Mercurial > repos > iuc > compleasm

annotate compleasm.xml @ 0:803d166831c8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm/ commit 025282d56217bb501fcae8500546dec4ddf63949
author iuc
date Wed, 24 Jul 2024 17:43:01 +0000
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803d166831c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm/ commit 025282d56217bb501fcae8500546dec4ddf63949
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1 <tool id="compleasm" name="compleasm" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
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2 <description>completeness of genome assemblies</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 <xrefs>
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7 <xref type="bio.tools">compleasm</xref>
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8 </xrefs>
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9 <requirements>
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10 <requirement type="package" version="@TOOL_VERSION@">compleasm</requirement>
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11 </requirements>
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12 <version_command>compleasm --version</version_command>
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13 <command><![CDATA[
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15 mkdir -p galaxy_db &&
803d166831c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm/ commit 025282d56217bb501fcae8500546dec4ddf63949
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16 cp -r '${busco_database.fields.path}/lineages/${lineage_dataset}/' 'galaxy_db/' &&
803d166831c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm/ commit 025282d56217bb501fcae8500546dec4ddf63949
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18 compleasm run
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19 -a '$input'
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20 -o galaxy_output
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21 --mode $mode
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22 -L 'galaxy_db'
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23 -l '$lineage_dataset'
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24 -t "\${GALAXY_SLOTS:-1}"
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26 #if str($specified_contigs) != '':
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27 --specified_contigs '$specified_contigs'
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28 #end if
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29
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30 ]]></command>
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31 <inputs>
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32 <param argument="-a" name="input" type="data" format="fasta" label="Input genome file"/>
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33 <param name="mode" type="select" label="The mode of evaluation" help="If you want to use hmmsearch, select BUSCO mode. Otherwise, select lite mode">
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34 <option value="busco" selected="true">BUSCO</option>
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35 <option value="lite">Lite</option>
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36 </param>
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37
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38 <param argument="--specified_contigs" type="text" label="Specify the contigs to be evaluated" optional="true" help="e.g. chr1 chr2 chr3. If not specified, all contigs will be evaluated">
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39 <sanitizer invalid_char="">
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40 <valid initial="string.letters,string.digits">
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41 <add value="_" />
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42 </valid>
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43 </sanitizer>
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44 <validator type="regex">[0-9a-zA-Z_ ]+</validator>
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45 </param>
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46
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47 <param name="outputs" type="select" multiple="true" label="Which outputs should be generated">
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48 <option value="full_table_busco" selected="true">full busco table</option>
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49 <option value="full_table">full table</option>
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50 <option value="miniprot">miniprot</option>
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51 <option value="translated_protein">translated proteins</option>
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52 </param>
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53
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54 <param name="busco_database" label="Choose the BUSCO database to be used" type="select" multiple="false">
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55 <options from_data_table="busco_database"/>
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56 </param>
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57
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58 <param name="lineage_dataset" type="select" label="Lineage">
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59 <expand macro="lineages"/>
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60 </param>
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61 </inputs>
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62
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63 <outputs>
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64 <data name='full_table_busco' format='tsv' label="${tool.name} on ${on_string}: full table BUSCO" from_work_dir="galaxy_output/*_odb10/full_table_busco_format.tsv">
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65 <filter>outputs and 'full_table_busco' in outputs</filter>
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66 </data>
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67 <data name='full_table' format='tsv' label="${tool.name} on ${on_string}: full table" from_work_dir="galaxy_output/*_odb10/full_table.tsv">
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68 <filter>outputs and 'full_table' in outputs</filter>
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69 </data>
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70 <data name='miniprot' format='gff3' label="${tool.name} on ${on_string}: Miniprot" from_work_dir="galaxy_output/*_odb10/miniprot_output.gff">
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71 <filter>outputs and 'miniprot' in outputs</filter>
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72 </data>
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73 <data name='translated_protein' format='fasta' label="${tool.name} on ${on_string}: Translated protein" from_work_dir="galaxy_output/*_odb10/translated_protein.fasta">
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74 <filter>outputs and 'translated_protein' in outputs</filter>
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75 </data>
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76 </outputs>
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77
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78 <tests>
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79 <test expect_num_outputs="4">
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80 <param name="input" value="small_genome.fasta"/>
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81 <param name="mode" value="busco"/>
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82 <param name="outputs" value="full_table_busco,full_table,miniprot,translated_protein"/>
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83 <param name="busco_database" value="eukaryota_odb10"/>
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84 <param name="lineage_dataset" value="eukaryota_odb10"/>
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85 <output name="full_table_busco">
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86 <assert_contents>
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87 <has_text text="Busco id"/>
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88 <has_text text="Missing"/>
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89 </assert_contents>
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90 </output>
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91 <output name="full_table">
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92 <assert_contents>
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93 <has_text text="Gene"/>
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94 <has_text text="Missing"/>
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95 </assert_contents>
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96 </output>
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97 <output name="miniprot">
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98 <assert_contents>
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99 <has_text text="##gff-version 3"/>
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100 </assert_contents>
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101 </output>
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102 <output name="translated_protein">
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103 <assert_contents>
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104 <has_text text="GGWLIGNGGAGGSGAAGVNGGAGGNGGAGGNGGAGG"/>
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105 <has_text text="AAVFADRGAHVVLAVRNLEKGNAARARIMAARPGAHVTLQQLDLCSLDSVRAAADALRTAYPRIDVLINNAGVMW"/>
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106 </assert_contents>
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107 </output>
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108 </test>
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109 </tests>
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110 <help><![CDATA[
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111
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112 compleasm_ assesses genome completeness based on genome assembly.
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113
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114 .. _compleasm: https://github.com/huangnengCSU/compleasm
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115
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116 ]]>
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117 </help>
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118 <expand macro="citation"/>
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119 </tool>