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comparison drep_dereplicate.xml @ 2:cb2fc9f60381 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit eaae9983f0339c4624431f4f843e319f83814490"
author jjohnson
date Wed, 08 Jan 2020 13:01:03 -0500
parents 7e2debc267eb
children
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1:7e2debc267eb 2:cb2fc9f60381
29 <collection name="dereplicated_genomes" type="list" label="dereplicated_genomes"> 29 <collection name="dereplicated_genomes" type="list" label="dereplicated_genomes">
30 <discover_datasets pattern="__designation__" directory="outdir/dereplicated_genomes" ext='fasta'/> 30 <discover_datasets pattern="__designation__" directory="outdir/dereplicated_genomes" ext='fasta'/>
31 </collection> 31 </collection>
32 <expand macro="drep_outputs" /> 32 <expand macro="drep_outputs" />
33 </outputs> 33 </outputs>
34 <tests>
35 <expand macro="test_defaults_log">
36 <has_text text="dRep dereplicate finished" />
37 </expand>
38 </tests>
34 <help><![CDATA[ 39 <help><![CDATA[
35 TODO: Fill in help.
36
37 usage: drep dereplicate [-p PROCESSORS] [-d] [-h] [-l LENGTH] 40 usage: drep dereplicate [-p PROCESSORS] [-d] [-h] [-l LENGTH]
38 [-comp COMPLETENESS] [-con CONTAMINATION] 41 [-comp COMPLETENESS] [-con CONTAMINATION]
39 [--ignoreGenomeQuality] [-ms MASH_SKETCH] 42 [--ignoreGenomeQuality] [-ms MASH_SKETCH]
40 [--S_algorithm {goANI,ANIn,ANImf,gANI}] 43 [--S_algorithm {goANI,ANIn,ANImf,gANI}]
41 [-n_PRESET {normal,tight}] [-pa P_ANI] [-sa S_ANI] 44 [-n_PRESET {normal,tight}] [-pa P_ANI] [-sa S_ANI]
51 [-g [GENOMES [GENOMES ...]]] 54 [-g [GENOMES [GENOMES ...]]]
52 [--checkM_method {taxonomy_wf,lineage_wf}] 55 [--checkM_method {taxonomy_wf,lineage_wf}]
53 [--genomeInfo GENOMEINFO] 56 [--genomeInfo GENOMEINFO]
54 work_directory 57 work_directory
55 58
59
56 @GENOMES_HELP@ 60 @GENOMES_HELP@
57 @FILTERING_HELP@ 61 @FILTERING_HELP@
58 @GENOME_COMPARISON_HELP@ 62 @GENOME_COMPARISON_HELP@
59 @CLUSTERING_HELP@ 63 @CLUSTERING_HELP@
60 @SCORING_HELP@ 64 @SCORING_HELP@