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changeset 2:efa724a29c40 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
author iuc
date Wed, 11 Sep 2019 12:37:04 -0400
parents 489850042c43
children c7894042022c
files biom_convert.xml test-data/input_abundance_1.tabular
diffstat 2 files changed, 10 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- 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:
--- 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