Mercurial > repos > iuc > biom_convert
changeset 2:584008e574b2 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f1b3e36f79747fca391321389276ac196d3f7cd0"
| author | iuc |
|---|---|
| date | Fri, 24 Jan 2020 16:40:37 -0500 |
| parents | 0de92f0b96ef |
| children | bd46669113b9 |
| files | biom_convert.xml test-data/output_abundance_1.tabular |
| diffstat | 2 files changed, 37 insertions(+), 3 deletions(-) [+] |
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--- a/biom_convert.xml Wed Sep 11 12:40:19 2019 -0400 +++ b/biom_convert.xml Fri Jan 24 16:40:37 2020 -0500 @@ -1,4 +1,4 @@ -<tool id="biom_convert" name="Convert" version="@VERSION@.2"> +<tool id="biom_convert" name="Convert" version="@VERSION@.3"> <description>between BIOM table formats</description> <macros> <import>macros.xml</import> @@ -24,9 +24,9 @@ #end if #if str( $output.type_selector ) == "tsv" --to-tsv - #if $output_type.header_key + #if $output.header_key --header-key '$output.header_key' - #if $output_type.output_metadata_id + #if $output.output_metadata_id --output-metadata-id '$output.output_metadata_id' #end if --tsv-metadata-formatter '$output.tsv_metadata_formatter' @@ -152,6 +152,19 @@ </conditional> <output name="output_fp" file="output_1.biom1.re" ftype="biom1" compare="re_match"/> </test> + <test> + <conditional name="input"> + <param name="type_selector" value="biom"/> + <param name="input_fp" value="input_abundance_1.biom1" ftype="biom1"/> + </conditional> + <conditional name="output"> + <param name="type_selector" value="tsv"/> + <param name="header_key"/> + <param name="output_metadata_id"/> + <param name="tsv_metadata_formatter" value="naive"/> + </conditional> + <output name="output_fp" file="output_abundance_1.tabular" ftype="tabular" /> + </test> </tests> <help><![CDATA[
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_abundance_1.tabular Fri Jan 24 16:40:37 2020 -0500 @@ -0,0 +1,21 @@ +# Constructed from biom file +#OTU ID SAMPLE_1 SAMPLE_2 +2 0.0 0.0 +3 160.0 242.0 +4 0.0 0.0 +5 0.0 0.0 +8 0.0 0.0 +9 0.0 0.0 +10 1.0 1.0 +11 3.0 4.0 +12 0.0 0.0 +14 0.0 0.0 +15 0.0 0.0 +16 0.0 0.0 +17 13.0 36.0 +18 0.0 0.0 +22 1.0 5.0 +23 1.0 0.0 +25 1.0 3.0 +28 0.0 0.0 +29 0.0 0.0 \ No newline at end of file