Mercurial > repos > jjohnson > drep
comparison drep_dereplicate.xml @ 0:cb142f79f424 draft default tip
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
| author | jjohnson |
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| date | Mon, 06 Jan 2020 15:37:18 +0000 |
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| -1:000000000000 | 0:cb142f79f424 |
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| 1 <tool id="drep_dereplicate" name="dRep dereplicate" version="@VERSION@.0" python_template_version="3.5"> | |
| 2 <description>De-replicate a list of genomes</description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements" /> | |
| 7 <command detect_errors="exit_code"><![CDATA[ | |
| 8 @PREPARE_GENOMES@ | |
| 9 dRep dereplicate outdir | |
| 10 @FILTER_OPTIONS@ | |
| 11 @GENOME_COMPARISON_OPTIONS@ | |
| 12 @CLUSTERING_OPTIONS@ | |
| 13 @SCORING_OPTIONS@ | |
| 14 @TAXONOMY_OPTIONS@ | |
| 15 @WARNING_OPTIONS@ | |
| 16 @GENOMES@ | |
| 17 ]]></command> | |
| 18 <inputs> | |
| 19 <expand macro="genomes"/> | |
| 20 <expand macro="filtering_options"/> | |
| 21 <expand macro="genome_comparison_options"/> | |
| 22 <expand macro="clustering_options"/> | |
| 23 <expand macro="scoring_options"/> | |
| 24 <expand macro="taxonomy_options"/> | |
| 25 <expand macro="warning_options"/> | |
| 26 </inputs> | |
| 27 <outputs> | |
| 28 <expand macro="common_outputs" /> | |
| 29 <collection name="dereplicated_genomes" type="list" label="dereplicated_genomes"> | |
| 30 <discover_datasets pattern="__designation__" directory="out_drep/dereplicated_genomes" ext='fasta'/> | |
| 31 </collection> | |
| 32 </outputs> | |
| 33 <help><![CDATA[ | |
| 34 TODO: Fill in help. | |
| 35 | |
| 36 usage: drep dereplicate [-p PROCESSORS] [-d] [-h] [-l LENGTH] | |
| 37 [-comp COMPLETENESS] [-con CONTAMINATION] | |
| 38 [--ignoreGenomeQuality] [-ms MASH_SKETCH] | |
| 39 [--S_algorithm {goANI,ANIn,ANImf,gANI}] | |
| 40 [-n_PRESET {normal,tight}] [-pa P_ANI] [-sa S_ANI] | |
| 41 [--SkipMash] [--SkipSecondary] [-nc COV_THRESH] | |
| 42 [-cm {total,larger}] [--clusterAlg CLUSTERALG] | |
| 43 [-comW COMPLETENESS_WEIGHT] | |
| 44 [-conW CONTAMINATION_WEIGHT] | |
| 45 [-strW STRAIN_HETEROGENEITY_WEIGHT] [-N50W N50_WEIGHT] | |
| 46 [-sizeW SIZE_WEIGHT] [--run_tax] | |
| 47 [--tax_method {percent,max}] [-per PERCENT] | |
| 48 [--cent_index CENT_INDEX] [--warn_dist WARN_DIST] | |
| 49 [--warn_sim WARN_SIM] [--warn_aln WARN_ALN] | |
| 50 [-g [GENOMES [GENOMES ...]]] | |
| 51 [--checkM_method {taxonomy_wf,lineage_wf}] | |
| 52 [--genomeInfo GENOMEINFO] | |
| 53 work_directory | |
| 54 | |
| 55 @GENOMES_HELP@ | |
| 56 @FILTERING_HELP@ | |
| 57 @GENOME_COMPARISON_HELP@ | |
| 58 @CLUSTERING_HELP@ | |
| 59 @SCORING_HELP@ | |
| 60 @TAXONOMY_HELP@ | |
| 61 @WARNINGS_HELP@ | |
| 62 | |
| 63 | |
| 64 ]]></help> | |
| 65 <expand macro="citations" /> | |
| 66 </tool> |