Mercurial > repos > iuc > biom_convert
comparison biom_convert.xml @ 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 |
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| 1:0de92f0b96ef | 2:584008e574b2 |
|---|---|
| 1 <tool id="biom_convert" name="Convert" version="@VERSION@.2"> | 1 <tool id="biom_convert" name="Convert" version="@VERSION@.3"> |
| 2 <description>between BIOM table formats</description> | 2 <description>between BIOM table formats</description> |
| 3 <macros> | 3 <macros> |
| 4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
| 5 </macros> | 5 </macros> |
| 6 <expand macro="requirements" /> | 6 <expand macro="requirements" /> |
| 22 --process-obs-metadata '$input.process_obs_metadata' | 22 --process-obs-metadata '$input.process_obs_metadata' |
| 23 #end if | 23 #end if |
| 24 #end if | 24 #end if |
| 25 #if str( $output.type_selector ) == "tsv" | 25 #if str( $output.type_selector ) == "tsv" |
| 26 --to-tsv | 26 --to-tsv |
| 27 #if $output_type.header_key | 27 #if $output.header_key |
| 28 --header-key '$output.header_key' | 28 --header-key '$output.header_key' |
| 29 #if $output_type.output_metadata_id | 29 #if $output.output_metadata_id |
| 30 --output-metadata-id '$output.output_metadata_id' | 30 --output-metadata-id '$output.output_metadata_id' |
| 31 #end if | 31 #end if |
| 32 --tsv-metadata-formatter '$output.tsv_metadata_formatter' | 32 --tsv-metadata-formatter '$output.tsv_metadata_formatter' |
| 33 #end if | 33 #end if |
| 34 #else: | 34 #else: |
| 150 <param name="sample_metadata_fp"/> | 150 <param name="sample_metadata_fp"/> |
| 151 <param name="observation_metadata_fp"/> | 151 <param name="observation_metadata_fp"/> |
| 152 </conditional> | 152 </conditional> |
| 153 <output name="output_fp" file="output_1.biom1.re" ftype="biom1" compare="re_match"/> | 153 <output name="output_fp" file="output_1.biom1.re" ftype="biom1" compare="re_match"/> |
| 154 </test> | 154 </test> |
| 155 <test> | |
| 156 <conditional name="input"> | |
| 157 <param name="type_selector" value="biom"/> | |
| 158 <param name="input_fp" value="input_abundance_1.biom1" ftype="biom1"/> | |
| 159 </conditional> | |
| 160 <conditional name="output"> | |
| 161 <param name="type_selector" value="tsv"/> | |
| 162 <param name="header_key"/> | |
| 163 <param name="output_metadata_id"/> | |
| 164 <param name="tsv_metadata_formatter" value="naive"/> | |
| 165 </conditional> | |
| 166 <output name="output_fp" file="output_abundance_1.tabular" ftype="tabular" /> | |
| 167 </test> | |
| 155 </tests> | 168 </tests> |
| 156 <help><![CDATA[ | 169 <help><![CDATA[ |
| 157 | 170 |
| 158 Usage: biom convert [OPTIONS]:: | 171 Usage: biom convert [OPTIONS]:: |
| 159 | 172 |