Mercurial > repos > jjohnson > contig_annotation_tool
comparison cat_bins.xml @ 3:18ece3d5bcde draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 3febcc9ba3d3717877c36bf96742209012a13ac4-dirty
| author | jjohnson |
|---|---|
| date | Tue, 26 Nov 2019 15:42:14 -0500 |
| parents | 9a01840eac52 |
| children | aaeb63501369 |
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| 2:9a01840eac52 | 3:18ece3d5bcde |
|---|---|
| 43 <outputs> | 43 <outputs> |
| 44 <expand macro="outputs" /> | 44 <expand macro="outputs" /> |
| 45 </outputs> | 45 </outputs> |
| 46 <tests> | 46 <tests> |
| 47 <test> | 47 <test> |
| 48 <param name="mags" ftype="fasta" value="genome2.fna"/> | |
| 49 <expand macro="test_catdb"/> | |
| 50 <param name="select_outputs" value="bin2classification"/> | |
| 51 <output name="bin2classification"> | |
| 52 <assert_contents> | |
| 53 <has_text text="666" /> | |
| 54 </assert_contents> | |
| 55 </output> | |
| 56 </test> | |
| 57 <test> | |
| 48 <param name="mags" ftype="fasta" value="genome3.fna"/> | 58 <param name="mags" ftype="fasta" value="genome3.fna"/> |
| 49 <expand macro="test_catdb"/> | 59 <expand macro="test_catdb"/> |
| 50 <param name="select_outputs" value="contig2classification"/> | 60 <param name="select_outputs" value="bin2classification"/> |
| 51 <output name="contig2classification"> | 61 <output name="bin2classification"> |
| 52 <assert_contents> | 62 <assert_contents> |
| 53 <has_text text="1639" /> | 63 <has_text text="1639" /> |
| 54 </assert_contents> | 64 </assert_contents> |
| 55 </output> | 65 </output> |
| 56 </test> | 66 </test> |
| 57 <test> | 67 <test> |
| 58 <param name="mags" ftype="fasta" value="genome2.fna,genome3.fna"/> | 68 <param name="mags" ftype="fasta" value="genome2.fna,genome3.fna"/> |
| 59 <expand macro="test_catdb"/> | 69 <expand macro="test_catdb"/> |
| 60 <param name="select_outputs" value="contig2classification"/> | 70 <param name="select_outputs" value="bin2classification"/> |
| 61 <output name="contig2classification"> | 71 <output name="bin2classification"> |
| 62 <assert_contents> | 72 <assert_contents> |
| 63 <has_text text="666" /> | 73 <has_text text="666" /> |
| 64 <has_text text="1639" /> | 74 <has_text text="1639" /> |
| 65 </assert_contents> | 75 </assert_contents> |
| 66 </output> | 76 </output> |
| 67 </test> | 77 </test> |
| 78 <test> | |
| 79 <param name="mags" ftype="fasta" value="genome2.fna,genome3.fna"/> | |
| 80 <expand macro="test_catdb"/> | |
| 81 <param name="select_outputs" value="bin2classification"/> | |
| 82 <param name="select_outputs" value="predicted_proteins_faa"/> | |
| 83 <conditional name="names"> | |
| 84 <param name="add_names" value="both"/> | |
| 85 </conditional> | |
| 86 <param name="summarise" value="classification"/> | |
| 87 <output name="predicted_proteins_faa"> | |
| 88 <assert_contents> | |
| 89 <has_text text="contig_11394" /> | |
| 90 <has_text text="contig_4403" /> | |
| 91 </assert_contents> | |
| 92 </output> | |
| 93 <output name="orf2lca_names"> | |
| 94 <assert_contents> | |
| 95 <has_text text="Listeria" /> | |
| 96 <has_text text="Vibrio" /> | |
| 97 </assert_contents> | |
| 98 </output> | |
| 99 <output name="classification_summary"> | |
| 100 <assert_contents> | |
| 101 <has_text text="Listeria" /> | |
| 102 </assert_contents> | |
| 103 </output> | |
| 104 </test> | |
| 105 | |
| 68 </tests> | 106 </tests> |
| 69 <help><![CDATA[ | 107 <help><![CDATA[ |
| 70 **CAT bin or bins** | 108 **CAT bin or bins** |
| 71 Classify metagenomics assembled genomes. | 109 Classify metagenomics assembled genomes. |
| 72 | 110 |