Mercurial > repos > iuc > dram_annotate
annotate dram_annotate.xml @ 0:cf3f6929b52c draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
author | iuc |
---|---|
date | Sat, 10 Dec 2022 21:14:46 +0000 |
parents | |
children | 4058af4457c0 |
rev | line source |
---|---|
0
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
1 <tool id="dram_annotate" name="DRAM annotate" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
2 <description>metagenome-assembled-genomes (MAGs)</description> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
3 <macros> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
4 <import>macros.xml</import> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
5 </macros> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
6 <expand macro="requirements"/> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
7 <expand macro="stdio"/> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
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
parents:
diff
changeset
|
9 #import os |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
10 |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
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
parents:
diff
changeset
|
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
parents:
diff
changeset
|
13 #set output_gbk_file_name = $input_fasta_file_name + '.gbk' |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
14 |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
15 DRAM.py annotate |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
16 --input_fasta '$input_fasta' |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
17 --output_dir 'output_dir' |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
18 --min_contig_size $min_contig_size |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
19 --prodigal_mode '$prodigal_mode' |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
20 --trans_table $trans_table |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
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
parents:
diff
changeset
|
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
parents:
diff
changeset
|
23 $kofam_use_dbcan2_thresholds |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
24 #if str($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
parents:
diff
changeset
|
25 #for additional_db in $custom_fasta_dbs_cond.custom_fasta_dbs: |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
26 --custom_db_name '$additional_db.custom_db_name' |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
27 --custom_fasta_loc '$additional_db.custom_fasta_loc' |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
28 #end for |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
29 #end if |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
30 #if str($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
parents:
diff
changeset
|
31 #for additional_db in $custom_hmm_dbs_cond.custom_hmm_dbs: |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
32 --custom_hmm_name '$additional_db.custom_hmm_name' |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
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
parents:
diff
changeset
|
34 #if $additional_db.custom_hmm_cutoffs_loc: |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
35 --custom_hmm_cutoffs_loc '$additional_db.custom_hmm_cutoffs_loc' |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
36 #end if |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
37 #end for |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
38 #end if |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
39 $use_uniref |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
40 $use_vogdb |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
41 $low_mem_mode |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
42 $skip_trnascan |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
43 --threads \${GALAXY_SLOTS:-10} |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
44 && test -f 'output_dir/genes.faa' && mv 'output_dir/genes.faa' '$output_genes_faa' || echo 'No genes.faa output produced' |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
45 && test -f 'output_dir/genes.fna' && mv 'output_dir/genes.fna' '$output_genes_fna' || echo 'No genes.fna output produced' |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
46 && test -f 'output_dir/genes.gff' && mv 'output_dir/genes.gff' '$output_genes_gff' || echo 'No genes.gff output produced' |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
47 && test -f 'output_dir/scaffolds.fna' && mv 'output_dir/scaffolds.fna' '$output_scaffolds_fna' || echo 'No scaffolds.fna output produced' |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
48 && test -f 'output_dir/rrnas.tsv' && mv 'output_dir/rrnas.tsv' '$output_rrnas' || echo 'No rrnas.tsv output produced' |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
49 && test -f 'output_dir/trnas.tsv' && mv 'output_dir/trnas.tsv' '$output_trnas' || echo 'No trnas.tsv output produced' |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
50 && test -f 'output_dir/genbank/$output_gbk_file_name' && mv 'output_dir/genbank/$output_gbk_file_name' '$output_genbank' || echo 'No genbank output produced' |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
51 && test -f 'output_dir/annotations.tsv' && mv 'output_dir/annotations.tsv' '$output_annotations' || echo 'No annotations.tsv output produced' |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
52 ]]></command> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
53 <inputs> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
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
parents:
diff
changeset
|
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
parents:
diff
changeset
|
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
parents:
diff
changeset
|
57 <option value="single" selected="true">single</option> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
58 <option value="meta">meta</option> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
59 <option value="train">train</option> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
60 </param> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
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
parents:
diff
changeset
|
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
parents:
diff
changeset
|
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
parents:
diff
changeset
|
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
parents:
diff
changeset
|
65 <conditional name="custom_fasta_dbs_cond"> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
66 <param name="custom_dbs_fasta" type="select" label="Specify additional fasta files against which to annotate?"> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
67 <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
parents:
diff
changeset
|
68 <option value="yes">Yes</option> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
69 </param> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
70 <when value="no"/> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
71 <when value="yes"> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
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
parents:
diff
changeset
|
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
parents:
diff
changeset
|
74 <validator type="empty_field"/> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
75 <expand macro="sanitizer"/> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
76 </param> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
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
parents:
diff
changeset
|
78 </repeat> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
79 </when> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
80 </conditional> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
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
parents:
diff
changeset
|
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
parents:
diff
changeset
|
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
parents:
diff
changeset
|
84 <option value="yes">Yes</option> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
85 </param> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
86 <when value="no"/> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
87 <when value="yes"> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
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
parents:
diff
changeset
|
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
parents:
diff
changeset
|
90 <validator type="empty_field"/> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
91 <expand macro="sanitizer"/> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
92 </param> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
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
iuc
parents:
diff
changeset
|
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
parents:
diff
changeset
|
95 </repeat> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
96 </when> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
97 </conditional> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
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
iuc
parents:
diff
changeset
|
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
iuc
parents:
diff
changeset
|
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
iuc
parents:
diff
changeset
|
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
iuc
parents:
diff
changeset
|
102 </inputs> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
103 <outputs> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
104 <data name="output_genes_faa" format="fasta" label="${tool.name} on ${on_string}: genes.faa"/> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
105 <data name="output_genes_fna" format="fasta" label="${tool.name} on ${on_string}: genes.fna"/> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
106 <data name="output_genes_gff" format="gff3" label="${tool.name} on ${on_string}: genes.gff"/> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
107 <data name="output_scaffolds_fna" format="fasta" label="${tool.name} on ${on_string}: scaffolds"/> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
108 <data name="output_rrnas" format="tabular" label="${tool.name} on ${on_string}: rrnas"/> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
109 <data name="output_trnas" format="tabular" label="${tool.name} on ${on_string}: trnas"/> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
110 <data name="output_genbank" format="genbank" label="${tool.name} on ${on_string}: genbank"/> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
111 <data name="output_annotations" format="tabular" label="${tool.name} on ${on_string}: annotations"/> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
112 </outputs> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
113 <tests> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
114 <test expect_num_outputs="8"> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
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
iuc
parents:
diff
changeset
|
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
parents:
diff
changeset
|
117 <output name="output_genes_faa"> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
118 <assert_contents> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
119 <has_text text="rank"/> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
120 </assert_contents> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
121 </output> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
122 <output name="output_genes_fna"> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
123 <assert_contents> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
124 <has_text text="rank"/> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
125 </assert_contents> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
126 </output> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
127 <output name="output_genes_gff"> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
128 <assert_contents> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
129 <has_text text="gff-version 3"/> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
130 </assert_contents> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
131 </output> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
132 <output name="output_scaffolds_fna"> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
133 <assert_contents> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
134 <has_text text="scaffold"/> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
135 </assert_contents> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
136 </output> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
137 <output name="output_rrnas"> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
138 <assert_contents> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
139 <has_text text="scaffold"/> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
140 </assert_contents> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
141 </output> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
142 <output name="output_trnas"> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
143 <assert_contents> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
144 <has_text text="fasta"/> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
145 </assert_contents> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
146 </output> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
147 <output name="output_genbank"> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
148 <assert_contents> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
149 <has_text text="LOCUS"/> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
150 </assert_contents> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
151 </output> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
152 <output name="output_annotations"> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
153 <assert_contents> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
154 <has_text text="fasta"/> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
155 </assert_contents> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
156 </output> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
157 </test> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
158 <!-- These settings require a db which doesn't exist in the test environment --> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
159 <test expect_failure="true"> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
160 <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
iuc
parents:
diff
changeset
|
161 <param name="custom_dbs_fasta" value="yes"/> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
162 <repeat name="custom_fasta_dbs"> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
163 <param name="custom_db_name" value="CF1"/> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
164 <param name="custom_fasta_loc" value="annotate_custom.fasta" ftype="fasta"/> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
165 </repeat> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
166 <param name="custom_dbs_hmm" value="yes"/> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
167 <repeat name="custom_hmm_dbs"> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
168 <param name="custom_hmm_name" value="CH1"/> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
169 <param name="custom_hmm_loc" value="annotate_custom.hmm" ftype="hmm3"/> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
170 </repeat> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
171 <param name="prodigal_mode" value="meta"/> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
172 <assert_stderr> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
173 <has_text text="returned non-zero exit status"/> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
174 </assert_stderr> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
175 </test> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
176 </tests> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
177 <help> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
178 **What it does** |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
179 |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
180 @WHATITDOESHEADER@ |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
181 |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
182 This tool annotates genes by assigning database identifiers to them. Short contigs (default less than 2,500 bp) are initially |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
183 removed and then Prodigal is used to detect open reading frames (ORFs) and to predict their amino acid sequences. Next, DRAM |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
184 searches all amino acid sequences against multiple databases, providing a single Raw output. When gene annotation is complete, |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
185 all results are merged in a single tabular annotation table, including the best hit for each database, for user comparison. |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
186 |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
187 This tool accepts assembly-derived fastA files which may come from unbinned data (metagenome contig or scaffold files) or |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
188 genome-resolved data from one or many organisms (isolate genomes, single-amplified genome (SAGs), MAGs). |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
189 |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
190 This tool produces the following outputs. |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
191 |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
192 * A tabular file with all annotations from Pfam, UniProt, dbCAN and MEROPS databases for all genes in the input genomes |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
193 * Genbank files for each genome |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
194 * A gff file of all annotations across genomes |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
195 * A fasta file of each open reading frame amino acid sequence and best ranked annotation |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
196 * Tabular files with tRNAs and rRNAs |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
197 |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
198 @WHATITDOESFOOTER@ |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
199 </help> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
200 <expand macro="citations"/> |
cf3f6929b52c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
201 </tool> |