Mercurial > repos > iuc > funannotate_compare

annotate funannotate_compare.xml @ 2:cf9367edad93 draft

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"planemo upload commit 9cbeba115a6e13dd4c007065b7d77dcb400f72fb"
author iuc
date Thu, 25 Nov 2021 09:38:45 +0000
parents 5760412495fb
children fc651e59ac34
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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 <requirements>
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7 <expand macro="requirements" />
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8 </requirements>
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9 <version_command>funannotate check --show-versions</version_command>
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10 <command><![CDATA[
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11 #set $inputs = ""
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12 #for i, f in enumerate($input):
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13 #set $inputs = $inputs + " input" + str($i) + ".gbk"
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14 ln -s '$f' input${i}.gbk &&
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15 #end for
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16
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17 funannotate compare
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18 --input
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19
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20 $inputs
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21
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22 --out output
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23
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24 --database '$database.fields.path'
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25
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26 #if $run_dnds in ['estimate', 'full']:
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27 --run_dnds ${run_dnds}
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28 #end if
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29
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30 ## TODO add --outgroup option some day (hard to get an up to date/customizable list)
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31
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32 --go_fdr ${go_fdr}
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33
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34 --heatmap_stdev ${heatmap_stdev}
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35
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36 --num_orthos ${num_orthos}
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37
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38 #if $proteinortho:
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39 --proteinortho '${proteinortho}'
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40 #end if
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41
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42 --ml_method ${ml.ml_method}
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43
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44 #if $ml.ml_method == 'raxml':
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45 --bootstrap '${ml.bootstrap}'
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46 #end if
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47
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48 --cpus \${GALAXY_SLOTS:-2}
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49
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50 &&
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51
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52 mkdir -p '$output.files_path' &&
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53 cp -R output/* '$output.files_path' &&
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54 cp output/index.html '$output'
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55 ]]></command>
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56 <inputs>
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57 <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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58
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59 <param name="database" label="Funannotate database" type="select">
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60 <options from_data_table="funannotate">
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61 <column name="value" index="0" />
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62 <column name="name" index="1" />
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63 <column name="path" index="3" />
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64 <filter type="sort_by" column="0" />
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65 <filter type="static_value" column="2" value="1.0" />
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66 </options>
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67 </param>
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68
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69 <param argument="--run_dnds" type="select" label="Calculate dN/dS ratio on all orthologs">
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70 <option value="no" selected="True">No</option>
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71 <option value="estimate">estimate</option>
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72 <option value="full">full</option>
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73 </param>
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74
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75 <param argument="--go_fdr" type="float" value="0.05" label="P-value for FDR GO-enrichment" />
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76 <param argument="--heatmap_stdev" type="float" value="1.0" label="Cut-off for heatmap" />
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77 <param argument="--num_orthos" type="integer" value="500" label="Number of Single-copy orthologs to use for ML" />
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78 <param argument="--proteinortho" type="data" format="tabular" optional="true" label="Proteinortho POFF results" help="TSV format, if available"/>
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79
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80 <conditional name="ml">
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81 <param argument="--ml_method" type="select" label="Maximum Likelihood method">
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82 <option value="iqtree" selected="True">iqtree</option>
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83 <option value="raxml">raxml</option>
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84 </param>
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85 <when value="iqtree" />
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86 <when value="raxml">
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87 <param argument="--bootstrap" type="integer" value="100" label="Number of boostrap replicates to run with RAxML" />
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88 </when>
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89 </conditional>
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90 </inputs>
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91 <outputs>
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92 <data name='output' format='html' label="${tool.name} on ${on_string}: report" />
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93 </outputs>
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94 <tests>
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95 <test>
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96 <param name="input" value="compare/Genus_species.gbk,compare/Other_species.gbk,compare/Other_beast.gbk,compare/Yet_another.gbk" />
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97 <param name="database" value="2021-07-20-120000" />
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98 <conditional name="ml">
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99 <param name="ml_method" value="raxml" />
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100 </conditional>
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101 <output name="output">
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102 <assert_contents>
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103 <has_text text="Report generated on:" />
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104 </assert_contents>
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105 </output>
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106 </test>
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107 </tests>
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108 <help><![CDATA[
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109 Funannotate_ compare
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110 --------------------
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111
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112 Funannotate_ is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes).
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113
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114 This script does light-weight comparative genomics between funannotated genomes. Output
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115 is graphs, phylogeny, CSV files, etc --> visualized in web-browser.
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116
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117 .. _Funannotate: http://funannotate.readthedocs.io
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118 ]]></help>
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119 <expand macro="citations" />
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120 </tool>