Mercurial > repos > jjohnson > contig_annotation_tool
comparison cat_contigs.xml @ 4:aaeb63501369 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit ec15da3a30507841856303de991cbe80c65128fd-dirty
| author | jjohnson |
|---|---|
| date | Wed, 27 Nov 2019 10:27:23 -0500 |
| parents | 18ece3d5bcde |
| children | 226949352e31 |
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| 3:18ece3d5bcde | 4:aaeb63501369 |
|---|---|
| 8 <command detect_errors="exit_code"><![CDATA[ | 8 <command detect_errors="exit_code"><![CDATA[ |
| 9 CAT contigs -c '$contigs_fasta' | 9 CAT contigs -c '$contigs_fasta' |
| 10 @CAT_DB@ | 10 @CAT_DB@ |
| 11 @USE_INTERMEDIATES@ | 11 @USE_INTERMEDIATES@ |
| 12 @CUSTOM_SETTINGS@ | 12 @CUSTOM_SETTINGS@ |
| 13 @DIAMOND_OPTIONS@ | |
| 13 && @TXT2TSV@ *.ORF2LCA.txt *.contig2classification.txt | 14 && @TXT2TSV@ *.ORF2LCA.txt *.contig2classification.txt |
| 14 @ADD_NAMES@ | 15 @ADD_NAMES@ |
| 15 @SUMMARISE@ | 16 @SUMMARISE@ |
| 16 ]]></command> | 17 ]]></command> |
| 17 <inputs> | 18 <inputs> |
| 18 <param name="contigs_fasta" type="data" format="fasta" label="Contigs fasta"/> | 19 <param name="contigs_fasta" type="data" format="fasta" label="Contigs fasta"/> |
| 19 <expand macro="cat_db" /> | 20 <expand macro="cat_db" /> |
| 20 <expand macro="use_intermediates" /> | 21 <expand macro="use_intermediates" /> |
| 21 <expand macro="custom_settings" /> | 22 <expand macro="custom_settings" /> |
| 23 <expand macro="diamond_options" /> | |
| 22 <expand macro="add_names" /> | 24 <expand macro="add_names" /> |
| 23 <expand macro="summarise" /> | 25 <expand macro="summarise" /> |
| 24 <expand macro="select_cat_outputs" /> | 26 <expand macro="select_cat_outputs" /> |
| 25 </inputs> | 27 </inputs> |
| 26 <outputs> | 28 <outputs> |