime_gneiss_ilr-transform.xml	Sun Jul 21 02:21:34 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,56 +0,0 @@
-<?xml version="1.0" ?>
-<tool id="qiime_gneiss_ilr-transform" name="qiime gneiss ilr-transform" version="2019.4">
-	<description> - Isometric Log-ratio Transform</description>
-	<requirements>
-		<requirement type="package" version="2019.4">qiime2</requirement>
-	</requirements>
-	<command>
-	<![CDATA[
-	qiime gneiss ilr-transform --i-table=$itable --i-tree=$itree --o-balances=obalances
-
-	#if str($cmdconfig) != 'None':
-	 --cmd-config=$cmdconfig
-	#end if
-	;
-	cp obalances.qza $obalances;
-	]]>
-	</command>
-	<inputs>
-		<param format="qza,no_unzip.zip" label="--i-table: FeatureTable[Composition] The feature table containing the samples in which the ilr transform will be performed. [required]" name="itable" optional="False" type="data"/>
-		<param format="qza,no_unzip.zip" label="--i-tree: Hierarchy A hierarchy of feature identifiers that defines the partitions of features.  Each tip in the hierarchycorresponds to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree.  This assumes that all of the internal nodes in the tree have labels.  [required]" name="itree" optional="False" type="data"/>
-		<param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
-	</inputs>
-	<outputs>
-		<data format="qza" label="${tool.name} on ${on_string}: balances.qza" name="obalances"/>
-	</outputs>
-	<help>
-		<![CDATA[
-Isometric Log-ratio Transform
-------------------------------
-
-Calculate balances given a hierarchy.
-
-Parameters
-----------
-table : FeatureTable[Composition]
-    The feature table containing the samples in which the ilr transform
-    will be performed.
-tree : Hierarchy
-    A hierarchy of feature identifiers that defines the partitions of
-    features.  Each tip in the hierarchycorresponds 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.  This assumes that all of the internal nodes in the tree
-    have labels.
-
-Returns
--------
-balances : FeatureTable[Balance]
-    The resulting balances from the ilr transform.
-    ]]>
-	</help>
-<macros>
-	<import>qiime_citation.xml</import>
-</macros>
-<expand macro="qiime_citation" />
-</tool>
diff -r 558645416841 -r 914fa4daf16a qiime2/qiime_gneiss_lme-regression.xml
--- a/qiime2/qiime_gneiss_lme-regression.xml	Sun Jul 21 02:21:34 2019 -0400
+++ b/qiime2/qiime_gneiss_lme-regression.xml	Wed Jul 31 03:06:00 2019 -0400
@@ -36,6 +36,11 @@
 		<param format="qza,no_unzip.zip" label="--i-tree: ARTIFACT    A hierarchy of feature identifiers where each tip Hierarchy          corresponds 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="itree" optional="False" type="data"/>
 		<param label="--p-formula: TEXT     Statistical formula specifying the statistical model. In other words, a list of the metadata categories that will be used in the linear mixed effect model, typically separated by '+'. For more information see https://patsy.readthedocs.io/en/latest/API-reference.ht ml                                           [required]" name="pformula" optional="False" type="text"/>
 		<param label="--p-groups: TEXT                                                   [required]" name="pgroups" optional="False" type="text"/>
+
+		<repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file  [required]">
+			<param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
+		</repeat>
+
 	</inputs>
 	<outputs>
 		<data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
diff -r 558645416841 -r 914fa4daf16a qiime2/qiime_gneiss_ols-regression.xml
--- a/qiime2/qiime_gneiss_ols-regression.xml	Sun Jul 21 02:21:34 2019 -0400
+++ b/qiime2/qiime_gneiss_ols-regression.xml	Wed Jul 31 03:06:00 2019 -0400
@@ -37,7 +37,7 @@
 		<param label="--p-formula: TEXT     Formula specifying the statistical model. In other words, a list of the metadata categories that will be used in the regression model, typically separated by '+'. For more information see https://patsy.readthedocs.io/en/latest/API-reference.html                                           [required]" name="pformula" optional="False" type="text"/>
 
 
-		<repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
+		<repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file  [required]">
 			<param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
 		</repeat>
 	</inputs>
diff -r 558645416841 -r 914fa4daf16a qiime2/qiime_longitudinal_anova.xml
--- a/qiime2/qiime_longitudinal_anova.xml	Sun Jul 21 02:21:34 2019 -0400
+++ b/qiime2/qiime_longitudinal_anova.xml	Wed Jul 31 03:06:00 2019 -0400
@@ -7,8 +7,18 @@
 	<command><![CDATA[
 qiime longitudinal anova
 
+
+
+
+#if 'X' in str($pformula):
+  #set $pformula_temp = $pformula.replace('X', "~")
+  #set $pformula = $pformula_temp
+#end if
+
 --p-formula="$pformula"
 
+
+
 #if str($psstype) != 'None':
  --p-sstype=$psstype
 #end if
diff -r 558645416841 -r 914fa4daf16a qiime2/qiime_longitudinal_feature-volatility.xml
--- a/qiime2/qiime_longitudinal_feature-volatility.xml	Sun Jul 21 02:21:34 2019 -0400
+++ b/qiime2/qiime_longitudinal_feature-volatility.xml	Wed Jul 31 03:06:00 2019 -0400
@@ -8,6 +8,8 @@
 qiime longitudinal feature-volatility
 
 --i-table=$itable
+
+
 --p-state-column="$pstatecolumn"
 
 #if str($pindividualidcolumn):
@@ -101,7 +103,7 @@
 			<option value="ignore">ignore</option>
 		</param>
 
-		<repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
+		<repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file  [required]">
 			<param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
 		</repeat>
 
diff -r 558645416841 -r 914fa4daf16a qiime2/qiime_longitudinal_first-differences.xml
--- a/qiime2/qiime_longitudinal_first-differences.xml	Sun Jul 21 02:21:34 2019 -0400
+++ b/qiime2/qiime_longitudinal_first-differences.xml	Wed Jul 31 03:06:00 2019 -0400
@@ -53,7 +53,7 @@
 		</param>
 		<param label="--p-baseline: NUMBER    A value listed in the state-column metadata column against which all other states should be compared. Toggles calculation of static differences instead of first differences (which are calculated if no value is given for baseline). If a 'baseline' value is provided, sample differences at each state are compared against the baseline state, instead of the previous state. Must be a value listed in the state-column.                              [optional]" name="pbaseline" optional="True" type="float"/>
 
-		<repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
+		<repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file  [required]">
 			<param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
 		</repeat>
 
diff -r 558645416841 -r 914fa4daf16a qiime2/qiime_longitudinal_first-distances.xml
--- a/qiime2/qiime_longitudinal_first-distances.xml	Sun Jul 21 02:21:34 2019 -0400
+++ b/qiime2/qiime_longitudinal_first-distances.xml	Wed Jul 31 03:06:00 2019 -0400
@@ -48,7 +48,7 @@
 			<option value="drop">drop</option>
 		</param>
 
-		<repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
+		<repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file  [required]">
 			<param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
 		</repeat>
 
diff -r 558645416841 -r 914fa4daf16a qiime2/qiime_longitudinal_linear-mixed-effects.xml
--- a/qiime2/qiime_longitudinal_linear-mixed-effects.xml	Sun Jul 21 02:21:34 2019 -0400
+++ b/qiime2/qiime_longitudinal_linear-mixed-effects.xml	Wed Jul 31 03:06:00 2019 -0400
@@ -47,7 +47,7 @@
  --p-lowess
 #end if
 
-#if $pci:
+#if str($pci):
  --p-ci=$pci
 #end if
 
@@ -93,7 +93,7 @@
 		<param label="--p-ci: NUMBER           Size of the confidence interval for the regression Range(0, 100)         estimate.                              [default: 95]" name="pci" optional="True" type="float" min="0" max="100" value="95"/>
 		<param label="--p-formula: TEXT        R-style formula to use for model specification. A formula must be used if the 'metric' parameter is None. Note that the metric and group columns specified in the formula will override metric and group columns that are passed separately as parameters to this method. Formulae will be in the format 'a ~ b + c', where 'a' is the metric (dependent variable) and 'b' and 'c' are independent covariates. Use '+' to add a variable; '+ a:b' to add an interaction between variables a and b; '*' to include a variable and all interactions; and '-' to subtract a particular term (e.g., an interaction term). See https://patsy.readthedocs.io/en/latest/formulas.html for full documentation of valid formula operators. Always enclose formulae in quotes to avoid unpleasant surprises.                     [optional]" name="pformula" optional="True" type="text"/>
 
-		<repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
+		<repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file  [required]">
 			<param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
 		</repeat>
 
diff -r 558645416841 -r 914fa4daf16a qiime2/qiime_longitudinal_maturity-index.xml
--- a/qiime2/qiime_longitudinal_maturity-index.xml	Sun Jul 21 02:21:34 2019 -0400
+++ b/qiime2/qiime_longitudinal_maturity-index.xml	Wed Jul 31 03:06:00 2019 -0400
@@ -24,11 +24,11 @@
  --p-n-estimators=$pnestimators
 #end if
 
-#if $ptestsize:
+#if str($ptestsize):
  --p-test-size=$ptestsize
 #end if
 
-#if $pstep:
+#if str($pstep):
  --p-step=$pstep
 #end if
 
@@ -62,7 +62,7 @@
  --p-missing-samples=$pmissingsamples
 #end if
 
-#if $pfeaturecount:
+#if str($pfeaturecount):
  --p-feature-count=$pfeaturecount
 #end if
 
@@ -139,7 +139,7 @@
 		</param>
 		<param label="--p-feature-count: INTEGER Range(0, None)       Filter feature table to include top N most important features. Set to zero to include all features. [default: 50]" name="pfeaturecount" optional="True" type="integer" min="0" value="50"/>
 
-		<repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
+		<repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file  [required]">
 			<param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
 		</repeat>	</inputs>
 
diff -r 558645416841 -r 914fa4daf16a qiime2/qiime_longitudinal_nmit.xml
--- a/qiime2/qiime_longitudinal_nmit.xml	Sun Jul 21 02:21:34 2019 -0400
+++ b/qiime2/qiime_longitudinal_nmit.xml	Wed Jul 31 03:06:00 2019 -0400
@@ -8,7 +8,21 @@
 qiime longitudinal nmit
 
 --i-table=$itable
---p-individual-id-column="$pindividualidcolumn"
+
+
+
+
+#if '__sq__' in str($pindividualidcolumn):
+  #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__sq__', "'")
+  #set $pindividualidcolumn = $pindividualidcolumn_temp
+#end if
+
+#if str($pindividualidcolumn):
+ --p-individual-id-column="$pindividualidcolumn"
+#end if
+
+
+
 
 #if str($pcorrmethod) != 'None':
  --p-corr-method=$pcorrmethod
@@ -50,7 +64,7 @@
 			<option value="nuc">nuc</option>
 		</param>
 
-		<repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
+		<repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file  [required]">
 			<param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
 		</repeat>
 
diff -r 558645416841 -r 914fa4daf16a qiime2/qiime_longitudinal_pairwise-differences.xml
--- a/qiime2/qiime_longitudinal_pairwise-differences.xml	Sun Jul 21 02:21:34 2019 -0400
+++ b/qiime2/qiime_longitudinal_pairwise-differences.xml	Wed Jul 31 03:06:00 2019 -0400
@@ -11,7 +11,17 @@
 --p-state-column="$pstatecolumn"
 --p-state-1="$pstate1"
 --p-state-2="$pstate2"
---p-individual-id-column="$pindividualidcolumn"
+
+
+#if '__sq__' in str($pindividualidcolumn):
+  #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__sq__', "'")
+  #set $pindividualidcolumn = $pindividualidcolumn_temp
+#end if
+#if str($pindividualidcolumn):
+ --p-individual-id-column="$pindividualidcolumn"
+#end if
+
+
 
 #if str($itable) != 'None':
  --i-table=$itable
diff -r 558645416841 -r 914fa4daf16a qiime2/qiime_longitudinal_pairwise-distances.xml
--- a/qiime2/qiime_longitudinal_pairwise-distances.xml	Sun Jul 21 02:21:34 2019 -0400
+++ b/qiime2/qiime_longitudinal_pairwise-distances.xml	Wed Jul 31 03:06:00 2019 -0400
@@ -12,7 +12,17 @@
 --p-state-column="$pstatecolumn"
 --p-state-1="$pstate1"
 --p-state-2="$pstate2"
---p-individual-id-column="$pindividualidcolumn"
+
+
+#if '__sq__' in str($pindividualidcolumn):
+  #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__sq__', "'")
+  #set $pindividualidcolumn = $pindividualidcolumn_temp
+#end if
+#if str($pindividualidcolumn):
+ --p-individual-id-column="$pindividualidcolumn"
+#end if
+
+
 
 #if $pparametric:
  --p-parametric
diff -r 558645416841 -r 914fa4daf16a qiime2/qiime_longitudinal_plot-feature-volatility.xml
--- a/qiime2/qiime_longitudinal_plot-feature-volatility.xml	Sun Jul 21 02:21:34 2019 -0400
+++ b/qiime2/qiime_longitudinal_plot-feature-volatility.xml	Wed Jul 31 03:06:00 2019 -0400
@@ -11,10 +11,20 @@
 --i-importances=$iimportances
 --p-state-column="$pstatecolumn"
 
+
+
+#if '__sq__' in str($pindividualidcolumn):
+  #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__sq__', "'")
+  #set $pindividualidcolumn = $pindividualidcolumn_temp
+#end if
+
 #if str($pindividualidcolumn):
  --p-individual-id-column="$pindividualidcolumn"
 #end if
 
+
+
+
 #if str($pdefaultgroupcolumn):
  --p-default-group-column="$pdefaultgroupcolumn"
 #end if
@@ -56,7 +66,7 @@
 			<option value="log">log</option>
 		</param>
 
-		<repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
+		<repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file  [required]">
 			<param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
 		</repeat>
 
diff -r 558645416841 -r 914fa4daf16a qiime2/qiime_longitudinal_volatility.xml
--- a/qiime2/qiime_longitudinal_volatility.xml	Sun Jul 21 02:21:34 2019 -0400
+++ b/qiime2/qiime_longitudinal_volatility.xml	Wed Jul 31 03:06:00 2019 -0400
@@ -13,10 +13,19 @@
  --i-table=$itable
 #end if
 
+
+
+#if '__sq__' in str($pindividualidcolumn):
+  #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__sq__', "'")
+  #set $pindividualidcolumn = $pindividualidcolumn_temp
+#end if
+
 #if str($pindividualidcolumn):
  --p-individual-id-column="$pindividualidcolumn"
 #end if
 
+
+
 #if str($pdefaultgroupcolumn):
  --p-default-group-column="$pdefaultgroupcolumn"
 #end if
@@ -62,7 +71,7 @@
 			<option value="log">log</option>
 		</param>
 
-		<repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
+		<repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file  [required]">
 			<param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
 		</repeat>
 
diff -r 558645416841 -r 914fa4daf16a qiime2/qiime_phylogeny_align-to-tree-mafft-fasttree.xml
--- a/qiime2/qiime_phylogeny_align-to-tree-mafft-fasttree.xml	Sun Jul 21 02:21:34 2019 -0400
+++ b/qiime2/qiime_phylogeny_align-to-tree-mafft-fasttree.xml	Wed Jul 31 03:06:00 2019 -0400
@@ -16,11 +16,11 @@
 #end if
 
 
-#if $pmaskmaxgapfrequency:
+#if str($pmaskmaxgapfrequency):
  --p-mask-max-gap-frequency=$pmaskmaxgapfrequency
 #end if
 
-#if $pmaskminconservation:
+#if str($pmaskminconservation):
  --p-mask-min-conservation=$pmaskminconservation
 #end if
 
diff -r 558645416841 -r 914fa4daf16a qiime2/qiime_phylogeny_iqtree-ultrafast-bootstrap.xml
--- a/qiime2/qiime_phylogeny_iqtree-ultrafast-bootstrap.xml	Sun Jul 21 02:21:34 2019 -0400
+++ b/qiime2/qiime_phylogeny_iqtree-ultrafast-bootstrap.xml	Wed Jul 31 03:06:00 2019 -0400
@@ -13,10 +13,13 @@
  --p-seed="$pseed"
 #end if
 
-#if $pncores:
- --p-n-cores=$pncores
+
+#set $pncores = '${GALAXY_SLOTS:-4}'
+#if str($pncores):
+--p-n-cores=$pncores
 #end if
 
+
 #if $pnruns:
  --p-n-runs=$pnruns
 #end if
@@ -100,7 +103,6 @@
 	<inputs>
 		<param format="qza,no_unzip.zip" label="--i-alignment: ARTIFACT FeatureData[AlignedSequence] Aligned sequences to be used for phylogenetic reconstruction.                           [required]" name="ialignment" optional="False" type="data"/>
 		<param label="--p-seed: INTEGER        Random number seed. If not set, program defaults will be used. See IQ-TREE manual for details. [optional]" name="pseed" optional="True" type="integer"/>
-		<param label="--p-n-cores: INTEGER     The number of cores to use for parallel processing. Range(0, None)        Use '0' to let IQ-TREE automatically determine the optimal number of cores to use.         [default: 1]" name="pncores" optional="True" type="integer" min="0" value="1"/>
 		<param label="--p-n-runs: INTEGER      Number of indepedent runs. Multiple  independent Range(1, None)        runs (e.g. 10) can outperform a single run in terms of likelihood maximisation.             [default: 1]" name="pnruns" optional="True" type="integer" min="1" value="1"/>
 		<param label="--p-substitution-model: " name="psubstitutionmodel" optional="True" type="select">
 			<option selected="True" value="None">Selection is Optional</option>
diff -r 558645416841 -r 914fa4daf16a qiime2/qiime_sample-classifier_split-table.xml
--- a/qiime2/qiime_sample-classifier_split-table.xml	Sun Jul 21 02:21:34 2019 -0400
+++ b/qiime2/qiime_sample-classifier_split-table.xml	Wed Jul 31 03:06:00 2019 -0400
@@ -47,7 +47,6 @@
 ;
 cp otrainingtable.qza $otrainingtable;
 cp otesttable.qza $otesttable;
-cp mmetadatafile.qza $mmetadatafile
 	]]></command>
 	<inputs>
 		<param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] Feature table containing all features that should be used for target prediction.                  [required]" name="itable" optional="False" type="data"/>
diff -r 558645416841 -r 914fa4daf16a qiime2/qiime_taxa_barplot.xml
--- a/qiime2/qiime_taxa_barplot.xml	Sun Jul 21 02:21:34 2019 -0400
+++ b/qiime2/qiime_taxa_barplot.xml	Wed Jul 31 03:06:00 2019 -0400
@@ -31,7 +31,7 @@
 		<param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] Feature table to visualize at various taxonomic levels.                                    [required]" name="itable" optional="False" type="data"/>
 		<param format="qza,no_unzip.zip" label="--i-taxonomy: ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored.                           [required]" name="itaxonomy" optional="False" type="data"/>
 
-		<repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
+		<repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file  [required]">
 			<param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
 		</repeat>
 
diff -r 558645416841 -r 914fa4daf16a qiime2/qiime_taxa_filter-seqs.xml
--- a/qiime2/qiime_taxa_filter-seqs.xml	Sun Jul 21 02:21:34 2019 -0400
+++ b/qiime2/qiime_taxa_filter-seqs.xml	Wed Jul 31 03:06:00 2019 -0400
@@ -59,7 +59,7 @@
 
 		<param label="--p-include: TEXT        One or more search terms that indicate which taxa should be included in the resulting sequences. If providing more than one term, terms should be delimited by the query-delimiter character. By default, all taxa will be included.       [optional]" name="pinclude" optional="True" type="text"/>
 		<param label="--p-exclude: TEXT        One or more search terms that indicate which taxa should be excluded from the resulting sequences. If providing more than one term, terms should be delimited by the query-delimiter character. By default, no taxa will be excluded.        [optional]" name="pexclude" optional="True" type="text"/>
-		<param label="--p-query-delimiter: TEXT The string used to delimit multiple search terms provided to include or exclude. This parameter should only need to be modified if the default delimiter (a comma) is used in the provided taxonomic annotations.                [default: ',']" name="pquerydelimiter" optional="True" type="text" value="','"/>
+		<param label="--p-query-delimiter: TEXT The string used to delimit multiple search terms provided to include or exclude. This parameter should only need to be modified if the default delimiter (a comma) is used in the provided taxonomic annotations.                [default: ',']" name="pquerydelimiter" optional="True" type="text" value=",'"/>
 		<param label="--p-mode: " name="pmode" optional="True" type="select">
 			<option selected="True" value="None">Selection is Optional</option>
 			<option value="exact">exact</option>
diff -r 558645416841 -r 914fa4daf16a qiime2/qiime_taxa_filter-table.xml
--- a/qiime2/qiime_taxa_filter-table.xml	Sun Jul 21 02:21:34 2019 -0400
+++ b/qiime2/qiime_taxa_filter-table.xml	Wed Jul 31 03:06:00 2019 -0400
@@ -59,7 +59,7 @@
 
 		<param label="--p-include: TEXT       One or more search terms that indicate which taxa should be included in the resulting table. If providing more than one term, terms should be delimited by the query-delimiter character. By default, all taxa will be included.        [optional]" name="pinclude" optional="True" type="text"/>
 		<param label="--p-exclude: TEXT       One or more search terms that indicate which taxa should be excluded from the resulting table. If providing more than one term, terms should be delimited by the query-delimiter character. By default, no taxa will be excluded.         [optional]" name="pexclude" optional="True" type="text"/>
-		<param label="--p-query-delimiter: TEXT The string used to delimit multiple search terms provided to include or exclude. This parameter should only need to be modified if the default delimiter (a comma) is used in the provided taxonomic annotations. [default: ',']" name="pquerydelimiter" optional="True" type="text" value="','"/>
+		<param label="--p-query-delimiter: TEXT The string used to delimit multiple search terms provided to include or exclude. This parameter should only need to be modified if the default delimiter (a comma) is used in the provided taxonomic annotations. [default: ',']" name="pquerydelimiter" optional="True" type="text" value=",'"/>
 		<param label="--p-mode: " name="pmode" optional="True" type="select">
 			<option selected="True" value="None">Selection is Optional</option>
 			<option value="exact">exact</option>
diff -r 558645416841 -r 914fa4daf16a qiime2/qiime_tools_export.xml
--- a/qiime2/qiime_tools_export.xml	Sun Jul 21 02:21:34 2019 -0400
+++ b/qiime2/qiime_tools_export.xml	Wed Jul 31 03:06:00 2019 -0400
@@ -4,7 +4,7 @@
 	<requirements>
 		<requirement type="package" version="2019.4">qiime2</requirement>
 	</requirements>
-	<command><![CDATA[qiime tools export --input-path $isequences --output-dir test
+	<command><![CDATA[qiime tools export --input-path $isequences --output-path test
 	]]></command>
 	<inputs>
 	<param format="qza,no_unzip.zip" label="Input artifact to export! [required]" name="isequences" optional="False" type="data"/></inputs>
diff -r 558645416841 -r 914fa4daf16a qiime2/qiime_tools_export_collection.xml
--- a/qiime2/qiime_tools_export_collection.xml	Sun Jul 21 02:21:34 2019 -0400
+++ b/qiime2/qiime_tools_export_collection.xml	Wed Jul 31 03:06:00 2019 -0400
@@ -4,7 +4,7 @@
    <requirements>
       <requirement type="package" version="2019.4">qiime2</requirement>
    </requirements>
-   <command><![CDATA[qiime tools export --input-path $isequences --output-dir test && cd test && gunzip *]]></command>
+   <command><![CDATA[qiime tools export --input-path $isequences --output-path test && cd test && gunzip *]]></command>
    <inputs>
       <param format="qza,no_unzip.zip" label="Input artifact to export! [required]" name="isequences" optional="False" type="data" />
    </inputs>
diff -r 558645416841 -r 914fa4daf16a qiime2/qiime_tools_export_paired_collection.xml
--- a/qiime2/qiime_tools_export_paired_collection.xml	Sun Jul 21 02:21:34 2019 -0400
+++ b/qiime2/qiime_tools_export_paired_collection.xml	Wed Jul 31 03:06:00 2019 -0400
@@ -4,7 +4,7 @@
    <requirements>
       <requirement type="package" version="2019.4">qiime2</requirement>
    </requirements>
-   <command><![CDATA[qiime tools export --input-path $isequences --output-dir test && cd test && gunzip *]]></command>
+   <command><![CDATA[qiime tools export --input-path $isequences --output-path test && cd test && gunzip *]]></command>
    <inputs>
       <param format="qza,no_unzip.zip" label="Input artifact to export! [required]" name="isequences" optional="False" type="data" />
    </inputs>
diff -r 558645416841 -r 914fa4daf16a qiime2/qiime_tools_import.xml
--- a/qiime2/qiime_tools_import.xml	Sun Jul 21 02:21:34 2019 -0400
+++ b/qiime2/qiime_tools_import.xml	Wed Jul 31 03:06:00 2019 -0400
@@ -44,7 +44,7 @@
 			ln -s ${f}  $file_for_processing;
 		#end if
 	#end for
-	#if 'SingleEndFastqManifestPhred' in str($sourceformat):
+	#if 'SingleEndFastqManifestPhred' in str($inputformat):
 			#set $cwd = str($outputpath.extra_files_path) + "_manifest_file.txt"
 			#set $m_file = open(str($cwd), 'w')
 			$m_file.write("sample-id,absolute-filepath,direction\n")
@@ -85,9 +85,9 @@
 
 	
 	$m_file.close()
-	#if 'PairedEndFastqManifestPhred' in str($sourceformat):
+	#if 'PairedEndFastqManifestPhred' in str($inputformat):
 		#set $in_= str($cwd)
-	#elif  'Casava' in str($sourceformat):
+	#elif  'Casava' in str($inputformat):
 		#set $in_= 'input'
 	#end if
 
@@ -119,20 +119,21 @@
 
 qiime tools import
 
---type="$semantic_type"
+--input-path=$in_
 
---input-path=$in_
+#if str($inputformat) != 'None':
+	#if '__ob__' in str($inputformat):
+  		#set $inputformat_temp = str($inputformat).replace('__ob__', '[')
+		#set $inputformat_temp = str($inputformat_temp).replace('__cb__', ']')
+  		#set $inputformat = $inputformat_temp
+	#end if
+ --input-format="$inputformat"
+#end if
+
+--type="$semantic_type"
 
 --output-path=outputpath.qza
 
-#if str($sourceformat) != 'None':
-	#if '__ob__' in str($sourceformat):
-  		#set $sourceformat_temp = str($sourceformat).replace('__ob__', '[')
-		#set $sourceformat_temp = str($sourceformat_temp).replace('__cb__', ']')
-  		#set $sourceformat = $sourceformat_temp
-	#end if
- --source-format="$sourceformat"
-#end if
 ;
 cp outputpath.qza $outputpath
 ]]>
@@ -161,13 +162,16 @@
 			<option value="DistanceMatrix">DistanceMatrix</option>
 			<option value="EMPPairedEndSequences">EMPPairedEndSequences</option>
 			<option value="EMPSingleEndSequences">EMPSingleEndSequences</option>
+			<option value="ErrorCorrectionDetails">ErrorCorrectionDetails</option>
 			<option value="FeatureData[AlignedSequence]">FeatureData[AlignedSequence]</option>
+			<option value="FeatureData[Importance]">FeatureData[Importance]</option>
 			<option value="FeatureData[PairedEndSequence]">FeatureData[PairedEndSequence]</option>
 			<option value="FeatureData[Sequence]">FeatureData[Sequence]</option>
 			<option value="FeatureData[Taxonomy]">FeatureData[Taxonomy]</option>
 			<option value="FeatureTable[Balance]">FeatureTable[Balance]</option>
 			<option value="FeatureTable[Composition]">FeatureTable[Composition]</option>
 			<option value="FeatureTable[Frequency]">FeatureTable[Frequency]</option>
+			<option value="FeatureTable[PercentileNormalized]">FeatureTable[PercentileNormalized]</option>
 			<option value="FeatureTable[PresenceAbsence]">FeatureTable[PresenceAbsence]</option>
 			<option value="FeatureTable[RelativeFrequency]">FeatureTable[RelativeFrequency]</option>
 			<option value="Hierarchy">Hierarchy</option>
@@ -176,21 +180,26 @@
 			<option value="PCoAResults">PCoAResults</option>
 			<option value="Phylogeny[Rooted]">Phylogeny[Rooted]</option>
 			<option value="Phylogeny[Unrooted]">Phylogeny[Unrooted]</option>
+			<option value="Placements">Placements</option>
 			<option value="QualityFilterStats">QualityFilterStats</option>
 			<option value="RawSequences">RawSequences</option>
 			<option value="SampleData[AlphaDiversity]">SampleData[AlphaDiversity]</option>
 			<option value="SampleData[BooleanSeries]">SampleData[BooleanSeries]</option>
+			<option value="SampleData[ClassifierPredictions]">SampleData[ClassifierPredictions]</option>
 			<option value="SampleData[DADA2Stats]">SampleData[DADA2Stats]</option>
 			<option value="SampleData[FirstDifferences]">SampleData[FirstDifferences]</option>
 			<option value="SampleData[JoinedSequencesWithQuality]">SampleData[JoinedSequencesWithQuality]</option>
 			<option selected="True" value="SampleData[PairedEndSequencesWithQuality]">SampleData[PairedEndSequencesWithQuality]</option>
+			<option value="SampleData[RegressorPredictions]">SampleData[RegressorPredictions]</option>
 			<option value="SampleData[SequencesWithQuality]">SampleData[SequencesWithQuality]</option>
 			<option value="SampleData[Sequences]">SampleData[Sequences]</option>
+			<option value="SampleData[Classifier]">SampleData[Classifier]</option>
+			<option value="SampleData[Regressor]">SampleData[Regressor]</option>
 			<option value="TaxonomicClassifier">TaxonomicClassifier</option>
 			<option value="UchimeStats">UchimeStats</option>
 		</param>
 
-		<param label="--source-format: The format of the data to be imported. If not provided, data must be in the format expected by the semantic type provided via --type." name="sourceformat" optional="True" type="select">
+		<param label="--input-format: The format of the data to be imported. If not provided, data must be in the format expected by the semantic type provided via --type." name="inputformat" optional="True" type="select">
 			<option value="AlignedDNAFASTAFormat">AlignedDNAFASTAFormat</option>
 			<option value="AlignedDNASequencesDirectoryFormat">AlignedDNASequencesDirectoryFormat</option>
 			<option value="AlphaDiversityDirectoryFormat">AlphaDiversityDirectoryFormat</option>
@@ -214,11 +223,14 @@
 			<option value="EMPPairedEndDirFmt">EMPPairedEndDirFmt</option>
 			<option value="EMPSingleEndCasavaDirFmt">EMPSingleEndCasavaDirFmt</option>
 			<option value="EMPSingleEndDirFmt">EMPSingleEndDirFmt</option>
+			<option value="ErrorCorrectionDetailsDirFmt">ErrorCorrectionDetailsDirFmt</option>
 			<option value="FastqGzFormat">FastqGzFormat</option>
 			<option value="FirstDifferencesDirectoryFormat">FirstDifferencesDirectoryFormat</option>
 			<option value="FirstDifferencesFormat">FirstDifferencesFormat</option>
 			<option value="HeaderlessTSVTaxonomyDirectoryFormat">HeaderlessTSVTaxonomyDirectoryFormat</option>
 			<option value="HeaderlessTSVTaxonomyFormat">HeaderlessTSVTaxonomyFormat</option>
+			<option value="ImportanceDirectoryFormat">ImportanceDirectoryFormat</option>
+			<option value="ImportanceFormat">ImportanceFormat</option>
 			<option value="LSMatFormat">LSMatFormat</option>
 			<option value="MultiplexedPairedEndBarcodeInSequenceDirFmt">MultiplexedPairedEndBarcodeInSequenceDirFmt</option>
 			<option value="MultiplexedSingleEndBarcodeInSequenceDirFmt">MultiplexedSingleEndBarcodeInSequenceDirFmt</option>
@@ -227,14 +239,23 @@
 			<option value="OrdinationDirectoryFormat">OrdinationDirectoryFormat</option>
 			<option value="OrdinationFormat">OrdinationFormat</option>
 			<option value="PairedDNASequencesDirectoryFormat">PairedDNASequencesDirectoryFormat</option>
-			<option selected="True" value="PairedEndFastqManifestPhred33">PairedEndFastqManifestPhred33</option>
+			<option value="PairedEndFastqManifestPhred33">PairedEndFastqManifestPhred33</option>
+			<option value="PairedEndFastqManifestPhred33V2">PairedEndFastqManifestPhred33V2</option>
 			<option value="PairedEndFastqManifestPhred64">PairedEndFastqManifestPhred64</option>
+			<option value="PairedEndFastqManifestPhred64V2">PairedEndFastqManifestPhred64V2</option>
+			<option value="PlacementsDirFmt">PlacementsDirFmt</option>
+			<option value="PlacementsFormat">PlacementsFormat</option>
+			<option value="PredictionsDirectoryFormat">PredictionsDirectoryFormat</option>
+			<option value="PredictionsFormat">PredictionsFormat</option>
 			<option value="QIIME1DemuxDirFmt">QIIME1DemuxDirFmt</option>
 			<option value="QIIME1DemuxFormat">QIIME1DemuxFormat</option>
 			<option value="QualityFilterStatsDirFmt">QualityFilterStatsDirFmt</option>
 			<option value="QualityFilterStatsFmt">QualityFilterStatsFmt</option>
+			<option value="SampleEstimatorDirFmt">SampleEstimatorDirFmt</option>
 			<option value="SingleEndFastqManifestPhred33">SingleEndFastqManifestPhred33</option>
+			<option value="SingleEndFastqManifestPhred33V2">SingleEndFastqManifestPhred33V2</option>
 			<option value="SingleEndFastqManifestPhred64">SingleEndFastqManifestPhred64</option>
+			<option value="SingleEndFastqManifestPhred64V2">SingleEndFastqManifestPhred64V2</option>
 			<option value="SingleLanePerSamplePairedEndFastqDirFmt">SingleLanePerSamplePairedEndFastqDirFmt</option>
 			<option value="SingleLanePerSampleSingleEndFastqDirFmt">SingleLanePerSampleSingleEndFastqDirFmt</option>
 			<option value="TSVTaxonomyDirectoryFormat">TSVTaxonomyDirectoryFormat</option>