Mercurial > repos > leomrtns > dfast

annotate dfast.xml @ 0:6ddc8a6503e7 draft default tip

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