--- a/pick_otus.xml	Mon Jul 10 16:41:50 2017 -0400
+++ b/pick_otus.xml	Sat Aug 05 07:34:24 2017 -0400
@@ -1,5 +1,5 @@
-<tool id="qiime_pick_otus" name="Pick OTUs" version="@WRAPPER_VERSION@.0">
-    <description></description>
+<tool id="qiime_pick_otus" name="Perform OTU picking" version="@WRAPPER_VERSION@.0">
+    <description> (pick_otus)</description>
     <macros>
         <import>macros.xml</import>
     </macros>
@@ -11,95 +11,95 @@
     </expand>
     <version_command>pick_otus.py --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
-        pick_otus.py
-            --input_seqs_filepath '$input_seqs_filepath'
-            --output_dir pick_otus
-            --otu_picking_method '$method.otu_picking_method'
+pick_otus.py
+    --input_seqs_filepath '$input_seqs_filepath'
+    --output_dir pick_otus
+    --otu_picking_method '$method.otu_picking_method'
 
-            #if $method.otu_picking_method == "sortmerna"
-                #if $method.references.source_selector == 'history'
-                    --refseqs_fp '$method.references.refseqs_fp'
-                #else if $method.references.source_selector == 'cached'
-                    --refseqs_fp '$method.references.refseqs_fp.fields.path'
-                #end if
-                --sortmerna_e_value '$method.sortmerna_e_value'
-                --sortmerna_coverage '$method.sortmerna_coverage'
-                #if $method.sortmerna_tabular.test == 'yes'
-                    --sortmerna_tabular
-                    --sortmerna_best_N_alignments '$method.sortmerna_tabular.sortmerna_best_N_alignments'
-                #end if
-                --sortmerna_max_pos '$method.sortmerna_max_pos'
-                --similarity '$method.similarity'
-                $method.suppress_prefilter_exact_match
-                --threads \${GALAXY_SLOTS:-2}
-            #else if $method.otu_picking_method == "mothur"
-                --clustering_algorithm '$method.clustering_algorithm'
-            #else if $method.otu_picking_method == "trie"
-                $method.trie_reverse_seqs
-            #else if $method.otu_picking_method == "uclust_ref"
-                #if $method.references.source_selector == 'history'
-                    --refseqs_fp '$method.references.refseqs_fp'
-                #else if $method.references.source_selector == 'cached'
-                    --refseqs_fp '$method.references.refseqs_fp.fields.path'
-                #end if
-                --similarity '$method.similarity'
-                $method.enable_rev_strand_match
-                $method.suppress_presort_by_abundance_uclust
-                $method.suppress_new_clusters
-                --max_accepts '$method.max_accepts'
-                --max_rejects '$method.max_rejects'
-                --stepwords '$method.stepwords'
-                --word_length '$method.word_length'
-            #else if $method.otu_picking_method == "blast"
-                #if $method.references.source_selector == 'history'
-                    --refseqs_fp '$method.references.refseqs_fp'
-                #else if $method.references.source_selector == 'cached'
-                    --refseqs_fp '$method.references.refseqs_fp.fields.path'
-                #end if
-                --max_e_value_blast '$method.max_e_value_blast'
-                --min_aligned_percent '$method.min_aligned_percent'
-                --similarity '$method.similarity'
-            #else if $method.otu_picking_method == "sumaclust"
-                --similarity '$method.similarity'
-                '$method.sumaclust_exact'
-                --denovo_otu_id_prefix '$method.denovo_otu_id_prefix'
-                $method.suppress_prefilter_exact_match
-                --threads \${GALAXY_SLOTS:-2}
-            #else if $method.otu_picking_method == "swarm"
-                --denovo_otu_id_prefix '$method.denovo_otu_id_prefix'
-                --swarm_resolution '$method.swarm_resolution'
-                --threads \${GALAXY_SLOTS:-2}
-            #else if $method.otu_picking_method == "prefix_suffix"
-                --prefix_length '$method.prefix_length'
-                --suffix_length '$method.suffix_length'
-            #else if $method.otu_picking_method == "cdhit"
-                --similarity '$method.similarity'
-            #else if $method.otu_picking_method == "uclust"
-                --similarity '$method.similarity'
-                --denovo_otu_id_prefix '$method.denovo_otu_id_prefix'
-                $method.enable_rev_strand_match
-                $method.suppress_presort_by_abundance_uclust
-                $method.optimal_uclust
-                $method.exact_uclust
-                $method.user_sort
-                --max_accepts '$method.max_accepts'
-                --max_rejects '$method.max_rejects'
-                --stepwords '$method.stepwords'
-                --word_length '$method.word_length'
-                $method.suppress_uclust_stable_sort
-                $method.suppress_prefilter_exact_match
-            #end if
+    #if $method.otu_picking_method == "sortmerna"
+        #if $method.references.source_selector == 'history'
+            --refseqs_fp '$method.references.refseqs_fp'
+        #else if $method.references.source_selector == 'cached'
+            --refseqs_fp '$method.references.refseqs_fp.fields.path'
+        #end if
+        --sortmerna_e_value '$method.sortmerna_e_value'
+        --sortmerna_coverage '$method.sortmerna_coverage'
+        #if $method.sortmerna_tabular.test == 'yes'
+            --sortmerna_tabular
+            --sortmerna_best_N_alignments '$method.sortmerna_tabular.sortmerna_best_N_alignments'
+        #end if
+        --sortmerna_max_pos '$method.sortmerna_max_pos'
+        --similarity '$method.similarity'
+        $method.suppress_prefilter_exact_match
+        --threads \${GALAXY_SLOTS:-2}
+    #else if $method.otu_picking_method == "mothur"
+        --clustering_algorithm '$method.clustering_algorithm'
+    #else if $method.otu_picking_method == "trie"
+        $method.trie_reverse_seqs
+    #else if $method.otu_picking_method == "uclust_ref"
+        #if $method.references.source_selector == 'history'
+            --refseqs_fp '$method.references.refseqs_fp'
+        #else if $method.references.source_selector == 'cached'
+            --refseqs_fp '$method.references.refseqs_fp.fields.path'
+        #end if
+        --similarity '$method.similarity'
+        $method.enable_rev_strand_match
+        $method.suppress_presort_by_abundance_uclust
+        $method.suppress_new_clusters
+        --max_accepts '$method.max_accepts'
+        --max_rejects '$method.max_rejects'
+        --stepwords '$method.stepwords'
+        --word_length '$method.word_length'
+    #else if $method.otu_picking_method == "blast"
+        #if $method.references.source_selector == 'history'
+            --refseqs_fp '$method.references.refseqs_fp'
+        #else if $method.references.source_selector == 'cached'
+            --refseqs_fp '$method.references.refseqs_fp.fields.path'
+        #end if
+        --max_e_value_blast '$method.max_e_value_blast'
+        --min_aligned_percent '$method.min_aligned_percent'
+        --similarity '$method.similarity'
+    #else if $method.otu_picking_method == "sumaclust"
+        --similarity '$method.similarity'
+        '$method.sumaclust_exact'
+        --denovo_otu_id_prefix '$method.denovo_otu_id_prefix'
+        $method.suppress_prefilter_exact_match
+        --threads \${GALAXY_SLOTS:-2}
+    #else if $method.otu_picking_method == "swarm"
+        --denovo_otu_id_prefix '$method.denovo_otu_id_prefix'
+        --swarm_resolution '$method.swarm_resolution'
+        --threads \${GALAXY_SLOTS:-2}
+    #else if $method.otu_picking_method == "prefix_suffix"
+        --prefix_length '$method.prefix_length'
+        --suffix_length '$method.suffix_length'
+    #else if $method.otu_picking_method == "cdhit"
+        --similarity '$method.similarity'
+    #else if $method.otu_picking_method == "uclust"
+        --similarity '$method.similarity'
+        --denovo_otu_id_prefix '$method.denovo_otu_id_prefix'
+        $method.enable_rev_strand_match
+        $method.suppress_presort_by_abundance_uclust
+        $method.optimal_uclust
+        $method.exact_uclust
+        $method.user_sort
+        --max_accepts '$method.max_accepts'
+        --max_rejects '$method.max_rejects'
+        --stepwords '$method.stepwords'
+        --word_length '$method.word_length'
+        $method.suppress_uclust_stable_sort
+        $method.suppress_prefilter_exact_match
+    #end if
 
-            #if str($prefix_prefilter_length) != ''
-                --prefix_prefilter_length '$prefix_prefilter_length'
-            #end if
-            $trie_prefilter
-            --non_chimeras_retention '$non_chimeras_retention'
+    #if str($prefix_prefilter_length) != ''
+        --prefix_prefilter_length '$prefix_prefilter_length'
+    #end if
+    $trie_prefilter
+    --non_chimeras_retention '$non_chimeras_retention'
 
-        #if $method.otu_picking_method == "sortmerna"
-            &&
-            rm pick_otus/sortmerna_otus.log
-        #end if
+#if $method.otu_picking_method == "sortmerna"
+    &&
+    rm pick_otus/sortmerna_otus.log
+#end if
     ]]></command>
     <inputs>
         <param argument="--input_seqs_filepath" type="data" format="fasta" label="Input sequences file"/>
@@ -126,7 +126,7 @@
                         <option value="no" selected="true">No</option>
                     </param>
                     <when value="yes">
-                        <param argument="--sortmerna_best_N_alignments" type="integer" value="1" label="how many alignments per read will be written"/>
+                        <param argument="--sortmerna_best_N_alignments" type="integer" value="1" label="How many alignments per read will be written"/>
                     </when>
                     <when value="no"/>
                 </conditional>