Mercurial > repos > jjohnson > contig_annotation_tool
comparison cat_add_names.xml @ 0:ad7507073c3f draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
| author | jjohnson |
|---|---|
| date | Sun, 24 Nov 2019 21:56:00 -0500 |
| parents | |
| children | 226949352e31 |
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| -1:000000000000 | 0:ad7507073c3f |
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| 1 <tool id="cat_add_names" name="CAT add_names" version="@VERSION@.0"> | |
| 2 <description>annotate with taxonomic classification</description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements" /> | |
| 7 <expand macro="version_command" /> | |
| 8 <command detect_errors="exit_code"><![CDATA[ | |
| 9 CAT add_names -i '$input' | |
| 10 @CAT_TAXONOMY@ | |
| 11 @ADD_NAMES_OPTIONS@ | |
| 12 -o output_names.txt | |
| 13 && @TXT2TSV@ -i output_names.txt -o $output | |
| 14 ]]></command> | |
| 15 <inputs> | |
| 16 <param name="input" type="data" format="tabular,txt" label="classification.txt or ORF2LCA.txt"/> | |
| 17 <expand macro="cat_db" /> | |
| 18 <expand macro="add_names_options" /> | |
| 19 </inputs> | |
| 20 <outputs> | |
| 21 <data name="output" format="tabular"/> | |
| 22 </outputs> | |
| 23 <tests> | |
| 24 <test> | |
| 25 <param name="input" ftype="tabular" value="test_contig.contig2classification.txt"/> | |
| 26 <expand macro="test_catdb"/> | |
| 27 <output name="output"> | |
| 28 <assert_contents> | |
| 29 <has_text text="Firmicutes" /> | |
| 30 </assert_contents> | |
| 31 </output> | |
| 32 </test> | |
| 33 </tests> | |
| 34 <help><![CDATA[ | |
| 35 **CAT/BAT add_names** | |
| 36 Add names for the NCBI taxomy IDs. | |
| 37 | |
| 38 @COMMON_HELP@ | |
| 39 ]]></help> | |
| 40 <expand macro="citations" /> | |
| 41 </tool> |