# HG changeset patch
# User florianbegusch
# Date 1563466755 14400
# Node ID 51025741f326c5858f6523a771829f328ba6a0c6
# Parent  255f48db74f8492dd363eedd6ae59e803233866b
Uploaded

diff -r 255f48db74f8 -r 51025741f326 qiime2/.idea/workspace.xml
--- a/qiime2/.idea/workspace.xml	Wed Jul 17 03:26:16 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,517 +0,0 @@
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-          <caret line="47" column="65" selection-start-line="47" selection-start-column="65" selection-end-line="47" selection-end-column="65" />
-        </state>
-      </provider>
-    </entry>
-  </component>
-  <component name="masterDetails">
-    <states>
-      <state key="GlobalLibrariesConfigurable.UI">
-        <settings>
-          <splitter-proportions>
-            <option name="proportions">
-              <list>
-                <option value="0.2" />
-              </list>
-            </option>
-          </splitter-proportions>
-        </settings>
-      </state>
-      <state key="JdkListConfigurable.UI">
-        <settings>
-          <last-edited>1.8</last-edited>
-          <splitter-proportions>
-            <option name="proportions">
-              <list>
-                <option value="0.2" />
-              </list>
-            </option>
-          </splitter-proportions>
-        </settings>
-      </state>
-      <state key="ProjectJDKs.UI">
-        <settings>
-          <last-edited>1.8</last-edited>
-          <splitter-proportions>
-            <option name="proportions">
-              <list>
-                <option value="0.2" />
-              </list>
-            </option>
-          </splitter-proportions>
-        </settings>
-      </state>
-      <state key="ProjectLibrariesConfigurable.UI">
-        <settings>
-          <splitter-proportions>
-            <option name="proportions">
-              <list>
-                <option value="0.2" />
-              </list>
-            </option>
-          </splitter-proportions>
-        </settings>
-      </state>
-    </states>
-  </component>
-</project>
\ No newline at end of file
diff -r 255f48db74f8 -r 51025741f326 qiime2/qiime_composition_ancom.xml
--- a/qiime2/qiime_composition_ancom.xml	Wed Jul 17 03:26:16 2019 -0400
+++ b/qiime2/qiime_composition_ancom.xml	Thu Jul 18 12:19:15 2019 -0400
@@ -9,6 +9,7 @@
 
 --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:]:
@@ -16,6 +17,7 @@
   #end for
   #return $file_list
 #end def
+#end if
 
 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile) --m-metadata-column="$mmetadatacolumn"
 
diff -r 255f48db74f8 -r 51025741f326 qiime2/qiime_cutadapt_demux-paired.xml
--- a/qiime2/qiime_cutadapt_demux-paired.xml	Wed Jul 17 03:26:16 2019 -0400
+++ b/qiime2/qiime_cutadapt_demux-paired.xml	Thu Jul 18 12:19:15 2019 -0400
@@ -8,6 +8,7 @@
 qiime cutadapt demux-paired
 --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:]:
@@ -16,8 +17,13 @@
   #return $file_list
 #end def
 
+#if $input_files_mforwardbarcodesfile:
 --m-forward-barcodes-file=$list_dict_to_string("$input_files_mforwardbarcodesfile")
+#end if
+
+#if $input_files_mreversebarcodesfile:
 --m-reverse-barcodes-file=$list_dict_to_string("$input_files_mreversebarcodesfile")
+#end if
 
 --m-forward-barcodes-column="$mforwardbarcodescolumn"
 
diff -r 255f48db74f8 -r 51025741f326 qiime2/qiime_cutadapt_demux-single.xml
--- a/qiime2/qiime_cutadapt_demux-single.xml	Wed Jul 17 03:26:16 2019 -0400
+++ b/qiime2/qiime_cutadapt_demux-single.xml	Thu Jul 18 12:19:15 2019 -0400
@@ -12,6 +12,8 @@
 --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:]:
@@ -19,8 +21,8 @@
   #end for
   #return $file_list
 #end def
-
 --m-barcodes-file=$list_dict_to_string("$input_files_mbarcodesfile")
+#end if
 
 #if $perrorrate:
  --p-error-rate=$perrorrate
diff -r 255f48db74f8 -r 51025741f326 qiime2/qiime_demux_emp-paired.xml
--- a/qiime2/qiime_demux_emp-paired.xml	Wed Jul 17 03:26:16 2019 -0400
+++ b/qiime2/qiime_demux_emp-paired.xml	Thu Jul 18 12:19:15 2019 -0400
@@ -11,6 +11,7 @@
 --m-barcodes-column="$mbarcodescolumn"
 
 
+#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:]:
@@ -18,8 +19,8 @@
 #end for
 #return $file_list
 #end def
-
 --m-barcodes-file=$list_dict_to_string($input_files_mbarcodesfile)
+#end if
 
 
 #if $pnogolayerrorcorrection:
diff -r 255f48db74f8 -r 51025741f326 qiime2/qiime_demux_emp-single.xml
--- a/qiime2/qiime_demux_emp-single.xml	Wed Jul 17 03:26:16 2019 -0400
+++ b/qiime2/qiime_demux_emp-single.xml	Thu Jul 18 12:19:15 2019 -0400
@@ -11,6 +11,7 @@
 --m-barcodes-column="$mbarcodescolumn"
 
 
+#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:]:
@@ -18,8 +19,8 @@
 #end for
 #return $file_list
 #end def
-
 --m-barcodes-file=$list_dict_to_string($input_files_mbarcodesfile)
+#end if
 
 
 #if $pnogolayerrorcorrection:
diff -r 255f48db74f8 -r 51025741f326 qiime2/qiime_diversity_adonis.xml
--- a/qiime2/qiime_diversity_adonis.xml	Wed Jul 17 03:26:16 2019 -0400
+++ b/qiime2/qiime_diversity_adonis.xml	Thu Jul 18 12:19:15 2019 -0400
@@ -10,6 +10,7 @@
 --i-distance-matrix=$idistancematrix
 
 
+#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:]:
@@ -17,10 +18,8 @@
   #end for
   #return $file_list
 #end def
-
 --m-metadata-file=$list_dict_to_string("$input_files_mmetadatafile")
-
-
+#end if
 
 
 --p-formula="$pformula"
diff -r 255f48db74f8 -r 51025741f326 qiime2/qiime_diversity_alpha-group-significance.xml
--- a/qiime2/qiime_diversity_alpha-group-significance.xml	Wed Jul 17 03:26:16 2019 -0400
+++ b/qiime2/qiime_diversity_alpha-group-significance.xml	Thu Jul 18 12:19:15 2019 -0400
@@ -10,6 +10,7 @@
 --i-alpha-diversity=$ialphadiversity
 
 
+#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:]:
@@ -17,8 +18,9 @@
 #end for
 #return $file_list
 #end def
+--m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
+#end if
 
---m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
 
 --o-visualization=ovisualization
 ;
diff -r 255f48db74f8 -r 51025741f326 qiime2/qiime_diversity_beta-rarefaction.xml
--- a/qiime2/qiime_diversity_beta-rarefaction.xml	Wed Jul 17 03:26:16 2019 -0400
+++ b/qiime2/qiime_diversity_beta-rarefaction.xml	Thu Jul 18 12:19:15 2019 -0400
@@ -28,6 +28,7 @@
  --p-color-scheme=$pcolorscheme
 #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:]:
@@ -35,9 +36,8 @@
 #end for
 #return $file_list
 #end def
-
 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
-
+#end if
 
 --o-visualization=ovisualization
 ;
diff -r 255f48db74f8 -r 51025741f326 qiime2/qiime_diversity_core-metrics-phylogenetic.xml
--- a/qiime2/qiime_diversity_core-metrics-phylogenetic.xml	Wed Jul 17 03:26:16 2019 -0400
+++ b/qiime2/qiime_diversity_core-metrics-phylogenetic.xml	Thu Jul 18 12:19:15 2019 -0400
@@ -16,6 +16,8 @@
  --p-n-jobs="$pnjobs"
 #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:]:
@@ -23,8 +25,9 @@
 #end for
 #return $file_list
 #end def
+--m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
+#end if
 
---m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
 
 
 --o-rarefied-table=orarefiedtable
diff -r 255f48db74f8 -r 51025741f326 qiime2/qiime_diversity_core-metrics.xml
--- a/qiime2/qiime_diversity_core-metrics.xml	Wed Jul 17 03:26:16 2019 -0400
+++ b/qiime2/qiime_diversity_core-metrics.xml	Thu Jul 18 12:19:15 2019 -0400
@@ -15,6 +15,7 @@
  --p-n-jobs="$pnjobs"
 #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:]:
@@ -24,7 +25,7 @@
 #end def
 
 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
-
+#end if
 
 --o-rarefied-table=orarefiedtable
 --o-observed-otus-vector=oobservedotusvector
diff -r 255f48db74f8 -r 51025741f326 qiime2/qiime_emperor_biplot.xml
--- a/qiime2/qiime_emperor_biplot.xml	Wed Jul 17 03:26:16 2019 -0400
+++ b/qiime2/qiime_emperor_biplot.xml	Thu Jul 18 12:19:15 2019 -0400
@@ -18,8 +18,13 @@
 #return $file_list
 #end def
 
+#if $m_sample_metadatafile:
 --m-sample-metadata-file=$list_dict_to_string($m_sample_metadatafile)
+#end if
+
+if $m_feature_metadatafile:
 --m-feature-metadata-file=$list_dict_to_string($m_feature_metadatafile)
+#end if
 
 
 #if $pignoremissingsamples:
diff -r 255f48db74f8 -r 51025741f326 qiime2/qiime_feature-table_heatmap.xml
--- a/qiime2/qiime_feature-table_heatmap.xml	Wed Jul 17 03:26:16 2019 -0400
+++ b/qiime2/qiime_feature-table_heatmap.xml	Thu Jul 18 12:19:15 2019 -0400
@@ -9,6 +9,7 @@
 
 --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')
diff -r 255f48db74f8 -r 51025741f326 qiime2/qiime_feature-table_merge-seqs.xml
--- a/qiime2/qiime_feature-table_merge-seqs.xml	Wed Jul 17 03:26:16 2019 -0400
+++ b/qiime2/qiime_feature-table_merge-seqs.xml	Thu Jul 18 12:19:15 2019 -0400
@@ -7,6 +7,8 @@
 	<command><![CDATA[
 qiime feature-table merge-seqs
 
+
+#if $input_files_idata:
 #def list_dict_to_string(list_dict):
 	#set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
 	#for d in list_dict[1:]:
@@ -15,6 +17,7 @@
 	#return $file_list
 #end def
 --i-data=$list_dict_to_string($input_files_idata)
+#end if
 
 
 --o-merged-data=omergeddata
diff -r 255f48db74f8 -r 51025741f326 qiime2/qiime_feature-table_merge-taxa.xml
--- a/qiime2/qiime_feature-table_merge-taxa.xml	Wed Jul 17 03:26:16 2019 -0400
+++ b/qiime2/qiime_feature-table_merge-taxa.xml	Thu Jul 18 12:19:15 2019 -0400
@@ -7,6 +7,8 @@
 	<command><![CDATA[
 qiime feature-table merge-taxa
 
+
+#if $input_files_idata:
 #def list_dict_to_string(list_dict):
 	#set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
 	#for d in list_dict[1:]:
@@ -15,6 +17,7 @@
 	#return $file_list
 #end def
  --i-data=$list_dict_to_string($input_files_idata)
+#end if
 
 
 --o-merged-data=omergeddata
diff -r 255f48db74f8 -r 51025741f326 qiime2/qiime_feature-table_merge.xml
--- a/qiime2/qiime_feature-table_merge.xml	Wed Jul 17 03:26:16 2019 -0400
+++ b/qiime2/qiime_feature-table_merge.xml	Thu Jul 18 12:19:15 2019 -0400
@@ -7,6 +7,7 @@
 	<command><![CDATA[
 qiime feature-table merge
 
+#if $input_files_itables:
 #def list_dict_to_string(list_dict):
 	#set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
 	#for d in list_dict[1:]:
@@ -15,6 +16,7 @@
 	#return $file_list
 #end def
  --i-tables=$list_dict_to_string($input_files_itables)
+#end if
 
 
 #if str($poverlapmethod) != 'None':
diff -r 255f48db74f8 -r 51025741f326 qiime2/qiime_feature-table_summarize.xml
--- a/qiime2/qiime_feature-table_summarize.xml	Wed Jul 17 03:26:16 2019 -0400
+++ b/qiime2/qiime_feature-table_summarize.xml	Thu Jul 18 12:19:15 2019 -0400
@@ -9,6 +9,8 @@
 
 --i-table=$itable
 
+
+#if $m_sample_metadatafile:
 #def list_dict_to_string(list_dict):
 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
 #for d in list_dict[1:]:
@@ -17,6 +19,8 @@
 #return $file_list
 #end def
 --m-sample-metadata-file=$list_dict_to_string($m_sample_metadatafile)
+#end if
+
 
 --o-visualization=ovisualization
 ;
diff -r 255f48db74f8 -r 51025741f326 qiime2/qiime_gneiss_gradient-clustering.xml
--- a/qiime2/qiime_gneiss_gradient-clustering.xml	Wed Jul 17 03:26:16 2019 -0400
+++ b/qiime2/qiime_gneiss_gradient-clustering.xml	Thu Jul 18 12:19:15 2019 -0400
@@ -11,6 +11,7 @@
 --m-gradient-column="$mgradientcolumn"
 
 
+#if $input_files_mgradientfile:
 #def list_dict_to_string(list_dict):
 	#set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
 	#for d in list_dict[1:]:
@@ -18,9 +19,8 @@
 	#end for
 	#return $file_list
 #end def
-
 --m-gradient-file=$list_dict_to_string($input_files_mgradientfile)
-
+#end if
 
 #if $pnoweighted:
  --p-no-weighted
diff -r 255f48db74f8 -r 51025741f326 qiime2/qiime_metadata_tabulate.xml
--- a/qiime2/qiime_metadata_tabulate.xml	Wed Jul 17 03:26:16 2019 -0400
+++ b/qiime2/qiime_metadata_tabulate.xml	Thu Jul 18 12:19:15 2019 -0400
@@ -8,6 +8,7 @@
 qiime metadata tabulate
 
 
+#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:]:
@@ -16,6 +17,7 @@
 #return $file_list
 #end def
 --m-input-file=$list_dict_to_string($input_files_minputfile)
+#end if
 
 
 #if $ppagesize:
diff -r 255f48db74f8 -r 51025741f326 qiime2/qiime_quality-control_evaluate-composition.xml
--- a/qiime2/qiime_quality-control_evaluate-composition.xml	Wed Jul 17 03:26:16 2019 -0400
+++ b/qiime2/qiime_quality-control_evaluate-composition.xml	Thu Jul 18 12:19:15 2019 -0400
@@ -10,6 +10,7 @@
 --i-expected-features=$iexpectedfeatures
 --i-observed-features=$iobservedfeatures
 
+
 #if $input_files_mmetadatafile:
 #def list_dict_to_string(list_dict):
 	#set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
diff -r 255f48db74f8 -r 51025741f326 qiime2/qiime_sample-classifier_classify-samples-ncv.xml
--- a/qiime2/qiime_sample-classifier_classify-samples-ncv.xml	Wed Jul 17 03:26:16 2019 -0400
+++ b/qiime2/qiime_sample-classifier_classify-samples-ncv.xml	Thu Jul 18 12:19:15 2019 -0400
@@ -10,6 +10,7 @@
 --i-table=$itable
 --m-metadata-column="$mmetadatacolumn"
 
+
 #if $input_files_mmetadatafile:
 #def list_dict_to_string(list_dict):
 	#set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
@@ -21,6 +22,7 @@
  --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
 #end if
 
+
 #if $pcv:
  --p-cv=$pcv
 #end if
diff -r 255f48db74f8 -r 51025741f326 qiime2/qiime_sample-classifier_maturity-index.xml
--- a/qiime2/qiime_sample-classifier_maturity-index.xml	Wed Jul 17 03:26:16 2019 -0400
+++ b/qiime2/qiime_sample-classifier_maturity-index.xml	Thu Jul 18 12:19:15 2019 -0400
@@ -8,6 +8,7 @@
 	<![CDATA[
 	qiime sample-classifier maturity-index --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:]:
@@ -16,7 +17,11 @@
 		#return $file_list
 	#end def
 
-	 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile) --p-group-by="$pgroupby" --p-column="$pcolumn" --p-control="$pcontrol"
+	 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
+	#end fi
+
+
+	--p-group-by="$pgroupby" --p-column="$pcolumn" --p-control="$pcontrol"
 
 	#set $pnjobs = '${GALAXY_SLOTS:-4}'