Mercurial > repos > iuc > dram_annotate
annotate dram_annotate.xml @ 1:4058af4457c0 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit e0934fc66bfd742731505cacd18cbf53b26d4f2a
author | iuc |
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date | Tue, 11 Jul 2023 23:46:40 +0000 |
parents | cf3f6929b52c |
children | 0515750e7b10 |
rev | line source |
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1
4058af4457c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit e0934fc66bfd742731505cacd18cbf53b26d4f2a
iuc
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1 <tool id="dram_annotate" name="DRAM annotate" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> |
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cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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2 <description>metagenome-assembled-genomes (MAGs)</description> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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3 <macros> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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4 <import>macros.xml</import> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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5 </macros> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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6 <expand macro="requirements"/> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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7 <expand macro="stdio"/> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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8 <command detect_errors="exit_code"><![CDATA[ |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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9 #import os |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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10 |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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11 ## DRAM names the genbank output based on the input_fasta file name |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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12 #set input_fasta_file_name = $os.path.splitext($os.path.basename(str($input_fasta)))[0] |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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13 #set output_gbk_file_name = $input_fasta_file_name + '.gbk' |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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14 |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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15 DRAM.py annotate |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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16 --input_fasta '$input_fasta' |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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17 --output_dir 'output_dir' |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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18 --min_contig_size $min_contig_size |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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19 --prodigal_mode '$prodigal_mode' |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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20 --trans_table $trans_table |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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21 --bit_score_threshold $bit_score_threshold |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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22 --rbh_bit_score_threshold $rbh_bit_score_threshold |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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23 $kofam_use_dbcan2_thresholds |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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24 #if str($custom_fasta_dbs_cond.custom_dbs_fasta) == 'yes': |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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25 #for additional_db in $custom_fasta_dbs_cond.custom_fasta_dbs: |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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26 --custom_db_name '$additional_db.custom_db_name' |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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27 --custom_fasta_loc '$additional_db.custom_fasta_loc' |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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28 #end for |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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29 #end if |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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30 #if str($custom_hmm_dbs_cond.custom_dbs_hmm) == 'yes': |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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31 #for additional_db in $custom_hmm_dbs_cond.custom_hmm_dbs: |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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32 --custom_hmm_name '$additional_db.custom_hmm_name' |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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33 --custom_hmm_loc '$additional_db.custom_hmm_loc' |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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34 #if $additional_db.custom_hmm_cutoffs_loc: |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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35 --custom_hmm_cutoffs_loc '$additional_db.custom_hmm_cutoffs_loc' |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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36 #end if |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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37 #end for |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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38 #end if |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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39 $use_uniref |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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40 $use_vogdb |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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41 $low_mem_mode |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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42 $skip_trnascan |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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43 --threads \${GALAXY_SLOTS:-10} |
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4058af4457c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit e0934fc66bfd742731505cacd18cbf53b26d4f2a
iuc
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44 && (test -f 'output_dir/genes.faa' && mv 'output_dir/genes.faa' '$output_genes_faa' || echo 'No genes.faa output produced') |
4058af4457c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit e0934fc66bfd742731505cacd18cbf53b26d4f2a
iuc
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45 && (test -f 'output_dir/genes.fna' && mv 'output_dir/genes.fna' '$output_genes_fna' || echo 'No genes.fna output produced') |
4058af4457c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit e0934fc66bfd742731505cacd18cbf53b26d4f2a
iuc
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46 && (test -f 'output_dir/genes.gff' && mv 'output_dir/genes.gff' '$output_genes_gff' || echo 'No genes.gff output produced') |
4058af4457c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit e0934fc66bfd742731505cacd18cbf53b26d4f2a
iuc
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47 && (test -f 'output_dir/scaffolds.fna' && mv 'output_dir/scaffolds.fna' '$output_scaffolds_fna' || echo 'No scaffolds.fna output produced') |
4058af4457c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit e0934fc66bfd742731505cacd18cbf53b26d4f2a
iuc
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48 && (test -f 'output_dir/rrnas.tsv' && mv 'output_dir/rrnas.tsv' '$output_rrnas' || echo 'No rrnas.tsv output produced') |
4058af4457c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit e0934fc66bfd742731505cacd18cbf53b26d4f2a
iuc
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49 && (test -f 'output_dir/trnas.tsv' && mv 'output_dir/trnas.tsv' '$output_trnas' || echo 'No trnas.tsv output produced') |
4058af4457c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit e0934fc66bfd742731505cacd18cbf53b26d4f2a
iuc
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50 && (test -f 'output_dir/genbank/$output_gbk_file_name' && mv 'output_dir/genbank/$output_gbk_file_name' '$output_genbank' || echo 'No genbank output produced') |
4058af4457c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit e0934fc66bfd742731505cacd18cbf53b26d4f2a
iuc
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51 && (test -f 'output_dir/annotations.tsv' && mv 'output_dir/annotations.tsv' '$output_annotations' || echo 'No annotations.tsv output produced') |
0
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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52 ]]></command> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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53 <inputs> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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54 <param argument="--input_fasta" type="data" format="fasta,fasta.gz" label="FASTA file"/> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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55 <param argument="--min_contig_size" type="integer" value="2500" min="0" label="Minimum contig size to be used for gene prediction"/> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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56 <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 >3 Kbp)"> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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57 <option value="single" selected="true">single</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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58 <option value="meta">meta</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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59 <option value="train">train</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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60 </param> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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61 <param argument="--trans_table" type="integer" value="11" min="1" max="25" label="Translation table for prodigal to use for gene calling"/> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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62 <param argument="--bit_score_threshold" type="integer" value="60" min="1" label="Minimum bitScore of search to retain hits"/> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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63 <param argument="--rbh_bit_score_threshold" type="integer" value="350" min="1" label="Minimum bitScore of reverse best hits to retain hits"/> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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64 <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?"/> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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65 <conditional name="custom_fasta_dbs_cond"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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66 <param name="custom_dbs_fasta" type="select" label="Specify additional fasta files against which to annotate?"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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67 <option value="no" selected="true">No</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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68 <option value="yes">Yes</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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69 </param> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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70 <when value="no"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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71 <when value="yes"> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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72 <repeat name="custom_fasta_dbs" title="FASTA file" min="1"> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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73 <param argument="--custom_db_name" type="text" value="CF1" label="Custom FASTA database name"> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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74 <validator type="empty_field"/> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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75 <expand macro="sanitizer"/> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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76 </param> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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77 <param argument="--custom_fasta_loc" type="data" format="fasta,fasta.gz" label="Custom database FASTA file"/> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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78 </repeat> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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79 </when> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
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80 </conditional> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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81 <conditional name="custom_hmm_dbs_cond"> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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82 <param name="custom_dbs_hmm" type="select" label="Specify additional hmm files against which to annotate?"> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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83 <option value="no" selected="true">No</option> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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84 <option value="yes">Yes</option> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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85 </param> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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86 <when value="no"/> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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87 <when value="yes"> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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88 <repeat name="custom_hmm_dbs" title="HMM file" min="1"> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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89 <param argument="--custom_hmm_name" type="text" value="CH1" label="Custom HMM database name"> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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90 <validator type="empty_field"/> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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91 <expand macro="sanitizer"/> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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92 </param> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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93 <param argument="--custom_hmm_loc" type="data" format="hmm2,hmm3" label="Custom database HMM file"/> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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94 <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"/> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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95 </repeat> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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96 </when> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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97 </conditional> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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98 <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"/> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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99 <param argument="--use_vogdb" type="boolean" truevalue="--use_vogdb" falsevalue="" checked="false" label="Annotate the input FASTA files against VOGDB?" help="Decreases run time"/> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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100 <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"/> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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101 <param argument="--skip_trnascan" type="boolean" truevalue="--skip_trnascan" falsevalue="" checked="false" label="Skip transcan"/> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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102 </inputs> |
cf3f6929b52c
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103 <outputs> |
cf3f6929b52c
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104 <data name="output_genes_faa" format="fasta" label="${tool.name} on ${on_string}: genes.faa"/> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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105 <data name="output_genes_fna" format="fasta" label="${tool.name} on ${on_string}: genes.fna"/> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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106 <data name="output_genes_gff" format="gff3" label="${tool.name} on ${on_string}: genes.gff"/> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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107 <data name="output_scaffolds_fna" format="fasta" label="${tool.name} on ${on_string}: scaffolds"/> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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108 <data name="output_rrnas" format="tabular" label="${tool.name} on ${on_string}: rrnas"/> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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109 <data name="output_trnas" format="tabular" label="${tool.name} on ${on_string}: trnas"/> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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110 <data name="output_genbank" format="genbank" label="${tool.name} on ${on_string}: genbank"/> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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111 <data name="output_annotations" format="tabular" label="${tool.name} on ${on_string}: annotations"/> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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112 </outputs> |
cf3f6929b52c
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113 <tests> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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114 <test expect_num_outputs="8"> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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115 <param name="input_fasta" value="input_annotate1.fasta.gz" ftype="fasta.gz"/> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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116 <param name="prodigal_mode" value="meta"/> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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117 <output name="output_genes_faa"> |
cf3f6929b52c
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118 <assert_contents> |
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iuc
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119 <has_text text="rank"/> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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120 </assert_contents> |
cf3f6929b52c
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121 </output> |
cf3f6929b52c
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iuc
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122 <output name="output_genes_fna"> |
cf3f6929b52c
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iuc
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123 <assert_contents> |
cf3f6929b52c
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iuc
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124 <has_text text="rank"/> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
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125 </assert_contents> |
cf3f6929b52c
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126 </output> |
cf3f6929b52c
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iuc
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127 <output name="output_genes_gff"> |
cf3f6929b52c
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128 <assert_contents> |
cf3f6929b52c
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129 <has_text text="gff-version 3"/> |
cf3f6929b52c
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130 </assert_contents> |
cf3f6929b52c
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131 </output> |
cf3f6929b52c
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132 <output name="output_scaffolds_fna"> |
cf3f6929b52c
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133 <assert_contents> |
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134 <has_text text="scaffold"/> |
cf3f6929b52c
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135 </assert_contents> |
cf3f6929b52c
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136 </output> |
cf3f6929b52c
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iuc
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137 <output name="output_rrnas"> |
cf3f6929b52c
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138 <assert_contents> |
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139 <has_text text="scaffold"/> |
cf3f6929b52c
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140 </assert_contents> |
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141 </output> |
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142 <output name="output_trnas"> |
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143 <assert_contents> |
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144 <has_text text="fasta"/> |
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145 </assert_contents> |
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146 </output> |
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147 <output name="output_genbank"> |
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148 <assert_contents> |
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149 <has_text text="LOCUS"/> |
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150 </assert_contents> |
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151 </output> |
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152 <output name="output_annotations"> |
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153 <assert_contents> |
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154 <has_text text="fasta"/> |
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155 </assert_contents> |
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156 </output> |
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157 </test> |
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158 <!-- These settings require a db which doesn't exist in the test environment --> |
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159 <test expect_failure="true"> |
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160 <param name="input_fasta" value="input_annotate1.fasta.gz" ftype="fasta.gz"/> |
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161 <param name="custom_dbs_fasta" value="yes"/> |
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162 <repeat name="custom_fasta_dbs"> |
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163 <param name="custom_db_name" value="CF1"/> |
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164 <param name="custom_fasta_loc" value="annotate_custom.fasta" ftype="fasta"/> |
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165 </repeat> |
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166 <param name="custom_dbs_hmm" value="yes"/> |
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167 <repeat name="custom_hmm_dbs"> |
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168 <param name="custom_hmm_name" value="CH1"/> |
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169 <param name="custom_hmm_loc" value="annotate_custom.hmm" ftype="hmm3"/> |
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170 </repeat> |
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171 <param name="prodigal_mode" value="meta"/> |
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172 <assert_stderr> |
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173 <has_text text="returned non-zero exit status"/> |
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174 </assert_stderr> |
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175 </test> |
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176 </tests> |
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177 <help> |
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178 **What it does** |
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179 |
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180 @WHATITDOESHEADER@ |
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181 |
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182 This tool annotates genes by assigning database identifiers to them. Short contigs (default less than 2,500 bp) are initially |
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183 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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184 searches all amino acid sequences against multiple databases, providing a single Raw output. When gene annotation is complete, |
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185 all results are merged in a single tabular annotation table, including the best hit for each database, for user comparison. |
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186 |
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187 This tool accepts assembly-derived fastA files which may come from unbinned data (metagenome contig or scaffold files) or |
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188 genome-resolved data from one or many organisms (isolate genomes, single-amplified genome (SAGs), MAGs). |
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189 |
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190 This tool produces the following outputs. |
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191 |
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192 * A tabular file with all annotations from Pfam, UniProt, dbCAN and MEROPS databases for all genes in the input genomes |
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193 * Genbank files for each genome |
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194 * A gff file of all annotations across genomes |
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195 * A fasta file of each open reading frame amino acid sequence and best ranked annotation |
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196 * Tabular files with tRNAs and rRNAs |
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197 |
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198 @WHATITDOESFOOTER@ |
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199 </help> |
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200 <expand macro="citations"/> |
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201 </tool> |