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annotate compleasm.xml @ 2:95716c25b2ab draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm/ commit 9c5d5e6f1813e5c0fd496a828a1fb5e3120f188c
author iuc
date Thu, 25 Sep 2025 11:37:36 +0000
parents a5671f66f255
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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[
1
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14 mkdir -p 'galaxy_db/' &&
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15 ln -s '${busco_database.fields.path}/lineages/${lineage_dataset}/' 'galaxy_db/${lineage_dataset}' &&
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16 ## Create a compleasm-specific empty file to avoid redownloading the lineage data (https://github.com/huangnengCSU/compleasm/blob/0.2.6/compleasm.py#L165)
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17 touch 'galaxy_db/${lineage_dataset}.done' &&
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19 compleasm run
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20 -a '$input'
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21 -o galaxy_output
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22 --mode $mode
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23 -L 'galaxy_db'
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24 -l '$lineage_dataset'
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25 -t "\${GALAXY_SLOTS:-1}"
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27 #if str($specified_contigs) != '':
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28 --specified_contigs '$specified_contigs'
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29 #end if
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31 ]]></command>
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32 <inputs>
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33 <param argument="-a" name="input" type="data" format="fasta" label="Input genome file"/>
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34 <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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35 <option value="busco" selected="true">BUSCO</option>
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36 <option value="lite">Lite</option>
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37 </param>
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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
0
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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 <option value="summary">summary</option>
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53 </param>
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54
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55 <param name="busco_database" label="Choose the BUSCO database to be used" type="select" multiple="false">
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56 <options from_data_table="busco_database"/>
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57 </param>
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58
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59 <param name="lineage_dataset" type="select" label="Lineage">
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60 <expand macro="lineages"/>
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61 </param>
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62 </inputs>
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63
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64 <outputs>
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65 <data name='full_table_busco' format='tsv' label="${tool.name} on ${on_string}: full table BUSCO" from_work_dir="galaxy_output/*_odb10/full_table_busco_format.tsv">
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66 <filter>outputs and 'full_table_busco' in outputs</filter>
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67 </data>
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68 <data name='full_table' format='tsv' label="${tool.name} on ${on_string}: full table" from_work_dir="galaxy_output/*_odb10/full_table.tsv">
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69 <filter>outputs and 'full_table' in outputs</filter>
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70 </data>
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71 <data name='miniprot' format='gff3' label="${tool.name} on ${on_string}: Miniprot" from_work_dir="galaxy_output/*_odb10/miniprot_output.gff">
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72 <filter>outputs and 'miniprot' in outputs</filter>
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73 </data>
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74 <data name='translated_protein' format='fasta' label="${tool.name} on ${on_string}: Translated protein" from_work_dir="galaxy_output/*_odb10/translated_protein.fasta">
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75 <filter>outputs and 'translated_protein' in outputs</filter>
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76 </data>
2
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77 <data name='summary' format='txt' label="${tool.name} on ${on_string}: Summary" from_work_dir="galaxy_output/summary.txt">
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78 <filter>outputs and 'summary' in outputs</filter>
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79 </data>
0
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80 </outputs>
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81
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82 <tests>
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83 <test expect_num_outputs="4">
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84 <param name="input" value="small_genome.fasta"/>
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85 <param name="mode" value="busco"/>
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86 <param name="outputs" value="full_table_busco,full_table,miniprot,translated_protein"/>
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87 <param name="busco_database" value="entomoplasmatales_odb10"/>
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88 <param name="lineage_dataset" value="entomoplasmatales_odb10"/>
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89 <output name="full_table_busco">
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90 <assert_contents>
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91 <has_text text="Busco id"/>
1
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92 <has_text text="496at186328&#009;Missing"/>
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93 <has_text text="165at186328&#009;Complete"/>
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94 <has_text text="421at186328&#009;Complete"/>
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95 <has_text text="90at186328&#009;Complete"/>
0
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96 </assert_contents>
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97 </output>
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98 <output name="full_table">
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99 <assert_contents>
1
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100 <has_text text="Gene&#009;Status"/>
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101 <has_text text="496at186328&#009;Missing"/>
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102 <has_text text="165at186328&#009;Single"/>
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103 <has_text text="421at186328&#009;Single"/>
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104 <has_text text="90at186328&#009;Single"/>
0
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105 </assert_contents>
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106 </output>
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107 <output name="miniprot">
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108 <assert_contents>
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109 <has_text text="##gff-version 3"/>
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110 </assert_contents>
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111 </output>
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112 <output name="translated_protein">
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113 <assert_contents>
1
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114 <has_text text="EKDFYQELGVSSDASPEEIKRAYRKLARDLHPDANPGNPAA"/>
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115 <has_text text="AASITILEGLEAVRKRPGMYIGSTGERGLHHLIWEVVD"/>
0
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116 </assert_contents>
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117 </output>
1
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118 <assert_stdout>
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119 <has_text text="S:1.20%, 4"/>
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120 </assert_stdout>
0
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121 </test>
2
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122 <test expect_num_outputs="1">
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123 <param name="input" value="small_genome.fasta"/>
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124 <param name="mode" value="lite"/>
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125 <param name="outputs" value="summary"/>
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126 <param name="busco_database" value="entomoplasmatales_odb10"/>
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127 <param name="lineage_dataset" value="entomoplasmatales_odb10"/>
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128 <output name="summary">
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129 <assert_contents>
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130 <has_text text="## lineage: entomoplasmatales_odb10"/>
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131 <has_text text="M:96.08%, 319"/>
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132 <has_text text="N:332"/>
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133 </assert_contents>
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134 </output>
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135 <assert_stdout>
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136 <has_text text="S:3.01%, 10"/>
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137 </assert_stdout>
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138 </test>
0
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139 </tests>
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140 <help><![CDATA[
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141
1
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142 compleasm_ assesses genome completeness based on genome assembly.
0
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143
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144 .. _compleasm: https://github.com/huangnengCSU/compleasm
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145
1
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146 ]]>
0
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147 </help>
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148 <expand macro="citation"/>
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149 </tool>