--- a/pick_open_reference_otus.xml	Mon Jul 10 16:43:22 2017 -0400
+++ b/pick_open_reference_otus.xml	Sat Aug 05 07:24:40 2017 -0400
@@ -1,64 +1,63 @@
 <tool id="qiime_pick_open_reference_otus" name="Perform open-reference OTU picking" version="@WRAPPER_VERSION@.0">
-    <description></description>
+    <description>(pick_open_reference_otus)</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements"/>
     <version_command>pick_open_reference_otus.py --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
-        pick_open_reference_otus.py
-            --input_fps '$input_fps'
-            -o otus
-            --otu_picking_method '$otu_picking_method'
-            #if str( $ref_sequences.selector ) == 'history'
-                #set $ref = $ref_sequences.reference_fp
-            #else:
-                #set $ref = $ref_sequences.reference_fp.fields.path
-            #end if
-            --reference_fp '$ref'
-            #if str( $prefilter.use_prefilter ) == 'yes'
-                #if str( $prefilter.prefilter_ref_seq.selector ) == 'history'
-                    #set $ref = $prefilter.prefilter_ref_seq.prefilter_refseqs_fp
-                #else:
-                    #set $ref = $prefilter.prefilter_ref_seq.prefilter_refseqs_fp.fields.path
-                #end if
-                --prefilter_refseqs_fp '$ref'
-            #end if
-            --new_ref_set_id '$new_ref_set_id'
-            $parallel
-            -O "\${GALAXY_SLOTS:-4}"
-            --percent_subsample '$percent_subsample'
-            --prefilter_percent_id '$prefilter_percent_id'
-            #if str($step1_otu_map_fp) != 'None':
-                --step1_otu_map_fp '$step1_otu_map_fp'
-            #end if
-            #if str($step1_failures_fasta_fp) != 'None':
-                --step1_failures_fasta_fp='$step1_failures_fasta_fp'
-            #end if
-            --minimum_failure_threshold '$minimum_failure_threshold'
-            $suppress_step4
-            --min_otu_size '$min_otu_size'
-            $suppress_taxonomy_assignment
-            $suppress_align_and_tree
+pick_open_reference_otus.py
+    --input_fps '$input_fps'
+    -o otus
+    --otu_picking_method '$otu_picking_method'
+    #if str( $ref_sequences.selector ) == 'history'
+        #set $ref = $ref_sequences.reference_fp
+    #else:
+        #set $ref = $ref_sequences.reference_fp.fields.path
+    #end if
+    --reference_fp '$ref'
+    #if str( $prefilter.use_prefilter ) == 'yes'
+        #if str( $prefilter.prefilter_ref_seq.selector ) == 'history'
+            #set $ref = $prefilter.prefilter_ref_seq.prefilter_refseqs_fp
+        #else:
+            #set $ref = $prefilter.prefilter_ref_seq.prefilter_refseqs_fp.fields.path
+        #end if
+        --prefilter_refseqs_fp '$ref'
+    #end if
+    --new_ref_set_id '$new_ref_set_id'
+    $parallel
+    -O "\${GALAXY_SLOTS:-4}"
+    --percent_subsample '$percent_subsample'
+    --prefilter_percent_id '$prefilter_percent_id'
+    #if str($step1_otu_map_fp) != 'None':
+        --step1_otu_map_fp '$step1_otu_map_fp'
+    #end if
+    #if str($step1_failures_fasta_fp) != 'None':
+        --step1_failures_fasta_fp='$step1_failures_fasta_fp'
+    #end if
+    --minimum_failure_threshold '$minimum_failure_threshold'
+    $suppress_step4
+    --min_otu_size '$min_otu_size'
+    $suppress_taxonomy_assignment
+    $suppress_align_and_tree
 
-        #if str( $suppress_align_and_tree ) == ""
-            #if str( $suppress_taxonomy_assignment ) == ""
-                && mv otus/otu_table_mc*_w_tax.biom otus/otu_table_w_tax.biom
-                && mv otus/otu_table_mc*_w_tax_no_pynast_failures.biom otus/tu_table_w_tax_no_pynast_failures
-            #else
-                && mv otus/otu_table_mc*_no_pynast_failures.biom otus/otu_table_no_pynast_failures.biom
-            #end if
-        #end if
-
+#if str( $suppress_align_and_tree ) == ""
+    #if str( $suppress_taxonomy_assignment ) == ""
+        && mv otus/otu_table_mc*_w_tax.biom otus/otu_table_w_tax.biom
+        && mv otus/otu_table_mc*_w_tax_no_pynast_failures.biom otus/tu_table_w_tax_no_pynast_failures
+    #else
+        && mv otus/otu_table_mc*_no_pynast_failures.biom otus/otu_table_no_pynast_failures.biom
+    #end if
+#end if
     ]]></command>
     <inputs>
-        <param argument="--input_fps" type="data" format="fasta,fastq" multiple="True" label="Input sequence files"/>
+        <param argument="--input_fps" type="data" format="fasta,fastq" multiple="true" label="Input sequence files"/>
         <param argument="--otu_picking_method" type="select" label="The OTU picking method to use for reference and de novo steps">
-            <option value="uclust" selected="True">uclust</option>
+            <option value="uclust" selected="true">uclust</option>
         </param>
         <conditional name="ref_sequences">
-            <param name="selector" type="select"  label="Reference sequences to query">
-                <option value="cached" selected="True">Public databases</option>
+            <param name="selector" type="select" label="Reference sequences to query">
+                <option value="cached" selected="true">Public databases</option>
                 <option value="history">Databases from your history</option>
             </param>
             <when value="cached">
@@ -73,12 +72,12 @@
         <conditional name="prefilter">
             <param name="use_prefilter" type="select" label="Use different reference sequences for the prefilter?">
                 <option value="true">True</option>
-                <option value="false" selected="True">False</option>
+                <option value="false" selected="true">False</option>
             </param>
             <when value="true">
                 <conditional name="prefilter_ref_seq">
                     <param name="selector" type="select" label="Reference sequences to query">
-                        <option value="cached" selected="True">Public databases</option>
+                        <option value="cached" selected="true">Public databases</option>
                         <option value="history">Databases from your history</option>
                     </param>
                     <when value="cached">
@@ -94,16 +93,16 @@
             <when value="false"/>
         </conditional>
         <param argument="--new_ref_set_id" type="text" value="New" label="Unique identifier for OTUs that get created in this ref set" help="This is useful to support combining of reference sets"/>
-        <param argument="--parallel" type="boolean" truevalue="--parallel" falsevalue="" checked="False" label="Run in parallel where available?"/>
+        <param argument="--parallel" type="boolean" truevalue="--parallel" falsevalue="" checked="false" label="Run in parallel where available?"/>
         <param argument="--percent_subsample" type="float" value="0.001" min="0" max="1" label="Percent of failure sequences to include in the subsample to cluster de novo" help="Large numbers should give more comprehensive results but will be slower"/>
         <param argument="--prefilter_percent_id" type="float" value="0.0" min="0" max="1" label="Percent of sequence pre-cluster against the reference" help="Any reads which fail to hit are discarded (a quality filter)"/>
-        <param argument="--step1_otu_map_fp" type="data" format="txt" optional="True" label="Reference OTU picking OTU map to avoid rebuilding if one has already been built (optional)" help="This must be an OTU map generated by this workflow, not (for example) by pick_closed_reference_otus"/>
-        <param argument="--step1_failures_fasta_fp" type="data" format="fasta" optional="True" label="Reference OTU picking failures fasta filepath, to avoid rebuilding if one has already been built (optional)" help="This must be a failures file generated by this workflow, not (for example) by pick_closed_reference_otus"/>
+        <param argument="--step1_otu_map_fp" type="data" format="txt" optional="true" label="Reference OTU picking OTU map to avoid rebuilding if one has already been built (optional)" help="This must be an OTU map generated by this workflow, not (for example) by pick_closed_reference_otus"/>
+        <param argument="--step1_failures_fasta_fp" type="data" format="fasta" optional="true" label="Reference OTU picking failures fasta filepath, to avoid rebuilding if one has already been built (optional)" help="This must be a failures file generated by this workflow, not (for example) by pick_closed_reference_otus"/>
         <param argument="--minimum_failure_threshold" type="integer" value="100000" label="Minimum number of sequences that must fail to hit the reference for subsampling to be performed" help="If fewer than this number of sequences fail to hit the reference, the de novo clustering step will run serially rather than invoking the subsampled open reference approach to improve performance"/>
-        <param argument="--suppress_step4" type="boolean" truevalue="--suppress_step4" falsevalue="" checked="False" label="Suppress the final de novo OTU picking step?" help="It may be necessary for extremely large data sets"/>
-        <param argument="--min_otu_size" type="integer" value="2" label="Minimum otu size to retain the OTU" help=""/>
-        <param argument="--suppress_taxonomy_assignment" type="boolean" truevalue="--suppress_taxonomy_assignment" falsevalue="" checked="False" label="Skip the taxonomy assignment step?" help="It results in an OTU table without taxonomy"/>
-        <param argument="--suppress_align_and_tree" type="boolean" truevalue="--suppress_align_and_tree" falsevalue="" checked="False" label="Skip the sequence alignment and tree-building steps?" help=""/>
+        <param argument="--suppress_step4" type="boolean" truevalue="--suppress_step4" falsevalue="" checked="false" label="Suppress the final de novo OTU picking step?" help="It may be necessary for extremely large data sets"/>
+        <param argument="--min_otu_size" type="integer" value="2" label="Minimum otu size to retain the OTU"/>
+        <param argument="--suppress_taxonomy_assignment" type="boolean" truevalue="--suppress_taxonomy_assignment" falsevalue="" checked="false" label="Skip the taxonomy assignment step?" help="It results in an OTU table without taxonomy"/>
+        <param argument="--suppress_align_and_tree" type="boolean" truevalue="--suppress_align_and_tree" falsevalue="" checked="false" label="Skip the sequence alignment and tree-building steps?"/>
     </inputs>
     <outputs>
         <data name="final_otu_map" format="txt" from_work_dir="otus/final_otu_map.txt" label="${tool.name} on ${on_string}: Final OTU map"/>