diff qiime2/qiime_diversity_core-metrics.xml @ 4:71f124e02000 draft default tip

Fixes
author florianbegusch
date Tue, 13 Aug 2019 07:40:25 -0400
parents 149432539226
children
line wrap: on
line diff
--- a/qiime2/qiime_diversity_core-metrics.xml	Wed Jul 17 01:53:11 2019 -0400
+++ b/qiime2/qiime_diversity_core-metrics.xml	Tue Aug 13 07:40:25 2019 -0400
@@ -8,23 +8,26 @@
 qiime diversity core-metrics
 
 --i-table=$itable
---p-sampling-depth="$psamplingdepth"
+
+#if str($psamplingdepth):
+ --p-sampling-depth="$psamplingdepth"
+#end if
 
 #set $pnjobs = '${GALAXY_SLOTS:-4}'
 #if str($pnjobs):
  --p-n-jobs="$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:]:
-	#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
 
 --o-rarefied-table=orarefiedtable
 --o-observed-otus-vector=oobservedotusvector
@@ -56,7 +59,7 @@
 		<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>