Mercurial > repos > leomrtns > dfast
comparison dfast.xml @ 0:6ddc8a6503e7 draft default tip
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/dfast
author | leomrtns |
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date | Thu, 03 Oct 2019 12:41:36 -0400 |
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-1:000000000000 | 0:6ddc8a6503e7 |
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1 <tool id="dfast" name="dfast" version="@VERSION@"> | |
2 <description>prokaryotic genome annotation</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements" /> | |
7 <expand macro="version_command" /> | |
8 <command detect_errors="exit_code"><![CDATA[ | |
9 #import re | |
10 #if $ortho.use | |
11 #set $ref_set_str = '' | |
12 #set $divisor = '' | |
13 #for $i_file in $ortho.refs: | |
14 #set $ref_set_str = $ref_set_str + $divisor + "{}".format($i_file) | |
15 #set $divisor = ';' ### will create "A ; B ; C " | |
16 #end for | |
17 #end if | |
18 #if $genome_input.is_of_type('fasta'): | |
19 ln -s ${genome_input} in.fasta && | |
20 #elif $genome_input.is_of_type('fasta.gz'): | |
21 gunzip -c ${genome_input} > in.fasta && | |
22 #elif $genome_input.is_of_type('fasta.bz2'): | |
23 bunzip2 -c ${genome_input} > in.fasta && | |
24 #end if | |
25 dfast -g in.fasta | |
26 -o OUT | |
27 --cpu \${GALAXY_SLOTS:-1} | |
28 --aligner ${aligner} | |
29 --gcode ${gcode} | |
30 --use_original_name ${use_orig_name} | |
31 --sort_sequence ${sort_sequence} | |
32 --use_separate_tags ${separate_tags} | |
33 #if str($min_length) != "" | |
34 --minimum_length ${min_length} | |
35 #end if | |
36 #if $ortho.use | |
37 --references "${ref_set_str}" | |
38 #end if | |
39 ${fix_origin} | |
40 ]]></command> | |
41 <inputs> | |
42 <param name="genome_input" multiple="false" format="fasta, fasta.gz, fasta.bz2" type="data" label="Genome to be annotated, in fasta format (can be zipped)"/> | |
43 | |
44 <param name="aligner" type="select" label="Aligner" help="Safer to leave the default (ghostx)"> | |
45 <option value="ghostx" selected="true">ghostx (default)</option> | |
46 <option value="blastp">blastp (experimental, since didn't pass local tests) </option> | |
47 </param> | |
48 | |
49 <param name="gcode" type="select" label="Genetic code"> | |
50 <option value="11" selected="true">Default</option> | |
51 <option value="4">Mycoplasma</option> | |
52 </param> | |
53 | |
54 <param name="use_orig_name" type="boolean" truevalue="t" falsevalue="f" checked="false" help="--use_original_name" label="Use original sequence names in a query FASTA file"/> | |
55 | |
56 <param name="sort_sequence" type="boolean" truevalue="t" falsevalue="f" checked="true" help="--sort_sequence" label="Sort sequences by length"/> | |
57 | |
58 <param name="min_length" type="integer" label="Minimum sequence length (default:200)" help="--minimum_length" optional="true" /> | |
59 | |
60 <param name="separate_tags" type="boolean" truevalue="t" falsevalue="f" checked="true" help="--use_separate_tags" label="Use separate tags according to feature types"/> | |
61 | |
62 <param name="fix_origin" type="boolean" truevalue="--fix_origin" falsevalue="" checked="false" help="--fix_origin" | |
63 label="Rotate/flip the chromosome so that the dnaA gene comes first. (ONLY FOR A FINISHED GENOME)" /> | |
64 | |
65 <conditional name="ortho"> | |
66 <param name="use" type="boolean" checked="false" help="--references" label="orthologous gene assignment with OrthoSearch"/> | |
67 <when value="true"> | |
68 <param name="refs" type="data" multiple="true" format="genbank,embl,asn1" label="One or more genbank reference genomes"> | |
69 <help><![CDATA[ | |
70 OrthoSearch conducts all-against-all protein alignments between the given reference genomes to infer orthologous genes. | |
71 ]]></help> | |
72 </param> | |
73 </when> | |
74 <when value="false"> </when> | |
75 </conditional> | |
76 </inputs> | |
77 <outputs> | |
78 <data name="g_embl" format="embl" label="Annotated genome in EMBL format" from_work_dir="OUT/genome.embl"/> | |
79 <data name="g_gbk" format="genbank" label="Annotated genome in GENBANK format" from_work_dir="OUT/genome.gbk"/> | |
80 <data name="g_gff" format="gff" label="Annotated genome in GFF format" from_work_dir="OUT/genome.gff"/> | |
81 <data name="e_fsa" format="fasta" label="fsa file for Genbank submission" from_work_dir="OUT/genbank/genbank.fsa"/> | |
82 <data name="e_tbl" format="txt" label="tbl file for Genbank submission" from_work_dir="OUT/genbank/genbank.tbl"/> | |
83 <data name="e_fsa" format="fasta" label="fasta file for DDBJ submission" from_work_dir="OUT/ddbj/mss.fasta"/> | |
84 <data name="e_fsa" format="txt" label="ann file for DDBJ submission" from_work_dir="OUT/ddbj/mss.ann"/> | |
85 <data name="g_fna" format="fasta" label="Genome sequences in fasta format" from_work_dir="OUT/genome.fna"/> | |
86 <data name="p_faa" format="fasta" label="Predicted proteins (fasta)" from_work_dir="OUT/protein.faa"/> | |
87 <data name="r_fna" format="fasta" label="Predicted RNAs (fasta)" from_work_dir="OUT/rna.fna"/> | |
88 <data name="c_fna" format="fasta" label="Predicted CDs (fasta)" from_work_dir="OUT/cds.fna"/> | |
89 <data name="stats" format="tabular" label="overall statistics" from_work_dir="OUT/statistics.txt"/> | |
90 </outputs> | |
91 <tests> | |
92 <test> | |
93 <param name="genome_input" value="test.genome.fna"/> | |
94 <param name="fast" value="true"/> | |
95 <param name="inputtre" value="HOG1.tre,HOG2.tre,HOG3.tre,HOG4.tre,HOG5.tre"/> | |
96 <output name="stats" file="statistics.txt"/> | |
97 </test> | |
98 </tests> | |
99 <help><![CDATA[ | |
100 DFAST is a flexible and customizable pipeline for prokaryotic genome annotation as well as data submission to the | |
101 INSDC. It is originally developed as the background engine for the DFAST web service and is also available as a | |
102 stand-alone command-line tool. | |
103 | |
104 DFAST can annotate a typical-sized bacterial genome within several minutes. In addition to the conventional | |
105 homology search, it features unique functions such as orthologous gene assignment between reference genomes, | |
106 pseudo/frameshifted gene prediction, and conserved domain search. | |
107 | |
108 This galaxy tool may be incomplete, please let us know if there is any missing functionality. | |
109 ]]></help> | |
110 <expand macro="citations" /> | |
111 </tool> |