--- a/biom_add_metadata.xml	Tue Jun 07 17:25:44 2016 -0400
+++ b/biom_add_metadata.xml	Wed Sep 11 12:41:29 2019 -0400
@@ -1,75 +1,68 @@
-<tool id="biom_add_metadata" name="BIOM metadata" version="@VERSION@.0">
-    <description>add-metadata</description>
+<tool id="biom_add_metadata" name="Add metadata" version="@VERSION@.1">
+    <description>to a BIOM table</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
-    <expand macro="stdio" />
     <expand macro="version_command" />
-    <command>
+    <command detect_errors="exit_code">
         <![CDATA[
             biom add-metadata 
-                -i "${input_table}"
-                -o "${output_table}"
-                #if $input_sample_metadata:
-                    --sample-metadata-fp "${input_sample_metadata}"
+                --input-fp '$input_fp'
+                --output-fp '$output_fp'
+                #if $sample_metadata_fp
+                    --sample-metadata-fp '$sample_metadata_fp'
                 #end if
-                #if $input_observation_metadata:
-                    --observation-metadata-fp "${input_observation_metadata}"
+                #if $observation_metadata_fp
+                    --observation-metadata-fp '$observation_metadata_fp'
                 #end if
-                #if $sc_separated:
-                    --sc-separated "${sc_separated}"
+                #if $sc_separated
+                    --sc-separated '$sc_separated'
                 #end if
-                #if $sc_pipe_separated:
-                    --sc-pipe-separated "${sc_pipe_separated}"
+                #if $sc_pipe_separated
+                    --sc-pipe-separated '$sc_pipe_separated'
                 #end if
-                #if $int_fields:
-                    --int-fields "${int_fields}"
+                #if $int_fields
+                    --int-fields '$int_fields'
                 #end if
-                #if $float_fields:
-                    --float-fields "${float_fields}"
+                #if $float_fields
+                    --float-fields '$float_fields'
                 #end if
-                #if $sample_header:
-                    --sample-header "${sample_header}"
+                #if $sample_header
+                    --sample-header '$sample_header'
                 #end if
-                #if $observation_header:
-                    --observation-header "${observation_header}"
+                #if $observation_header
+                    --observation-header '$observation_header'
                 #end if
-                ${output_as_json}                
+                $output_as_json             
         ]]>
     </command>
     <inputs>
-        <param name="input_table" type="data" format="biom1" label="BIOM File" argument="--input-fp"/>
-        <param name="input_sample_metadata" type="data" format="tabular" optional="True" label="Sample Metadata Tabular File" argument="--sample-metadata-fp PATH"/>
-        <param name="input_observation_metadata" type="data" format="tabular" optional="True" label="Observation Metadata Tabular File" argument="--observation-metadata-fp"/>
-        <param name="sc_separated" type="text" value="" label="Comma-separated list of the metadata fields to split on semicolons" argument="--sc-separated"/>
-        <param name="sc_pipe_separated" type="text" value="" label="Comma-separated list of the metadata fields to split on semicolons and pipes (|)" argument="--sc-pipe-separated"/>
-        <param name="int_fields" type="text" value="" label="Comma-separated list of the metadata fields to cast to integers" argument="--int-fields"/>
-        <param name="float_fields" type="text" value="" label="Comma-separated list of the metadata fields to cast to floating point numbers" argument="--float-fields"/>
-        <param name="sample_header" type="text" value="" label="Comma-separated list of the sample metadata field names" argument="--sample-header"/>
-        <param name="observation_header" type="text" value="" label="Comma-separated list of the observation metadata field names" argument="--observation-header"/>
-        <param name="output_as_json" type="boolean" checked="True" truevalue="--output-as-json" falsevalue="" label="Write the output file in JSON format (biom1)" argument="--output-as-json"/>
+        <param name="input_fp" argument="--input-fp" type="data" format="biom1" label="BIOM File"/>
+        <param name="sample_metadata_fp" argument="--sample-metadata-fp" type="data" format="tabular" optional="True" label="Sample Metadata Tabular File" />
+        <param name="observation_metadata_fp" argument="--observation-metadata-fp" type="data" format="tabular" optional="True" label="Observation Metadata Tabular File"/>
+        <param name="sc_separated" argument="--sc-separated" type="text" value="" label="Comma-separated list of the metadata fields to split on semicolons" />
+        <param name="sc_pipe_separated" argument="--sc-pipe-separated" type="text" value="" label="Comma-separated list of the metadata fields to split on semicolons and pipes (|)"/>
+        <param name="int_fields" argument="--int-fields" type="text" value="" label="Comma-separated list of the metadata fields to cast to integers" />
+        <param name="float_fields" argument="--float-fields" type="text" value="" label="Comma-separated list of the metadata fields to cast to floating point numbers" />
+        <param name="sample_header" argument="--sample-header" type="text" value="" label="Comma-separated list of the sample metadata field names" />
+        <param name="observation_header" argument="--observation-header" type="text" value="" label="Comma-separated list of the observation metadata field names" />
+        <param name="output_as_json" argument="--output-as-json" type="boolean" checked="True" truevalue="--output-as-json" falsevalue="" label="Write the output file in JSON format (biom1)" />
     </inputs>
     <outputs>
-        <data format="biom1" name="output_table">
+        <data format="biom1" name="output_fp">
             <change_format>
-                <when input="${str( $output_as_json )}" value="" format="biom2" />
+                <when input="${str( $output_as_json )}" value="" format="h5" />
             </change_format>
         </data>
     </outputs>
     <tests>
         <test>
-            <param name="input_table" value="input_abundance_1.biom1" ftype="biom1"/>
-            <param name="input_observation_metadata" value="input_taxonomy_1.tabular" ftype="tabular"/>
+            <param name="input_fp" value="input_abundance_1.biom1" ftype="biom1"/>
+            <param name="observation_metadata_fp" value="input_taxonomy_1.tabular" ftype="tabular"/>
             <param name="sc_separated" value="taxonomy"/>
-            <param name="input_sample_metadata"/>
-            <param name="sc_pipe_separated" value=""/>
-            <param name="int_fields" value=""/>
-            <param name="float_fields" value=""/>
-            <param name="sample_header" value=""/>
-            <param name="observation_header" value=""/>
-            <param name="output_as_json" value="True"/>
-            <output name="output_table" file="output_taxonomy_1.biom1.re" ftype="biom1" compare="re_match"/>
+            <param name="output_as_json" value="--output-as-json"/>
+            <output name="output_fp" file="output_taxonomy_1.biom1.re" ftype="biom1" compare="re_match"/>
         </test>
     </tests>
     <help><![CDATA[
@@ -127,8 +120,6 @@
                                   provided here.
   --output-as-json                Write the output file in JSON format.
   --help                          Show this message and exit.
-
-
     ]]></help>
     <expand macro="citations" />
 </tool>