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annotate braker.xml @ 0:e50ea151f221 draft

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"planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
author genouest
date Tue, 05 Oct 2021 12:35:42 +0000
parents
children ca7c12566894
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e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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1 <tool id="braker" name="Braker genome annotation" profile="20.01" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
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2 <description></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 <requirements>
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7 <expand macro="requirements" />
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8 </requirements>
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9 <version_command><![CDATA[braker.pl --version; $GENEMARK_PATH/gmes_petap.pl | grep version]]></version_command>
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10 <command><![CDATA[
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11 if [ -z "\$GENEMARK_PATH" ] ; then echo "GeneMark is not installed on this Galaxy server." >&2 ; exit 1 ; fi &&
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12 if [ ! -f "\$GENEMARK_PATH/gmes_petap.pl" ] ; then echo "GeneMark is not installed properly on this Galaxy server." >&2 ; exit 1 ; fi &&
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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13 ## GeneMark only search for license in ~/.gm_key
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14 cp '${genemark_license}' ~/.gm_key &&
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15
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16 braker.pl
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17 --genome '${genome}'
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18
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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19 $softmasking
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20
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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21 #if $evidences.bam:
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22 --bam ${evidences.bam}
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23 #end if
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24
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25 #if $evidences.prot_seq:
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26 --prot_seq ${evidences.prot_seq}
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27 #end if
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28
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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29 ## No hints, use esmode
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30 #if not $evidences.bam and not $evidences.prot_seq
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31 --esmode
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32 #end if
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33
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34 #if $output_format == 'gff3'
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35 --gff3
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36 #end if
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37
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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38 $genemark.fungus
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39
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40 $augustus.crf
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41 --rounds $augustus.rounds
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42
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43 $advanced.UTR
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44
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45 $advanced.filterOutShort
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46
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47 #if $advanced.eval:
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48 --eval ${advanced.eval}
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49 #end if
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50
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51 #if $advanced.eval_pseudo:
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52 --eval_pseudo ${advanced.eval_pseudo}
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53 #end if
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54
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55 --cores \${GALAXY_SLOTS:-2}
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56 ]]></command>
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57 <inputs>
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58 <param name="genemark_license" type="data" format="txt" label="GeneMark license file" help="Braker uses GeneMark, which is not a free software, to use it download and unzip a license from http://topaz.gatech.edu/GeneMark/license_download.cgi (ES/ET/EP version). GeneMark needs to be installed manually by Galaxy administrators." />
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59
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60 <param argument="--genome" type="data" format="fasta" label="Assembly to annotate" help="The assembly should be soft-masked (with RepeatMasker for example)" />
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61
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62 <param argument="--softmasking" type="boolean" checked="false" truevalue="--softmasking" falsevalue="" label="Genome sequence is soft-masked" />
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63
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64 <section name="evidences" expanded="true" title="Evidences">
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65 <param argument="--bam" type="data" format="bam" optional="true" label="RNA-seq mapped to genome to train Augustus/GeneMark" />
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66 <param argument="--prot_seq" type="data" format="fasta" optional="true" label="Proteins to map to genome" />
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67 </section>
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68
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69 <section name="genemark" expanded="true" title="GeneMark">
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70 <param argument="--fungus" type="boolean" checked="false" truevalue="--fungus" falsevalue="" label="Fungal genome" help="GeneMark-EX option, run algorithm with branch point model (most useful for fungal genomes)" />
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71 </section>
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72
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73 <section name="augustus" expanded="true" title="Augustus">
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74 <param argument="--crf" type="boolean" checked="false" truevalue="--crf" falsevalue="" label="Use CRF training for Augustus" help="Alternate training method (Conditional Random Field)" />
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75 <param argument="--rounds" type="integer" value="5" label="Number of optimization rounds used in optimize_augustus.pl" />
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76 </section>
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77
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78 <section name="advanced" expanded="false" title="Advanced">
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79 <param argument="--UTR" type="boolean" checked="false" truevalue="--UTR=on" falsevalue="" label="" help="Experimental, requires RNASeq data (bam) and a softmasked genome" />
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80 <param argument="--filterOutShort" type="boolean" checked="false" truevalue="--filterOutShort" falsevalue="" label="Filter out too short traingin gene predicted by GeneMark-EX" />
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81 <param argument="--eval" type="data" format="gtf" optional="true" label="Reference set to evaluate predictions" help="using evaluation scripts from GaTech" />
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82 <param argument="--eval_pseudo" type="data" format="gff3" optional="true" label="File with pseudogenes that will be excluded from accuracy evaluation" />
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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83 </section>
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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84
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85 <param name="output_format" type="select" label="Output format">
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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86 <option value="gtf" selected="true">GTF</option>
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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87 <option value="gff3">GFF3</option>
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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88 </param>
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89 </inputs>
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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90 <outputs>
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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91 <data name='output_gtf' format='gtf' label="${tool.name} on ${on_string}: annotation" from_work_dir="braker/braker.gtf">
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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92 <filter>output_format == 'gtf'</filter>
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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93 </data>
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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94 <data name='output_gff' format='gff3' label="${tool.name} on ${on_string}: annotation" from_work_dir="braker/braker.gff3">
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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95 <filter>output_format == 'gff3'</filter>
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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96 </data>
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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97 </outputs>
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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98 <tests>
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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99 <!-- Disable next 2 for CI (it should pass locally)-->
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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100 <!--test>
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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101 <param name="genome" value="genome_masked.fa" />
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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102 <param name="softmasking" value="true" />
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103 <param name="genemark_license" value="genemark_license.gm_key" />
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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104 <output name="output_gtf" file="out_genome/braker.gtf" sort="true" />
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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105 </test>
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106 <test>
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107 <param name="genome" value="genome_masked.fa" />
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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108 <param name="softmasking" value="true" />
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109 <param name="genemark_license" value="genemark_license.gm_key" />
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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110 <param name="output_format" value="gff3" />
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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111 <output name="output_gff" file="out_genome/braker.gff3" sort="true" />
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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112 </test-->
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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113 <!-- following 2 tests throw an error because test dataset is too small -->
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114 <!--test>
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115 <param name="genome" value="genome_masked.fa" />
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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116 <param name="softmasking" value="true" />
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117 <param name="genemark_license" value="genemark_license.gm_key" />
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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118 <section name="evidences">
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119 <param name="bam" value="SRR7458692.bam" />
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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120 </section>
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121 <output name="output_gtf" file="out_bam/braker.gtf" sort="true" />
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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122 </test>
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123 <test>
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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124 <param name="genome" value="genome_masked.fa" />
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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125 <param name="softmasking" value="true" />
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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126 <param name="genemark_license" value="genemark_license.gm_key" />
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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127 <section name="evidences">
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128 <param name="prot_seq" value="proteins.fa" />
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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129 </section>
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130 <output name="output_gtf" file="out_prot/braker.gtf" sort="true" />
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131 </test-->
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132 </tests>
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133 <help><![CDATA[
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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134 Braker_
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135 -------
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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136
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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137 Braker_ allows for fully automated training of the gene prediction tools GeneMark-EX and AUGUSTUS from RNA-Seq and/or protein homology information, and that integrates the extrinsic evidence from RNA-Seq and protein homology information into the prediction.
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138
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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139 In contrast to other available methods that rely on protein homology information, BRAKER reaches high gene prediction accuracy even in the absence of the annotation of very closely related species and in the absence of RNA-Seq data.
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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140
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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141 .. _Braker: https://github.com/Gaius-Augustus/BRAKER
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142 ]]></help>
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143 <expand macro="citations" />
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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144 </tool>