diff dada2_assignTaxonomyAddspecies.xml @ 5:caa2bdb8a431 draft

planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38

--- a/dada2_assignTaxonomyAddspecies.xml	Mon Apr 29 09:53:04 2019 -0400
+++ b/dada2_assignTaxonomyAddspecies.xml	Sun May 05 12:39:41 2019 -0400
@@ -152,9 +152,9 @@
             <param name="addSpecies_cond|addSpecies_select" value="TRUE"/>
             <param name="addSpecies_cond|speciesreference_cond|speciesreference_select" value="history"/>
             <param name="addSpecies_cond|speciesreference_cond|speciesrefFasta" ftype="fasta" value="reference_species.fa" />
-            <param argument="addSpecies_cond|allowMultiple" value="TRUE"/>
-            <param argument="addSpecies_cond|tryRC" value="TRUE" />
-            <output name="output" value="assignTaxonomyAddspecies_F3D0.tab" ftype="tabular" />
+            <param name="addSpecies_cond|allowMultiple" value="TRUE"/>
+            <param name="addSpecies_cond|tryRC" value="TRUE" />
+            <output name="output" value="assignTaxonomyAddspecies_F3D0.tab" ftype="tabular" compare="sim_size" />
             <output name="bootstraps" value="assignTaxonomyAddspecies_F3D0_boot.tab" ftype="tabular" />
         </test>
 
@@ -175,11 +175,11 @@
 **Input**
 
 - A list of sequences contained in the results of removeBimeraDenovo or sequenceTable (note that also the results of derep, dada, and mergePairs are accepted).
-- Reference data bases for taxonomic and species/genus level assignment. Several chached data bases can be chosen (ask your Galaxy admin if they are missing). For using custom data bases see below.
+- Reference data bases for taxonomic and species/genus level assignment. Several cached data bases can be chosen (ask your Galaxy admin if they are missing). For using custom data bases see below.
 
 **Output**
 
-- A table containing the assigned taxonomies exceeding the minBoot level of bootstrapping confidence. Rows correspond to the provided sequences, columns to the taxonomic levels. NA indicates that the sequence was not consistently classified at that level at the minBoot threshhold.
+- A table containing the assigned taxonomies exceeding the minBoot level of bootstrapping confidence. Rows correspond to the provided sequences, columns to the taxonomic levels. NA indicates that the sequence was not consistently classified at that level at the minBoot threshold.
 - Optionally two columns for the genus and species taxonomic levels can be added. NA indicates that the sequence was not classified at that level.
 - If outputBootstraps checked, a table containing the assigned taxonomies (named "taxa") and the bootstrap values (named "boot") will be returned.