Mercurial > repos > florianbegusch > qiime2_suite

changeset 5:a025a4a89e07 draft

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Uploaded
author florianbegusch
date Mon, 05 Aug 2019 01:29:30 -0400
parents 914fa4daf16a
children de4c22a52df4
files qiime2/qiime_composition_add-pseudocount.xml qiime2/qiime_cutadapt_trim-paired.xml qiime2/qiime_cutadapt_trim-single.xml qiime2/qiime_demux_summarize.xml qiime2/qiime_feature-table_filter-samples.xml qiime2/qiime_phylogeny_raxml-rapid-bootstrap.xml qiime2/qiime_quality-control_evaluate-composition.xml qiime2/qiime_quality-control_exclude-seqs.xml qiime2/qiime_quality-filter_q-score-joined.xml qiime2/qiime_sample-classifier_classify-samples-from-dist.xml qiime2/qiime_sample-classifier_classify-samples-ncv.xml qiime2/qiime_sample-classifier_classify-samples.xml qiime2/qiime_sample-classifier_fit-classifier.xml qiime2/qiime_sample-classifier_fit-regressor.xml qiime2/qiime_sample-classifier_heatmap.xml qiime2/qiime_sample-classifier_regress-samples-ncv.xml qiime2/qiime_sample-classifier_regress-samples.xml qiime2/qiime_sample-classifier_scatterplot.xml qiime2/qiime_sample-classifier_split-table.xml qiime2/qiime_taxa_filter-seqs.xml qiime2/qiime_taxa_filter-table.xml qiime2/qiime_vsearch_cluster-features-closed-reference.xml qiime2/qiime_vsearch_join-pairs.xml qiime2/qiime_vsearch_uchime-denovo.xml qiime2/qiime_vsearch_uchime-ref.xml
diffstat 25 files changed, 113 insertions(+), 176 deletions(-) [+]
line wrap: on
line diff
--- a/qiime2/qiime_composition_add-pseudocount.xml	Wed Jul 31 03:06:00 2019 -0400
+++ b/qiime2/qiime_composition_add-pseudocount.xml	Mon Aug 05 01:29:30 2019 -0400
@@ -10,7 +10,7 @@
 --i-table=$itable
 --o-composition-table=ocompositiontable
 
-#if $ppseudocount:
+#if str($ppseudocount):
  --p-pseudocount=$ppseudocount
 #end if
 ;
--- a/qiime2/qiime_cutadapt_trim-paired.xml	Wed Jul 31 03:06:00 2019 -0400
+++ b/qiime2/qiime_cutadapt_trim-paired.xml	Mon Aug 05 01:29:30 2019 -0400
@@ -96,7 +96,7 @@
 
 
 
-#if $perrorrate:
+#if str($perrorrate):
  --p-error-rate=$perrorrate
 #end if
 
@@ -108,7 +108,7 @@
  --p-times=$ptimes
 #end if
 
-#if $poverlap:
+#if str($poverlap):
  --p-overlap=$poverlap
 #end if
 
--- a/qiime2/qiime_cutadapt_trim-single.xml	Wed Jul 31 03:06:00 2019 -0400
+++ b/qiime2/qiime_cutadapt_trim-single.xml	Mon Aug 05 01:29:30 2019 -0400
@@ -57,7 +57,7 @@
 
 
 
-#if $perrorrate:
+#if str($perrorrate):
  --p-error-rate=$perrorrate
 #end if
 
@@ -65,11 +65,11 @@
  --p-no-indels
 #end if
 
-#if $ptimes:
+#if str($ptimes):
  --p-times=$ptimes
 #end if
 
-#if $poverlap:
+#if str($poverlap):
  --p-overlap=$poverlap
 #end if
 
@@ -81,7 +81,7 @@
  --p-no-match-adapter-wildcards
 #end if
 
-#if $pminimumlength:
+#if str($pminimumlength):
  --p-minimum-length=$pminimumlength
 #end if
 
--- a/qiime2/qiime_demux_summarize.xml	Wed Jul 31 03:06:00 2019 -0400
+++ b/qiime2/qiime_demux_summarize.xml	Mon Aug 05 01:29:30 2019 -0400
@@ -9,7 +9,7 @@
 
 --i-data=$idata
 
-#if $pn:
+#if str($pn):
  --p-n=$pn
 #end if
 
--- a/qiime2/qiime_feature-table_filter-samples.xml	Wed Jul 31 03:06:00 2019 -0400
+++ b/qiime2/qiime_feature-table_filter-samples.xml	Mon Aug 05 01:29:30 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 $pminfeatures:
+#if str($pminfeatures):
  --p-min-features=$pminfeatures
 #end if
 
--- a/qiime2/qiime_phylogeny_raxml-rapid-bootstrap.xml	Wed Jul 31 03:06:00 2019 -0400
+++ b/qiime2/qiime_phylogeny_raxml-rapid-bootstrap.xml	Mon Aug 05 01:29:30 2019 -0400
@@ -17,7 +17,7 @@
  --p-rapid-bootstrap-seed="$prapidbootstrapseed"
 #end if
 
-#if $pbootstrapreplicates:
+#if str($pbootstrapreplicates):
  --p-bootstrap-replicates=$pbootstrapreplicates
 #end if
 
--- a/qiime2/qiime_quality-control_evaluate-composition.xml	Wed Jul 31 03:06:00 2019 -0400
+++ b/qiime2/qiime_quality-control_evaluate-composition.xml	Mon Aug 05 01:29:30 2019 -0400
@@ -11,19 +11,12 @@
 --i-observed-features=$iobservedfeatures
 
 
-#if $input_files_mmetadatafile:
-#def list_dict_to_string(list_dict):
-	#set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
-	#for d in list_dict[1:]:
-		#set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
-	#end for
-	#return $file_list
-#end def
- --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
+#if $metadatafile:
+ --m-metadata-file=$metadatafile
 #end if
 
 
-#if $pdepth:
+#if str($pdepth):
  --p-depth=$pdepth
 #end if
 
@@ -59,8 +52,8 @@
  --p-plot-observed-features
 #end if
 
-#if $pplotobservedfeaturesratio:
- --p-plot-observed-features-ratio
+#if $pnoplotobservedfeaturesratio:
+ --p-no-plot-observed-features-ratio
 #end if
 
 #if str($mmetadatacolumn):
@@ -108,9 +101,8 @@
 		<param label="--p-no-plot-observed-features-ratio: Do not plot ratio of observed:expected features on score plot.                                   [default: False]" name="pnoplotobservedfeaturesratio" selected="False" type="boolean"/>
 		<param label="--m-metadata-column: COLUMN  MetadataColumn[Categorical] Optional sample metadata that maps observed-features sample IDs to expected-features sample IDs.  [optional]" name="mmetadatacolumn" optional="True" type="text"/>
 
-		<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 METADATA" name="metadatafile" type="data" format="tabular,qza,no_unzip.zip" />
+
 
 	</inputs>
 	<outputs>
--- a/qiime2/qiime_quality-control_exclude-seqs.xml	Wed Jul 31 03:06:00 2019 -0400
+++ b/qiime2/qiime_quality-control_exclude-seqs.xml	Mon Aug 05 01:29:30 2019 -0400
@@ -14,7 +14,7 @@
  --p-method=$pmethod
 #end if
 
-#if $ppercidentity:
+#if str($ppercidentity):
  --p-perc-identity=$ppercidentity
 #end if
 
@@ -22,7 +22,7 @@
  --p-evalue="$pevalue"
 #end if
 
-#if $ppercqueryaligned:
+#if str($ppercqueryaligned):
  --p-perc-query-aligned=$ppercqueryaligned
 #end if
 
@@ -47,7 +47,7 @@
 			<option value="blastn-short">blastn-short</option>
 		</param>
 		<param label="--p-perc-identity: PROPORTION Range(0.0, 1.0, inclusive_end=True) Reject match if percent identity to reference is lower. Must be in range [0.0, 1.0]      [default: 0.97]" name="ppercidentity" optional="True" type="float" value="0.97" min="0" max="1" exclusive_end="False"/>
-		<param label="--p-evalue: NUMBER    BLAST expectation (E) value threshold for saving hits. Reject if E value is higher than threshold. This threshold is disabled by default.            [optional]" name="pevalue" optional="True" type="text"/>
+		<param label="--p-evalue: NUMBER    BLAST expectation (E) value threshold for saving hits. Reject if E value is higher than threshold. This threshold is disabled by default.            [optional]" name="pevalue" optional="True" type="float"/>
 		<param label="--p-perc-query-aligned: NUMBER Percent of query sequence that must align to reference in order to be accepted as a hit.       [default: 0.97]" name="ppercqueryaligned" optional="True" type="float" value="0.97"/>
 	</inputs>
 	<outputs>
--- a/qiime2/qiime_quality-filter_q-score-joined.xml	Wed Jul 31 03:06:00 2019 -0400
+++ b/qiime2/qiime_quality-filter_q-score-joined.xml	Mon Aug 05 01:29:30 2019 -0400
@@ -9,19 +9,19 @@
 
 --i-demux=$idemux
 
-#if $pminquality:
+#if str($pminquality):
  --p-min-quality=$pminquality
 #end if
 
-#if $pqualitywindow:
+#if str($pqualitywindow):
  --p-quality-window=$pqualitywindow
 #end if
 
-#if $pminlengthfraction:
+#if str($pminlengthfraction):
  --p-min-length-fraction=$pminlengthfraction
 #end if
 
-#if $pmaxambiguous:
+#if str($pmaxambiguous):
  --p-max-ambiguous=$pmaxambiguous
 #end if
 
--- a/qiime2/qiime_sample-classifier_classify-samples-from-dist.xml	Wed Jul 31 03:06:00 2019 -0400
+++ b/qiime2/qiime_sample-classifier_classify-samples-from-dist.xml	Mon Aug 05 01:29:30 2019 -0400
@@ -10,7 +10,7 @@
 --i-distance-matrix=$idistancematrix
 --m-metadata-column="$mmetadatacolumn"
 
-#if $pk:
+#if str($pk):
  --p-k=$pk
 #end if
 
@@ -19,15 +19,8 @@
 #end if
 
 
-#if $input_files_mmetadatafile:
-#def list_dict_to_string(list_dict):
-	#set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
-	#for d in list_dict[1:]:
-		#set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
-	#end for
-	#return $file_list
-#end def
- --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
+#if $metadatafile:
+ --m-metadata-file=$metadatafile
 #end if
 
 
@@ -77,9 +70,7 @@
 			<option value="greyscale">greyscale</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 METADATA" name="metadatafile" type="data" format="tabular,qza,no_unzip.zip" />
 
 	</inputs>
 	<outputs>
--- a/qiime2/qiime_sample-classifier_classify-samples-ncv.xml	Wed Jul 31 03:06:00 2019 -0400
+++ b/qiime2/qiime_sample-classifier_classify-samples-ncv.xml	Mon Aug 05 01:29:30 2019 -0400
@@ -11,15 +11,9 @@
 --m-metadata-column="$mmetadatacolumn"
 
 
-#if $input_files_mmetadatafile:
-#def list_dict_to_string(list_dict):
-	#set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
-	#for d in list_dict[1:]:
-		#set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
-	#end for
-	#return $file_list
-#end def
- --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
+
+#if $metadatafile:
+ --m-metadata-file=$metadatafile
 #end if
 
 
@@ -83,9 +77,8 @@
 			<option value="ignore">ignore</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 METADATA" name="metadatafile" type="data" format="tabular,qza,no_unzip.zip" />
+
 	</inputs>
 	<outputs>
 		<data format="qza" label="${tool.name} on ${on_string}: predictions.qza" name="opredictions"/>
--- a/qiime2/qiime_sample-classifier_classify-samples.xml	Wed Jul 31 03:06:00 2019 -0400
+++ b/qiime2/qiime_sample-classifier_classify-samples.xml	Mon Aug 05 01:29:30 2019 -0400
@@ -10,15 +10,15 @@
 --i-table=$itable
 --m-metadata-column="$mmetadatacolumn"
 
-#if $ptestsize:
+#if str($ptestsize):
  --p-test-size=$ptestsize
 #end if
 
-#if $pstep:
+#if str($pstep):
  --p-step=$pstep
 #end if
 
-#if $pcv:
+#if str($pcv):
  --p-cv=$pcv
 #end if
 
@@ -58,18 +58,12 @@
 #end if
 
 
-#if $input_files_mmetadatafile:
-#def list_dict_to_string(list_dict):
-	#set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
-	#for d in list_dict[1:]:
-		#set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
-	#end for
-	#return $file_list
-#end def
- --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
+#if $metadatafile:
+ --m-metadata-file=$metadatafile
 #end if
 
 
+
 --o-sample-estimator=osampleestimator
 --o-feature-importance=ofeatureimportance
 --o-predictions=opredictions
@@ -145,9 +139,7 @@
 			<option value="ignore">ignore</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 METADATA" name="metadatafile" type="data" format="tabular,qza,no_unzip.zip" />
 
 	</inputs>
 	<outputs>
--- a/qiime2/qiime_sample-classifier_fit-classifier.xml	Wed Jul 31 03:06:00 2019 -0400
+++ b/qiime2/qiime_sample-classifier_fit-classifier.xml	Mon Aug 05 01:29:30 2019 -0400
@@ -10,7 +10,7 @@
 --i-table=$itable
 --m-metadata-column="$mmetadatacolumn"
 
-#if $pstep:
+#if str($pstep):
  --p-step=$pstep
 #end if
 
@@ -50,18 +50,13 @@
 #end if
 
 
-#if $input_files_mmetadatafile:
-#def list_dict_to_string(list_dict):
-	#set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
-	#for d in list_dict[1:]:
-		#set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
-	#end for
-	#return $file_list
-#end def
- --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
+
+#if $metadatafile:
+ --m-metadata-file=$metadatafile
 #end if
 
 
+
 --o-sample-estimator=osampleestimator
 --o-feature-importance=ofeatureimportance
 ;
@@ -93,9 +88,7 @@
 			<option value="ignore">ignore</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 METADATA" name="metadatafile" type="data" format="tabular,qza,no_unzip.zip" />
 
 	</inputs>
 	<outputs>
--- a/qiime2/qiime_sample-classifier_fit-regressor.xml	Wed Jul 31 03:06:00 2019 -0400
+++ b/qiime2/qiime_sample-classifier_fit-regressor.xml	Mon Aug 05 01:29:30 2019 -0400
@@ -10,7 +10,7 @@
 --i-table=$itable
 --m-metadata-column="$mmetadatacolumn"
 
-#if $pstep:
+#if str($pstep):
  --p-step=$pstep
 #end if
 
@@ -49,18 +49,14 @@
 #end if
 
 
-#if $input_files_mmetadatafile:
-#def list_dict_to_string(list_dict):
-	#set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
-	#for d in list_dict[1:]:
-		#set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
-	#end for
-	#return $file_list
-#end def
- --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
+
+
+#if $metadatafile:
+ --m-metadata-file=$metadatafile
 #end if
 
 
+
 --o-sample-estimator=osampleestimator
 --o-feature-importance=ofeatureimportance
 ;
@@ -95,9 +91,7 @@
 			<option value="ignore">ignore</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 METADATA" name="metadatafile" type="data" format="tabular,qza,no_unzip.zip" />
 
 	</inputs>
 	<outputs>
--- a/qiime2/qiime_sample-classifier_heatmap.xml	Wed Jul 31 03:06:00 2019 -0400
+++ b/qiime2/qiime_sample-classifier_heatmap.xml	Mon Aug 05 01:29:30 2019 -0400
@@ -11,28 +11,25 @@
 --i-importance=$iimportance
 
 
-#if $input_files_mmetadatafile:
-#def list_dict_to_string(list_dict):
-	#set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
-	#for d in list_dict[1:]:
-		#set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
-	#end for
-	#return $file_list
-#end def
- --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
+
+
+#if $metadatafile:
+ --m-metadata-file=$metadatafile
 #end if
 
 
 
+
+
 #if str($mmetadatacolumn):
  --m-metadata-column="$mmetadatacolumn"
 #end if
 
-#if $pfeaturecount:
+#if str($pfeaturecount):
  --p-feature-count=$pfeaturecount
 #end if
 
-#if $pimportancethreshold:
+#if str($pimportancethreshold):
  --p-importance-threshold=$pimportancethreshold
 #end if
 
@@ -297,9 +294,9 @@
 			<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 METADATA" name="metadatafile" type="data" format="tabular,qza,no_unzip.zip" />
+
 
 	</inputs>
 	<outputs>
--- a/qiime2/qiime_sample-classifier_regress-samples-ncv.xml	Wed Jul 31 03:06:00 2019 -0400
+++ b/qiime2/qiime_sample-classifier_regress-samples-ncv.xml	Mon Aug 05 01:29:30 2019 -0400
@@ -46,18 +46,13 @@
 #end if
 
 
-#if $input_files_mmetadatafile:
-#def list_dict_to_string(list_dict):
-	#set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
-	#for d in list_dict[1:]:
-		#set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
-	#end for
-	#return $file_list
-#end def
- --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
+
+#if $metadatafile:
+ --m-metadata-file=$metadatafile
 #end if
 
 
+
 --o-predictions=opredictions
 --o-feature-importance=ofeatureimportance
 ;
@@ -91,9 +86,9 @@
 			<option value="ignore">ignore</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 METADATA" name="metadatafile" type="data" format="tabular,qza,no_unzip.zip" />
+
 	</inputs>
 	<outputs>
 		<data format="qza" label="${tool.name} on ${on_string}: predictions.qza" name="opredictions"/>
--- a/qiime2/qiime_sample-classifier_regress-samples.xml	Wed Jul 31 03:06:00 2019 -0400
+++ b/qiime2/qiime_sample-classifier_regress-samples.xml	Mon Aug 05 01:29:30 2019 -0400
@@ -10,11 +10,11 @@
 --i-table=$itable
 --m-metadata-column="$mmetadatacolumn"
 
-#if $ptestsize:
+#if str($ptestsize):
  --p-test-size=$ptestsize
 #end if
 
-#if $pstep:
+#if str($pstep):
  --p-step=$pstep
 #end if
 
@@ -33,7 +33,7 @@
 #end if
 
 
-#if $pnestimators:
+#if str($pnestimators):
  --p-n-estimators=$pnestimators
 #end if
 
@@ -58,18 +58,15 @@
 #end if
 
 
-#if $input_files_mmetadatafile:
-#def list_dict_to_string(list_dict):
-	#set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
-	#for d in list_dict[1:]:
-		#set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
-	#end for
-	#return $file_list
-#end def
- --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
+
+
+#if $metadatafile:
+ --m-metadata-file=$metadatafile
 #end if
 
 
+
+
 --o-sample-estimator=osampleestimator
 --o-feature-importance=ofeatureimportance
 --o-predictions=opredictions
@@ -89,9 +86,9 @@
 	<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"/>
 		<param label="--m-metadata-column: COLUMN  MetadataColumn[Numeric] Numeric metadata column to use as prediction target. [required]" name="mmetadatacolumn" optional="False" type="text"/>
-		<param label="--p-test-size: PROPORTION Range(0.0, 1.0, inclusive_start=False) Fraction of input samples to exclude from training set and use for classifier testing.          [default: 0.2]" name="ptestsize" optional="True" type="float" value="0.2"/>
-		<param label="--p-step: PROPORTION Range(0.0, 1.0, inclusive_start=False) If optimize-feature-selection is True, step is the percentage of features to remove at each iteration. [default: 0.05]" name="pstep" optional="True" type="float" value="0.05"/>
-		<param label="--p-cv: INTEGER       Number of k-fold cross-validations to perform. Range(1, None)                                                [default: 5]" name="pcv" optional="True" type="integer" value="5"/>
+		<param label="--p-test-size: PROPORTION Range(0.0, 1.0, inclusive_start=False) Fraction of input samples to exclude from training set and use for classifier testing.          [default: 0.2]" name="ptestsize" optional="True" type="float" value="0.2" min="0" max="1" />
+		<param label="--p-step: PROPORTION Range(0.0, 1.0, inclusive_start=False) If optimize-feature-selection is True, step is the percentage of features to remove at each iteration. [default: 0.05]" name="pstep" optional="True" type="float" value="0.05" min="0" max="1" />
+		<param label="--p-cv: INTEGER       Number of k-fold cross-validations to perform. Range(1, None)                                                [default: 5]" name="pcv" optional="True" type="integer" value="5" min="1"/>
 		<param label="--p-random-state: INTEGER Seed used by random number generator.        [optional]" name="prandomstate" optional="True" type="integer"/>
 		<param label="--p-n-estimators: INTEGER Range(1, None)     Number of trees to grow for estimation. More trees will improve predictive accuracy up to a threshold level, but will also increase time and memory requirements. This parameter only affects ensemble estimators, such as Random Forest, AdaBoost, ExtraTrees, and GradientBoosting.        [default: 100]" name="pnestimators" optional="True" type="integer" value="100" min="1"/>
 		<param label="--p-estimator: " name="pestimator" optional="True" type="select">
@@ -116,9 +113,9 @@
 			<option value="ignore">ignore</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 METADATA" name="metadatafile" type="data" format="tabular,qza,no_unzip.zip" />
+
 
 	</inputs>
 	<outputs>
--- a/qiime2/qiime_sample-classifier_scatterplot.xml	Wed Jul 31 03:06:00 2019 -0400
+++ b/qiime2/qiime_sample-classifier_scatterplot.xml	Mon Aug 05 01:29:30 2019 -0400
@@ -10,7 +10,7 @@
 --i-predictions=$ipredictions
 --m-truth-column="$mtruthcolumn"
 
---m-truth-file="$metadatafile"
+--m-truth-file="$mtruthfile"
 
 #if str($pmissingsamples) != 'None':
  --p-missing-samples=$pmissingsamples
@@ -21,7 +21,6 @@
 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';
-cp mtruthfile.qza $mtruthfile
 	]]></command>
 	<inputs>
 		<param format="qza,no_unzip.zip" label="--i-predictions: ARTIFACT SampleData[RegressorPredictions] Predicted values to plot on y axis. Must be predictions of numeric data produced by a sample regressor.                                   [required]" name="ipredictions" optional="False" type="data"/>
@@ -32,7 +31,7 @@
 			<option value="ignore">ignore</option>
 		</param>
 
-		<param label="--m-truth-file: Metadata file or artifact viewable as metadata." name="metadatafile" type="data" format="tabular,qza,no_unzip.zip" />
+		<param label="--m-truth-file: Metadata file or artifact viewable as metadata." name="mtruthfile" type="data" format="tabular,qza,no_unzip.zip" />
 
 	</inputs>
 	<outputs>
--- a/qiime2/qiime_sample-classifier_split-table.xml	Wed Jul 31 03:06:00 2019 -0400
+++ b/qiime2/qiime_sample-classifier_split-table.xml	Mon Aug 05 01:29:30 2019 -0400
@@ -12,21 +12,14 @@
 
 
 
-#if $input_files_mmetadatafile:
-#def list_dict_to_string(list_dict):
-	#set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
-	#for d in list_dict[1:]:
-		#set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
-	#end for
-	#return $file_list
-#end def
-
- --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
+#if $metadatafile:
+ --m-metadata-file=$metadatafile
 #end if
 
 
 
-#if $ptestsize:
+
+#if str($ptestsize):
  --p-test-size=$ptestsize
 #end if
 
@@ -60,9 +53,7 @@
 			<option value="ignore">ignore</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 METADATA" name="metadatafile" type="data" format="tabular,qza,no_unzip.zip" />
 
 	</inputs>
 	<outputs>
--- a/qiime2/qiime_taxa_filter-seqs.xml	Wed Jul 31 03:06:00 2019 -0400
+++ b/qiime2/qiime_taxa_filter-seqs.xml	Mon Aug 05 01:29:30 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>
--- a/qiime2/qiime_taxa_filter-table.xml	Wed Jul 31 03:06:00 2019 -0400
+++ b/qiime2/qiime_taxa_filter-table.xml	Mon Aug 05 01:29:30 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>
--- a/qiime2/qiime_vsearch_cluster-features-closed-reference.xml	Wed Jul 31 03:06:00 2019 -0400
+++ b/qiime2/qiime_vsearch_cluster-features-closed-reference.xml	Mon Aug 05 01:29:30 2019 -0400
@@ -9,7 +9,10 @@
 --i-sequences=$isequences
 --i-table=$itable
 --i-reference-sequences=$ireferencesequences
---p-perc-identity="$ppercidentity"
+
+#if str($ppercidentity):
+  --p-perc-identity="$ppercidentity"
+#end if
 
 #if str($pstrand) != 'None':
  --p-strand=$pstrand
--- a/qiime2/qiime_vsearch_join-pairs.xml	Wed Jul 31 03:06:00 2019 -0400
+++ b/qiime2/qiime_vsearch_join-pairs.xml	Mon Aug 05 01:29:30 2019 -0400
@@ -13,7 +13,7 @@
  --p-truncqual="$ptruncqual"
 #end if
 
-#if $pminlen:
+#if str($pminlen):
  --p-minlen=$pminlen
 #end if
 
@@ -25,11 +25,11 @@
  --p-allowmergestagger
 #end if
 
-#if $pminovlen:
+#if str($pminovlen):
  --p-minovlen=$pminovlen
 #end if
 
-#if $pmaxdiffs:
+#if str($pmaxdiffs):
  --p-maxdiffs=$pmaxdiffs
 #end if
 
@@ -45,19 +45,19 @@
  --p-maxee="$pmaxee"
 #end if
 
-#if $pqmin:
+#if str($pqmin):
  --p-qmin=$pqmin
 #end if
 
-#if $pqminout:
+#if str($pqminout):
  --p-qminout=$pqminout
 #end if
 
-#if $pqmax:
+#if str($pqmax):
  --p-qmax=$pqmax
 #end if
 
-#if $pqmaxout:
+#if str($pqmaxout):
  --p-qmaxout=$pqmaxout
 #end if
 
--- a/qiime2/qiime_vsearch_uchime-denovo.xml	Wed Jul 31 03:06:00 2019 -0400
+++ b/qiime2/qiime_vsearch_uchime-denovo.xml	Mon Aug 05 01:29:30 2019 -0400
@@ -10,7 +10,7 @@
 --i-sequences=$isequences
 --i-table=$itable
 
-#if $pdn:
+#if str($pdn):
  --p-dn=$pdn
 #end if
 
@@ -18,11 +18,11 @@
  --p-mindiffs=$pmindiffs
 #end if
 
-#if $pmindiv:
+#if str($pmindiv):
  --p-mindiv=$pmindiv
 #end if
 
-#if $pminh:
+#if str($pminh):
  --p-minh=$pminh
 #end if
 
--- a/qiime2/qiime_vsearch_uchime-ref.xml	Wed Jul 31 03:06:00 2019 -0400
+++ b/qiime2/qiime_vsearch_uchime-ref.xml	Mon Aug 05 01:29:30 2019 -0400
@@ -11,7 +11,7 @@
 --i-table=$itable
 --i-reference-sequences=$ireferencesequences
 
-#if $pdn:
+#if str($pdn):
  --p-dn=$pdn
 #end if
 
@@ -19,11 +19,11 @@
  --p-mindiffs=$pmindiffs
 #end if
 
-#if $pmindiv:
+#if str($pmindiv):
  --p-mindiv=$pmindiv
 #end if
 
-#if $pminh:
+#if str($pminh):
  --p-minh=$pminh
 #end if