Mercurial > repos > iuc > compleasm

annotate compleasm.xml @ 2:47f9f4d13d2c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm/ commit ae898f7550e37679f70156ce8244b35a31b496de
author iuc
date Mon, 18 Mar 2024 16:05:48 +0000
parents 79413aecc398
children cfec9601b25d
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1 <tool id="compleasm" name="compleasm" version="@TOOL_VERSION@+galaxy0" 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 <command><![CDATA[
1
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14 mkdir -p galaxy_db &&
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15 cp -r '${busco_database.fields.path}/lineages/${lineage_dataset}/' 'galaxy_db/' &&
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16
0
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17 compleasm run
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18 -a '$input'
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19 -o galaxy_output
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20 --mode $mode
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21 -L 'galaxy_db'
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22 -l '$lineage_dataset'
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24 #if str($specified_contigs) != '':
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25 --specified_contigs '$specified_contigs'
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26 #end if
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28 ]]></command>
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29 <inputs>
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30 <param argument="-a" name="input" type="data" format="fasta" label="Input genome file"/>
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31 <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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32 <option value="busco" selected="true">BUSCO</option>
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33 <option value="lite">Lite</option>
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34 </param>
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35
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36 <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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37 <sanitizer invalid_char="">
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38 <valid initial="string.letters,string.digits">
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39 <add value="_" />
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40 </valid>
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41 </sanitizer>
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42 <validator type="regex">[0-9a-zA-Z_ ]+</validator>
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43 </param>
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44
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45 <param name="outputs" type="select" multiple="true" label="Which outputs should be generated">
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46 <option value="full_table_busco" selected="true">full busco table</option>
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47 <option value="full_table">full table</option>
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48 <option value="miniprot">miniprot</option>
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49 <option value="translated_protein">translated proteins</option>
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50 </param>
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51
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52 <param name="busco_database" label="Choose the BUSCO database to be used" type="select" multiple="false">
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53 <options from_data_table="busco_database"/>
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54 </param>
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55
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56 <param name="lineage_dataset" type="select" label="Lineage">
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57 <expand macro="lineages"/>
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58 </param>
0
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59 </inputs>
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61 <outputs>
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62 <data name='full_table_busco' format='tsv' label="${tool.name} on ${on_string}: full table BUSCO" from_work_dir="galaxy_output/*_odb10/full_table_busco_format.tsv">
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63 <filter>outputs and 'full_table_busco' in outputs</filter>
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64 </data>
1
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65 <data name='full_table' format='tsv' label="${tool.name} on ${on_string}: full table" from_work_dir="galaxy_output/*_odb10/full_table.tsv">
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66 <filter>outputs and 'full_table' in outputs</filter>
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67 </data>
1
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68 <data name='miniprot' format='gff3' label="${tool.name} on ${on_string}: Miniprot" from_work_dir="galaxy_output/*_odb10/miniprot_output.gff">
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69 <filter>outputs and 'miniprot' in outputs</filter>
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70 </data>
1
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71 <data name='translated_protein' format='fasta' label="${tool.name} on ${on_string}: Translated protein" from_work_dir="galaxy_output/*_odb10/translated_protein.fasta">
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72 <filter>outputs and 'translated_protein' in outputs</filter>
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73 </data>
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74 </outputs>
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75
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76 <tests>
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77 <test expect_num_outputs="4">
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78 <param name="input" value="small_genome.fasta"/>
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79 <param name="mode" value="busco"/>
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80 <param name="outputs" value="full_table_busco,full_table,miniprot,translated_protein"/>
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81 <param name="busco_database" value="eukaryota_odb10"/>
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82 <param name="lineage_dataset" value="eukaryota_odb10"/>
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83 <output name="full_table_busco">
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84 <assert_contents>
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85 <has_text text="Busco id"/>
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86 <has_text text="Missing"/>
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87 </assert_contents>
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88 </output>
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89 <output name="full_table">
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90 <assert_contents>
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91 <has_text text="Gene"/>
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92 <has_text text="Missing"/>
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93 </assert_contents>
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94 </output>
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95 <output name="miniprot">
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96 <assert_contents>
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97 <has_text text="##gff-version 3"/>
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98 </assert_contents>
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99 </output>
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100 <output name="translated_protein">
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101 <assert_contents>
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102 <has_text text="GGWLIGNGGAGGSGAAGVNGGAGGNGGAGGNGGAGG"/>
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103 <has_text text="AAVFADRGAHVVLAVRNLEKGNAARARIMAARPGAHVTLQQLDLCSLDSVRAAADALRTAYPRIDVLINNAGVMW"/>
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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
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110 compleasm_ assesses genome completeness based on genome assembly.
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111
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112 .. _compleasm: https://github.com/huangnengCSU/compleasm
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113
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114 ]]>
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115 </help>
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116 <expand macro="citation"/>
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117 </tool>