Mercurial > repos > jjohnson > contig_annotation_tool

comparison cat_bins.xml @ 4:aaeb63501369 draft

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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
21 bin -b '$mags' 21 bin -b '$mags'
22 #end if 22 #end if
23 @CAT_DB@ 23 @CAT_DB@
24 @USE_INTERMEDIATES@ 24 @USE_INTERMEDIATES@
25 @CUSTOM_SETTINGS@ 25 @CUSTOM_SETTINGS@
26 @DIAMOND_OPTIONS@
26 && @TXT2TSV@ *.ORF2LCA.txt *.bin2classification.txt 27 && @TXT2TSV@ *.ORF2LCA.txt *.bin2classification.txt
27 #if len($mags) > 1: 28 #if len($mags) > 1:
28 #set pat = '$' + '{i/concatenated./}' 29 #set pat = '$' + '{i/concatenated./}'
29 && (for i in *.concatenated.*; do ln -s "\$i" "${pat}"; done) 30 && (for i in *.concatenated.*; do ln -s "\$i" "${pat}"; done)
30 #end if 31 #end if
34 <inputs> 35 <inputs>
35 <param name="mags" type="data" format="fasta" multiple="true" label="metagenome assembled genomes (MAGs/bins)"/> 36 <param name="mags" type="data" format="fasta" multiple="true" label="metagenome assembled genomes (MAGs/bins)"/>
36 <expand macro="cat_db" /> 37 <expand macro="cat_db" />
37 <expand macro="use_intermediates" /> 38 <expand macro="use_intermediates" />
38 <expand macro="custom_settings" /> 39 <expand macro="custom_settings" />
40 <expand macro="diamond_options" />
39 <expand macro="add_names" /> 41 <expand macro="add_names" />
40 <expand macro="summarise" /> 42 <expand macro="summarise" />
41 <expand macro="select_bat_outputs" /> 43 <expand macro="select_bat_outputs" />
42 </inputs> 44 </inputs>
43 <outputs> 45 <outputs>