Mercurial > repos > iuc > funannotate_compare

annotate funannotate_compare.xml @ 9:d6f107f8e241 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate commit 0b6712733bce2e4ec6b276a6dec9c7b4bff5a5cd
author iuc
date Sun, 09 Mar 2025 09:33:27 +0000
parents ea5944e50e36
children
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1 <tool id="funannotate_compare" name="Funannotate compare" profile="20.01" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
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2 <description>annotations</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="biotools" />
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7 <requirements>
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8 <expand macro="requirements" />
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9 </requirements>
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10 <version_command>funannotate check --show-versions</version_command>
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11 <command><![CDATA[
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12 ## Needed by some subprocess invoked internally
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13 ## https://github.com/nextgenusfs/funannotate/issues/905
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14 export FUNANNOTATE_DB='$database.fields.path' &&
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16 ## show detailed info about the reference DB on stdout
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17 funannotate database &&
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18
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19 #set $inputs = ""
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20 #for i, f in enumerate($input):
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21 #set $inputs = $inputs + " input" + str($i) + ".gbk"
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22 ln -s '$f' input${i}.gbk &&
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23 #end for
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24
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25 funannotate compare
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26 --input
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27
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28 $inputs
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29
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30 --out output
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31
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32 --database '$database.fields.path'
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33
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34 #if $run_dnds in ['estimate', 'full']:
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35 --run_dnds ${run_dnds}
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36 #end if
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37
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38 #if $outgroup
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39 --outgroup '$outgroup'
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40 #end if
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41
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42 --go_fdr ${go_fdr}
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43
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44 --heatmap_stdev ${heatmap_stdev}
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45
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46 --num_orthos ${num_orthos}
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47
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48 #if $proteinortho:
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49 --proteinortho '${proteinortho}'
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50 #end if
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51
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52 --ml_method ${ml.ml_method}
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53
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54 #if $ml.ml_method == 'raxml':
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55 --bootstrap '${ml.bootstrap}'
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56 #end if
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57
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58 --cpus \${GALAXY_SLOTS:-2}
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59
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60 &&
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61
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62 mkdir -p '$output.files_path' &&
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63 cp -R output/* '$output.files_path' &&
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64 cp output/index.html '$output'
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65 ]]></command>
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66 <inputs>
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67 <param argument="--input" type="data" format="genbank" multiple="true" label="Genome annotations in genbank format" help="Outputs from 'Funannotate predict annotation' tool" />
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68
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69 <param name="database" label="Funannotate database" type="select">
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70 <options from_data_table="funannotate">
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71 <column name="value" index="0" />
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72 <column name="name" index="1" />
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73 <column name="path" index="3" />
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74 <filter type="sort_by" column="0" reverse_sort_order="true"/>
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75 <filter type="static_value" column="2" value="1.0" />
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76 </options>
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77 </param>
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78
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79 <param argument="--run_dnds" type="select" label="Calculate dN/dS ratio on all orthologs">
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80 <option value="no" selected="True">No</option>
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81 <option value="estimate">estimate</option>
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82 <option value="full">full</option>
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83 </param>
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84
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85 <param argument="--go_fdr" type="float" value="0.05" label="P-value for FDR GO-enrichment" />
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86 <param argument="--heatmap_stdev" type="float" value="1.0" label="Cut-off for heatmap" />
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87 <param argument="--num_orthos" type="integer" value="500" label="Number of Single-copy orthologs to use for ML" />
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88 <param argument="--outgroup" type="select" optional="true" label="Outgroup species" help="Name of species to use for ML outgroup. Default: no outgroup">
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89 <options from_data_table="funannotate_options">
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90 <column name="value" index="0" />
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91 <column name="name" index="1" />
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92 <filter type="static_value" column="2" value="outgroup"/>
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93 <filter type="param_value" column="3" ref="database"/>
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94 </options>
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95 </param>
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96 <param argument="--proteinortho" type="data" format="tabular" optional="true" label="Proteinortho POFF results" help="TSV format, if available"/>
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97
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98 <conditional name="ml">
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99 <param argument="--ml_method" type="select" label="Maximum Likelihood method">
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100 <option value="iqtree" selected="True">iqtree</option>
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101 <option value="raxml">raxml</option>
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102 </param>
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103 <when value="iqtree" />
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104 <when value="raxml">
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105 <param argument="--bootstrap" type="integer" value="100" label="Number of boostrap replicates to run with RAxML" />
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106 </when>
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107 </conditional>
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108 </inputs>
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109 <outputs>
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110 <data name='output' format='html' label="${tool.name} on ${on_string}: report" />
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111 </outputs>
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112 <tests>
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113 <test>
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114 <param name="input" value="compare/Genus_species.gbk,compare/Other_species.gbk,compare/Other_beast.gbk,compare/Yet_another.gbk" />
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115 <param name="database" value="2021-07-20-120000" />
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116 <conditional name="ml">
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117 <param name="ml_method" value="raxml" />
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118 </conditional>
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119 <output name="output">
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120 <assert_contents>
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121 <has_text text="Report generated on:" />
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122 </assert_contents>
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123 </output>
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124 </test>
3
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125 <test>
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126 <param name="input" value="compare/Genus_species.gbk,compare/Other_species.gbk,compare/Other_beast.gbk,compare/Yet_another.gbk" />
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127 <param name="database" value="2021-07-20-120000" />
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128 <param name="run_dnds" value="estimate" />
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129 <conditional name="ml">
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130 <param name="ml_method" value="raxml" />
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131 </conditional>
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132 <output name="output">
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133 <assert_contents>
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134 <has_text text="Report generated on:" />
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135 </assert_contents>
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136 </output>
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137 </test>
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138 <test>
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139 <param name="input" value="compare/Genus_species.gbk,compare/Other_species.gbk,compare/Other_beast.gbk,compare/Yet_another.gbk" />
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140 <param name="database" value="2021-07-20-120000" />
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141 <param name="run_dnds" value="full" />
8
ea5944e50e36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4
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142 <param name="outgroup" value="botrytis_cinerea.dikarya"/>
3
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143 <conditional name="ml">
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144 <param name="ml_method" value="raxml" />
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145 </conditional>
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146 <output name="output">
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147 <assert_contents>
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148 <has_text text="Report generated on:" />
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149 </assert_contents>
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150 </output>
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151 </test>
0
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152 </tests>
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153 <help><![CDATA[
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154 Funannotate_ compare
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155 --------------------
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156
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157 Funannotate_ is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes).
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158
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159 This script does light-weight comparative genomics between funannotated genomes. Output
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160 is graphs, phylogeny, CSV files, etc --> visualized in web-browser.
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161
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162 .. _Funannotate: http://funannotate.readthedocs.io
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163 ]]></help>
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164 <expand macro="citations" />
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165 </tool>