Mercurial > repos > galaxyp > eggnog_mapper

annotate eggnog_mapper_annotate.xml @ 14:d9c3016f7283 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 192779247c3385704ebd98a2cc47a210fb1f4d0c
author galaxyp
date Thu, 07 Sep 2023 18:51:23 +0000 (18 months ago)
parents 844fa988236b
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1 <tool id="eggnog_mapper_annotate" name="eggNOG Mapper" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>annotation phase</description>
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3 <macros>
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4 <import>eggnog_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="version_command"/>
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8 <command detect_errors="aggressive"><![CDATA[
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9 @MERGE_ANNOTATIONS@
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10
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11 emapper.py
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12 @DB_TOKEN@
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13 -m no_search
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14 @ORTHO_SEARCH_TOKEN@
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16 @ANNOTATION_TOKEN@
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17 $output_options.no_file_comments
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18 $output_options.report_orthologs
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19 $output_options.md5
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20 --output='results'
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21 --cpu "\${GALAXY_SLOTS:-1}"
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22 --scratch_dir \${TEMP:-\$_GALAXY_JOB_TMP_DIR}
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23 --temp_dir \${TEMP:-\$_GALAXY_JOB_TMP_DIR}
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24 ]]></command>
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25 <inputs>
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26 <expand macro="db_macro"/>
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27 <expand macro="ortho_annotate_macro"/>
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29 <section name="annotation_options" title="Annotation options">
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30 <expand macro="annotation_options_macro"/>
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31 </section>
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33 <expand macro="output_options_annotate_macro"/>
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34 </inputs>
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35 <outputs>
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36 <expand macro="annotation_output_macro"/>
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37 <expand macro="annotation_orthologs_output_macro"/>
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38 </outputs>
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39 <tests>
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40 <!-- test producing annotations form seed orthologs -->
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41 <test expect_num_outputs="1">
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42 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work -->
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43 <param name="annotate_hits_table" value="DIA_nlim.emapper.seed_orthologs" ftype="tabular">
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44 <!-- this has no effect at the moment since column_names can not be set in uploads <metadata name="column_names" value="@SEED_ORTHOLOG_COLUMNS@"/> -->
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45 </param>
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46 <conditional name="annotation_options">
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47 </conditional>
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48 <section name="output_options">
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49 <param name="report_orthologs" value="false"/>
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50 <param name="no_file_comments" value="true"/>
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51 </section>
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52 <expand macro="annotations_assertion"/>
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53 <expand macro="stdout_assertion"/>
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54 </test>
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55
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56 <!-- test using chached annotations from previous run -->
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57 <test expect_num_outputs="2">
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58 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work -->
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59 <conditional name="ortho_method">
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60 <param name="m" value="cache"/>
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61 <param name="input" value="Nmar_0135.fa" ftype="fasta"/>
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62 <param name="cache" value="DIA_nlim.emapper.annotations_cached" ftype="tabular"/>
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63 </conditional>
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64 <section name="output_options">
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65 <param name="report_orthologs" value="true"/>
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66 <param name="no_file_comments" value="true"/>
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67 <param name="md5" value="true"/>
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68 </section>
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69 <expand macro="annotations_assertion" columns="22" add_metadata_columm_names=",md5" add_column_names="&#009;md5" add_column_re="\t[\d\w]+"/>
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70 <output name="no_annotations" ftype="fasta">
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71 <assert_contents>
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72 <has_n_lines n="0"/>
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73 </assert_contents>
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74 </output>
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75 <expand macro="stdout_assertion"/>
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76 </test>
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77
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78 <!-- test setting tax scope-->
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79 <test expect_num_outputs="2">
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80 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work -->
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81 <param name="annotate_hits_table" value="DIA_nlim.emapper.seed_orthologs" ftype="tabular">
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82 <!-- this has no effect at the moment since column_names can not be set in uploads <metadata name="column_names" value="@SEED_ORTHOLOG_COLUMNS@"/> -->
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83 </param>
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84 <section name="annotation_options">
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85 <param name="tax_scope" value="651137" />
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86 </section>
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87 <section name="output_options">
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88 <param name="report_orthologs" value="true"/>
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89 <param name="no_file_comments" value="true"/>
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90 </section>
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91 <expand macro="annotations_assertion"/>
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92 <expand macro="annotations_orthologs_assertion"/>
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93 <expand macro="stdout_assertion">
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94 <has_text text="--tax_scope=651137"/>
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95 </expand>
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96 </test>
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97 </tests>
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98 <help><![CDATA[
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99
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100 eggnog-mapper
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101 =============
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102 Overview
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103 --------
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104
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105 ``eggnog-mapper`` is a tool for fast functional annotation of novel sequences (genes or proteins) using precomputed eggNOG-based orthology assignments.
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106 Obvious examples include the annotation of novel genomes, transcriptomes or even metagenomic gene catalogs.
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107 The use of orthology predictions for functional annotation is considered more precise than traditional homology searches,
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108 as it avoids transferring annotations from paralogs (duplicate genes with a higher chance of being involved in functional divergence).
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109
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110 EggNOG-mapper is also available as a public online resource: `<http://beta-eggnogdb.embl.de/#/app/emapper>`_.
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111
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112 Outputs
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113 -------
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114
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115 @HELP_ANNOTATION_OUTPUTS@
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116
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117 **Recommentation for large input data**
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118
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119 EggNOG-mapper consists of two phases
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120
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121 1. finding seed orthologous sequences (compute intensive)
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122 2. expanding annotations (IO intensive)
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123
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124 by default (i.e. if *Method to search seed orthologs* is not *Skip search stage...* and *Annotate seed orthologs* is *Yes*)
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125 both phases are executed within one tool run.
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126
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127 For large input FASTA datasets in can be favourable to split this in two separate
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128 tool runs as follows:
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129
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130 1. Split the FASTA (e.g. 1M seqs per data set)
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131 2. Run the search phase only (set *Annotate seed orthologs* to *No*) on the separate FASTA files.
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132 3. Run the annotation phase (set *Method to search seed orthologs* to *Skip search stage...*)
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133
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134 See [also](https://github.com/eggnogdb/eggnog-mapper/wiki/eggNOG-mapper-v2.1.5-to-v2.1.8#Setting_up_large_annotation_jobs)
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135
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136 Another alternative is to use cached annotations (produced in a run with --md5 enabled).
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137
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138
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139 ]]></help>
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140 <expand macro="citations"/>
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141 </tool>