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annotate braker.xml @ 1:ca7c12566894 draft

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"planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit 85d503dfb53a60847034bfc655d334e1e6307d28"
author genouest
date Thu, 21 Oct 2021 09:56:31 +0000
parents e50ea151f221
children
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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@">
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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2 <description></description>
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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6 <requirements>
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7 <expand macro="requirements" />
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8 </requirements>
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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9 <version_command><![CDATA[braker.pl --version; $GENEMARK_PATH/gmes_petap.pl | grep version]]></version_command>
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10 <command><![CDATA[
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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11 if [ -z "\$GENEMARK_PATH" ] ; then echo "GeneMark is not installed on this Galaxy server." >&2 ; exit 1 ; fi &&
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12 if [ ! -f "\$GENEMARK_PATH/gmes_petap.pl" ] ; then echo "GeneMark is not installed properly on this Galaxy server." >&2 ; exit 1 ; fi &&
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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13 ## GeneMark only search for license in ~/.gm_key
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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14 cp '${genemark_license}' ~/.gm_key &&
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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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16 braker.pl
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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17 --genome '${genome}'
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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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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
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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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
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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30 #if not $evidences.bam and not $evidences.prot_seq
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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31 --esmode
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32 #end if
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33
1
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34 ## Both proteins and rnaseq hints, use etpmode
ca7c12566894 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit 85d503dfb53a60847034bfc655d334e1e6307d28"
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35 #if $evidences.bam and $evidences.prot_seq
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36 --etpmode
ca7c12566894 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit 85d503dfb53a60847034bfc655d334e1e6307d28"
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37 #end if
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38
0
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39 #if $output_format == 'gff3'
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40 --gff3
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41 #end if
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42
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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43 $genemark.fungus
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44
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45 $augustus.crf
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46 --rounds $augustus.rounds
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47
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48 $advanced.UTR
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49
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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50 $advanced.filterOutShort
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51
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52 #if $advanced.eval:
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53 --eval ${advanced.eval}
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54 #end if
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55
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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56 #if $advanced.eval_pseudo:
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57 --eval_pseudo ${advanced.eval_pseudo}
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58 #end if
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59
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60 --cores \${GALAXY_SLOTS:-2}
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61 ]]></command>
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62 <inputs>
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63 <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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64
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65 <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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66
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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67 <param argument="--softmasking" type="boolean" checked="false" truevalue="--softmasking" falsevalue="" label="Genome sequence is soft-masked" />
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68
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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69 <section name="evidences" expanded="true" title="Evidences">
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70 <param argument="--bam" type="data" format="bam" optional="true" label="RNA-seq mapped to genome to train Augustus/GeneMark" />
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71 <param argument="--prot_seq" type="data" format="fasta" optional="true" label="Proteins to map to genome" />
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72 </section>
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73
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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74 <section name="genemark" expanded="true" title="GeneMark">
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75 <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)" />
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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76 </section>
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77
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78 <section name="augustus" expanded="true" title="Augustus">
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79 <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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80 <param argument="--rounds" type="integer" value="5" label="Number of optimization rounds used in optimize_augustus.pl" />
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81 </section>
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82
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83 <section name="advanced" expanded="false" title="Advanced">
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84 <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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85 <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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86 <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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87 <param argument="--eval_pseudo" type="data" format="gff3" optional="true" label="File with pseudogenes that will be excluded from accuracy evaluation" />
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88 </section>
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89
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90 <param name="output_format" type="select" label="Output format">
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91 <option value="gtf" selected="true">GTF</option>
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92 <option value="gff3">GFF3</option>
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93 </param>
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94 </inputs>
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95 <outputs>
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96 <data name='output_gtf' format='gtf' label="${tool.name} on ${on_string}: annotation" from_work_dir="braker/braker.gtf">
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97 <filter>output_format == 'gtf'</filter>
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98 </data>
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99 <data name='output_gff' format='gff3' label="${tool.name} on ${on_string}: annotation" from_work_dir="braker/braker.gff3">
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100 <filter>output_format == 'gff3'</filter>
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101 </data>
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102 </outputs>
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103 <tests>
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104 <!-- Disable next 2 for CI (it should pass locally)-->
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105 <!--test>
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106 <param name="genome" value="genome_masked.fa" />
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107 <param name="softmasking" value="true" />
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108 <param name="genemark_license" value="genemark_license.gm_key" />
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109 <output name="output_gtf" file="out_genome/braker.gtf" sort="true" />
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110 </test>
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111 <test>
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112 <param name="genome" value="genome_masked.fa" />
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113 <param name="softmasking" value="true" />
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114 <param name="genemark_license" value="genemark_license.gm_key" />
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115 <param name="output_format" value="gff3" />
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116 <output name="output_gff" file="out_genome/braker.gff3" sort="true" />
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117 </test-->
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118 <!-- following 2 tests throw an error because test dataset is too small -->
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119 <!--test>
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120 <param name="genome" value="genome_masked.fa" />
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121 <param name="softmasking" value="true" />
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122 <param name="genemark_license" value="genemark_license.gm_key" />
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123 <section name="evidences">
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124 <param name="bam" value="SRR7458692.bam" />
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125 </section>
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126 <output name="output_gtf" file="out_bam/braker.gtf" sort="true" />
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127 </test>
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128 <test>
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129 <param name="genome" value="genome_masked.fa" />
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130 <param name="softmasking" value="true" />
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131 <param name="genemark_license" value="genemark_license.gm_key" />
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132 <section name="evidences">
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133 <param name="prot_seq" value="proteins.fa" />
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134 </section>
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135 <output name="output_gtf" file="out_prot/braker.gtf" sort="true" />
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136 </test-->
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137 </tests>
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138 <help><![CDATA[
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139 Braker_
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140 -------
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141
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142 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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143
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144 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.
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145
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146 .. _Braker: https://github.com/Gaius-Augustus/BRAKER
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147 ]]></help>
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148 <expand macro="citations" />
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149 </tool>