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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit 3234c3d93fa294fa9c2c5148eae4b399d42904d8
author iuc
date Fri, 23 Aug 2024 08:16:56 +0000
parents 3925138d40bf
children
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a8ec43f1fc88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit 3234c3d93fa294fa9c2c5148eae4b399d42904d8
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1 <tool id="dram_annotate" name="DRAM annotate" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
0
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2 <description>metagenome-assembled-genomes (MAGs)</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
2
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6 <expand macro="bio_tools"/>
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7 <expand macro="requirements">
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8 </expand>
0
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9 <expand macro="stdio"/>
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10 <command detect_errors="exit_code"><![CDATA[
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11 #import os
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12
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13 ## DRAM names the genbank output based on the input_fasta file name
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14 #set input_fasta_file_name = $os.path.splitext($os.path.basename(str($input_fasta)))[0]
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15 #set output_gbk_file_name = $input_fasta_file_name + '.gbk'
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16
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17 #if str($custom_hmm_dbs_cond.custom_dbs_hmm) == 'yes':
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18 #for count, additional_db in enumerate($custom_hmm_dbs_cond.custom_hmm_dbs):
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19 ln -s '$additional_db.custom_hmm_loc' ${count}.hmm &&
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20 #end for
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21 #end if
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23
0
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24 DRAM.py annotate
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25 --input_fasta '$input_fasta'
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26 --output_dir 'output_dir'
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27 --min_contig_size $min_contig_size
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28 --prodigal_mode '$prodigal_mode'
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29 --trans_table $trans_table
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30 --bit_score_threshold $bit_score_threshold
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31 --rbh_bit_score_threshold $rbh_bit_score_threshold
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32 $kofam_use_dbcan2_thresholds
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33 #if str($custom_fasta_dbs_cond.custom_dbs_fasta) == 'yes':
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34 #for additional_db in $custom_fasta_dbs_cond.custom_fasta_dbs:
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35 --custom_db_name '$additional_db.custom_db_name'
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36 --custom_fasta_loc '$additional_db.custom_fasta_loc'
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37 #end for
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38 #end if
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39 #if str($custom_hmm_dbs_cond.custom_dbs_hmm) == 'yes':
2
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40 #for count, additional_db in enumerate($custom_hmm_dbs_cond.custom_hmm_dbs):
0
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41 --custom_hmm_name '$additional_db.custom_hmm_name'
2
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42 --custom_hmm_loc ${count}.hmm
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43 #if $additional_db.custom_hmm_cutoffs_loc:
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44 --custom_hmm_cutoffs_loc '$additional_db.custom_hmm_cutoffs_loc'
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45 #end if
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46 #end for
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47 #end if
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48 $use_uniref
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49 $use_vogdb
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50 $low_mem_mode
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51 $skip_trnascan
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52 --threads \${GALAXY_SLOTS:-10}
1
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53 && (test -f 'output_dir/genes.faa' && mv 'output_dir/genes.faa' '$output_genes_faa' || echo 'No genes.faa output produced')
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54 && (test -f 'output_dir/genes.fna' && mv 'output_dir/genes.fna' '$output_genes_fna' || echo 'No genes.fna output produced')
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55 && (test -f 'output_dir/genes.gff' && mv 'output_dir/genes.gff' '$output_genes_gff' || echo 'No genes.gff output produced')
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56 && (test -f 'output_dir/scaffolds.fna' && mv 'output_dir/scaffolds.fna' '$output_scaffolds_fna' || echo 'No scaffolds.fna output produced')
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57 && (test -f 'output_dir/rrnas.tsv' && mv 'output_dir/rrnas.tsv' '$output_rrnas' || echo 'No rrnas.tsv output produced')
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58 && (test -f 'output_dir/trnas.tsv' && mv 'output_dir/trnas.tsv' '$output_trnas' || echo 'No trnas.tsv output produced')
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59 && (test -f 'output_dir/genbank/$output_gbk_file_name' && mv 'output_dir/genbank/$output_gbk_file_name' '$output_genbank' || echo 'No genbank output produced')
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60 && (test -f 'output_dir/annotations.tsv' && mv 'output_dir/annotations.tsv' '$output_annotations' || echo 'No annotations.tsv output produced')
0
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61 ]]></command>
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62 <inputs>
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63 <param argument="--input_fasta" type="data" format="fasta,fasta.gz" label="FASTA file"/>
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64 <param argument="--min_contig_size" type="integer" min="0" value="2500" label="Minimum contig size to be used for gene prediction"/>
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65 <param argument="--prodigal_mode" type="select" label="Select mode of prodigal to use for gene calling" help="Single mode requires genomes which are high quality with low contamination and long contigs (average length &gt;3 Kbp)">
0
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66 <option value="single" selected="true">single</option>
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67 <option value="meta">meta</option>
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68 <option value="train">train</option>
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69 </param>
2
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70 <param argument="--trans_table" type="integer" min="1" max="25" value="11" label="Translation table for prodigal to use for gene calling"/>
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71 <param argument="--bit_score_threshold" type="integer" min="1" value="60" label="Minimum bitScore of search to retain hits"/>
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72 <param argument="--rbh_bit_score_threshold" type="integer" min="1" value="350" label="Minimum bitScore of reverse best hits to retain hits"/>
0
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73 <param argument="--kofam_use_dbcan2_thresholds" type="boolean" truevalue="--kofam_use_dbcan2_thresholds" falsevalue="" checked="false" label="Use dbcan2 suggested HMM cutoffs for KOfam annotation instead of KOfam recommended cutoffs?"/>
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74 <conditional name="custom_fasta_dbs_cond">
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75 <param name="custom_dbs_fasta" type="select" label="Specify additional fasta files against which to annotate?">
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76 <option value="no" selected="true">No</option>
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77 <option value="yes">Yes</option>
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78 </param>
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79 <when value="no"/>
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80 <when value="yes">
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81 <repeat name="custom_fasta_dbs" title="FASTA file" min="1">
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82 <param argument="--custom_db_name" type="text" value="CF1" label="Custom FASTA database name">
3f9129750546 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
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83 <validator type="empty_field"/>
3f9129750546 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
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84 <expand macro="sanitizer"/>
3f9129750546 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
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85 </param>
3f9129750546 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
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86 <param argument="--custom_fasta_loc" type="data" format="fasta,fasta.gz" label="Custom database FASTA file"/>
3f9129750546 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
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87 </repeat>
3f9129750546 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff changeset
88 </when>
3f9129750546 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff changeset
89 </conditional>
3f9129750546 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
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90 <conditional name="custom_hmm_dbs_cond">
3f9129750546 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
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91 <param name="custom_dbs_hmm" type="select" label="Specify additional hmm files against which to annotate?">
3f9129750546 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
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92 <option value="no" selected="true">No</option>
3f9129750546 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
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93 <option value="yes">Yes</option>
3f9129750546 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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94 </param>
3f9129750546 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff changeset
95 <when value="no"/>
3f9129750546 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
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96 <when value="yes">
3f9129750546 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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97 <repeat name="custom_hmm_dbs" title="HMM file" min="1">
3f9129750546 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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98 <param argument="--custom_hmm_name" type="text" value="CH1" label="Custom HMM database name">
3f9129750546 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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99 <validator type="empty_field"/>
3f9129750546 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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100 <expand macro="sanitizer"/>
3f9129750546 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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101 </param>
3f9129750546 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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102 <param argument="--custom_hmm_loc" type="data" format="hmm2,hmm3" label="Custom database HMM file"/>
3f9129750546 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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103 <param argument="--custom_hmm_cutoffs_loc" type="data" format="tabular,tsv" optional="true" label="Custom HMM cutoffs and descriptions file" help="Optional, leave blank to ignore"/>
3f9129750546 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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104 </repeat>
3f9129750546 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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105 </when>
3f9129750546 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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106 </conditional>
3f9129750546 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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107 <param argument="--use_uniref" type="boolean" truevalue="--use_uniref" falsevalue="" checked="false" label="Annotate the input FASTA files against UniRef?" help="Increases run time and memory requirements"/>
3f9129750546 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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108 <param argument="--use_vogdb" type="boolean" truevalue="--use_vogdb" falsevalue="" checked="false" label="Annotate the input FASTA files against VOGDB?" help="Decreases run time"/>
3f9129750546 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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109 <param argument="--low_mem_mode" type="boolean" truevalue="--low_mem_mode" falsevalue="" checked="false" label="Skip annotating with uniref and use kofam?" help="Decreases memory requirements"/>
3f9129750546 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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110 <param argument="--skip_trnascan" type="boolean" truevalue="--skip_trnascan" falsevalue="" checked="false" label="Skip transcan"/>
3f9129750546 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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111 </inputs>
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iuc
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112 <outputs>
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113 <data name="output_genes_faa" format="fasta" label="${tool.name} on ${on_string}: genes.faa"/>
3f9129750546 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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114 <data name="output_genes_fna" format="fasta" label="${tool.name} on ${on_string}: genes.fna"/>
3f9129750546 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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115 <data name="output_genes_gff" format="gff3" label="${tool.name} on ${on_string}: genes.gff"/>
3f9129750546 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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116 <data name="output_scaffolds_fna" format="fasta" label="${tool.name} on ${on_string}: scaffolds"/>
3f9129750546 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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117 <data name="output_rrnas" format="tabular" label="${tool.name} on ${on_string}: rrnas"/>
3f9129750546 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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118 <data name="output_trnas" format="tabular" label="${tool.name} on ${on_string}: trnas"/>
3f9129750546 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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119 <data name="output_genbank" format="genbank" label="${tool.name} on ${on_string}: genbank"/>
3f9129750546 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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120 <data name="output_annotations" format="tabular" label="${tool.name} on ${on_string}: annotations"/>
3f9129750546 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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121 </outputs>
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iuc
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122 <tests>
3f9129750546 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
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123 <test expect_num_outputs="8">
3f9129750546 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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124 <param name="input_fasta" value="input_annotate1.fasta.gz" ftype="fasta.gz"/>
3f9129750546 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
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125 <param name="prodigal_mode" value="meta"/>
3f9129750546 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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126 <output name="output_genes_faa">
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iuc
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127 <assert_contents>
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iuc
parents:
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128 <has_text text="rank"/>
3f9129750546 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
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129 </assert_contents>
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iuc
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130 </output>
3f9129750546 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
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131 <output name="output_genes_fna">
3f9129750546 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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132 <assert_contents>
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iuc
parents:
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133 <has_text text="rank"/>
3f9129750546 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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134 </assert_contents>
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iuc
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135 </output>
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iuc
parents:
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136 <output name="output_genes_gff">
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iuc
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137 <assert_contents>
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iuc
parents:
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138 <has_text text="gff-version 3"/>
3f9129750546 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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139 </assert_contents>
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iuc
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140 </output>
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iuc
parents:
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141 <output name="output_scaffolds_fna">
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iuc
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142 <assert_contents>
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iuc
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143 <has_text text="scaffold"/>
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iuc
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144 </assert_contents>
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145 </output>
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iuc
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146 <output name="output_rrnas">
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iuc
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147 <assert_contents>
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iuc
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148 <has_text text="scaffold"/>
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iuc
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149 </assert_contents>
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150 </output>
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iuc
parents:
diff changeset
151 <output name="output_trnas">
3f9129750546 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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152 <assert_contents>
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iuc
parents:
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153 <has_text text="fasta"/>
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iuc
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154 </assert_contents>
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iuc
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155 </output>
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iuc
parents:
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156 <output name="output_genbank">
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iuc
parents:
diff changeset
157 <assert_contents>
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iuc
parents:
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158 <has_text text="LOCUS"/>
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parents:
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159 </assert_contents>
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iuc
parents:
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160 </output>
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iuc
parents:
diff changeset
161 <output name="output_annotations">
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iuc
parents:
diff changeset
162 <assert_contents>
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iuc
parents:
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163 <has_text text="fasta"/>
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iuc
parents:
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164 </assert_contents>
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165 </output>
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iuc
parents:
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166 </test>
2
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iuc
parents: 1
diff changeset
167 <test>
0
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iuc
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168 <param name="input_fasta" value="input_annotate1.fasta.gz" ftype="fasta.gz"/>
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169 <param name="custom_dbs_fasta" value="yes"/>
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170 <repeat name="custom_fasta_dbs">
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171 <param name="custom_db_name" value="CF1"/>
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172 <param name="custom_fasta_loc" value="annotate_custom.fasta" ftype="fasta"/>
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173 </repeat>
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174 <param name="custom_dbs_hmm" value="yes"/>
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175 <repeat name="custom_hmm_dbs">
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176 <param name="custom_hmm_name" value="CH1"/>
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177 <param name="custom_hmm_loc" value="annotate_custom.hmm" ftype="hmm3"/>
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178 </repeat>
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179 <param name="prodigal_mode" value="meta"/>
2
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180 <output name="output_genbank">
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181 <assert_contents>
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182 <has_text text="LOCUS"/>
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183 <has_text text="gc_cont"/>
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184 </assert_contents>
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185 </output>
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186 <output name="output_annotations">
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187 <assert_contents>
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188 <has_text text="fasta"/>
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189 <has_text text="gene_position"/>
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190 <has_n_columns n="9"/>
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191 </assert_contents>
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192 </output>
0
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193 </test>
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194 </tests>
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195 <help>
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196 **What it does**
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197
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198 @WHATITDOESHEADER@
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199
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200 This tool annotates genes by assigning database identifiers to them. Short contigs (default less than 2,500 bp) are initially
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201 removed and then Prodigal is used to detect open reading frames (ORFs) and to predict their amino acid sequences. Next, DRAM
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202 searches all amino acid sequences against multiple databases, providing a single Raw output. When gene annotation is complete,
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203 all results are merged in a single tabular annotation table, including the best hit for each database, for user comparison.
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204
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205 This tool accepts assembly-derived fastA files which may come from unbinned data (metagenome contig or scaffold files) or
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206 genome-resolved data from one or many organisms (isolate genomes, single-amplified genome (SAGs), MAGs).
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207
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208 This tool produces the following outputs.
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209
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210 * A tabular file with all annotations from Pfam, UniProt, dbCAN and MEROPS databases for all genes in the input genomes
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211 * Genbank files for each genome
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212 * A gff file of all annotations across genomes
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213 * A fasta file of each open reading frame amino acid sequence and best ranked annotation
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214 * Tabular files with tRNAs and rRNAs
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215
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216 @WHATITDOESFOOTER@
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217 </help>
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218 <expand macro="citations"/>
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219 </tool>