# HG changeset patch
# User iuc
# Date 1568219824 14400
# Node ID efa724a29c408bef2e893b9acdc6faa6a18d9a69
# Parent  489850042c43a58a11059d3b3e7ea20a88a5eb4f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"

diff -r 489850042c43 -r efa724a29c40 biom_convert.xml
--- a/biom_convert.xml	Wed May 31 11:18:47 2017 -0400
+++ b/biom_convert.xml	Wed Sep 11 12:37:04 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="biom_convert" name="Convert" version="@VERSION@.1">
+<tool id="biom_convert" name="Convert" version="@VERSION@.2">
     <description>between BIOM table formats</description>
     <macros>
         <import>macros.xml</import>
@@ -7,8 +7,15 @@
     <expand macro="version_command" />
     <command detect_errors="exit_code">
         <![CDATA[
+            ## biom convert requires the header to start with a #
+            ## so we just add one if its missing
+            #if $input.type_selector == "tsv"
+                sed '1s/^\([^#].*\)/#\1/' '$input.input_fp' > input &&
+            #else
+                ln -s '$input.input_fp' input &&
+            #end if
             biom convert 
-                --input-fp '$input.input_fp'
+                --input-fp input
                 --output-fp '$output_fp'
                 #if str( $input.type_selector ) == "tsv"
                     #if $input.process_obs_metadata:
diff -r 489850042c43 -r efa724a29c40 test-data/input_abundance_1.tabular
--- a/test-data/input_abundance_1.tabular	Wed May 31 11:18:47 2017 -0400
+++ b/test-data/input_abundance_1.tabular	Wed Sep 11 12:37:04 2019 -0400
@@ -1,4 +1,4 @@
-#ID	SAMPLE_1	SAMPLE_2
+ID	SAMPLE_1	SAMPLE_2
 2	0	0
 3	160	242
 4	0	0