Mercurial > repos > galaxyp > eggnog_mapper

annotate eggnog_mapper.xml @ 13:844fa988236b draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
author galaxyp
date Mon, 04 Sep 2023 12:47:09 +0000
parents 9d1fbff733cf
children
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13
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
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1 <tool id="eggnog_mapper" name="eggNOG Mapper" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>functional sequence annotation by orthology</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 @ORTHO_SEARCH_TOKEN@
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14 #if $annotation_options.no_annot == "--no_annot"
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15 --no_annot
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16 #else
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17 @ANNOTATION_TOKEN@
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18 #end if
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19 $output_options.no_file_comments
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20 $output_options.report_orthologs
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21 $output_options.md5
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22 --output='results'
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23 --cpu "\${GALAXY_SLOTS:-4}"
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24 --scratch_dir \${TEMP:-\$_GALAXY_JOB_TMP_DIR}
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25 --temp_dir \${TEMP:-\$_GALAXY_JOB_TMP_DIR}
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26 ]]></command>
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27 <inputs>
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28 <expand macro="db_macro"/>
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29 <expand macro="ortho_full_macro"/>
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30 <conditional name="annotation_options">
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31 <param argument="--no_annot" type="select" label="Annotate seed orthologs">
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32 <option value="">Yes</option>
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33 <option value="--no_annot">No</option>
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34 </param>
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35 <when value="">
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36 <expand macro="annotation_options_macro"/>
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37 </when>
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38 <when value="--no_annot"/>
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39 </conditional>
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40
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41 <expand macro="output_options_annotate_macro"/>
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42 </inputs>
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43 <outputs>
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44 <expand macro="ortho_search_output_macro"/>
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45 <expand macro="annotation_output_macro">
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46 <filter>annotation_options['no_annot'] == ''</filter>
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47 </expand>
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48 <expand macro="annotation_orthologs_output_macro"/>
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49 </outputs>
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50 <tests>
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51 <!-- test producing only seed orthologs-->
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52 <test expect_num_outputs="1">
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53 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/>
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54 <conditional name="ortho_method">
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55 <param name="input" value="Nmar_0135.fa" ftype="fasta"/>
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56 </conditional>
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57 <conditional name="annotation_options">
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58 <param name="no_annot" value="--no_annot"/>
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59 </conditional>
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60 <section name="output_options">
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61 </section>
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62 <expand macro="seed_orthologs_assertion"/>
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63 <expand macro="stdout_assertion"/>
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64 </test>
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65
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66 <!-- test producing annotations form seed orthologs -->
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67 <test expect_num_outputs="2">
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68 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work -->
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69 <conditional name="ortho_method">
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70 <param name="m" value="no_search"/>
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71 <param name="annotate_hits_table" value="DIA_nlim.emapper.seed_orthologs" ftype="tabular">
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72 <!-- 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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73 </param>
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74 </conditional>
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75 <conditional name="annotation_options">
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76 </conditional>
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77 <section name="output_options">
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78 <param name="report_orthologs" value="true"/>
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79 </section>
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80 <expand macro="annotations_assertion"/>
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81 <expand macro="annotations_orthologs_assertion"/>
11
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82 <expand macro="stdout_assertion"/>
0
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83 </test>
12
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84
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85 <!-- test producing seed orthologs and annotations at once (ie the same as the previous two tests but in a single tool run) -->
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86 <test expect_num_outputs="3">
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87 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work -->
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88 <conditional name="ortho_method">
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89 <param name="input" value="Nmar_0135.fa" ftype="fasta"/>
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90 </conditional>
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91 <section name="output_options">
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92 <param name="report_orthologs" value="true"/>
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93 <param name="no_file_comments" value="false"/>
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94 <param name="md5" value="true"/>
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95 </section>
13
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96 <expand macro="seed_orthologs_assertion" nocomments="false"/>
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97 <expand macro="annotations_assertion" columns="22" add_metadata_columm_names=",md5" add_column_names="&#009;md5" add_column_re="\t[\d\w]+" nocomments="false"/>
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98 <expand macro="annotations_orthologs_assertion" nocomments="false"/>
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99 <expand macro="stdout_assertion"/>
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100 </test>
12
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101
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102 <!-- test using chached annotations from previous run -->
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103 <test expect_num_outputs="2">
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104 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work -->
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105 <conditional name="ortho_method">
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106 <param name="m" value="cache"/>
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107 <param name="input" value="Nmar_0135.fa" ftype="fasta"/>
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108 <param name="cache" value="DIA_nlim.emapper.annotations_cached" ftype="tabular"/>
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109 </conditional>
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110 <section name="output_options">
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111 <param name="report_orthologs" value="true"/>
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112 <param name="md5" value="true"/>
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113 </section>
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114 <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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115 <output name="no_annotations" ftype="fasta">
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116 <assert_contents>
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117 <has_n_lines n="0"/>
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118 </assert_contents>
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119 </output>
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120 <expand macro="stdout_assertion"/>
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121 </test>
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122
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123 <!-- test setting tax scope-->
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124 <test expect_num_outputs="3">
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125 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work -->
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126 <conditional name="ortho_method">
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127 <param name="input" value="Nmar_0135.fa" ftype="fasta"/>
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128 </conditional>
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129 <section name="annotation_options">
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130 <param name="tax_scope" value="651137" />
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131 </section>
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132 <section name="output_options">
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133 <param name="report_orthologs" value="true"/>
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134 </section>
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135 <expand macro="seed_orthologs_assertion"/>
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136 <expand macro="annotations_assertion"/>
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137 <expand macro="annotations_orthologs_assertion"/>
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138 <expand macro="stdout_assertion">
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139 <has_text text="--tax_scope=651137"/>
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140 </expand>
0
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141 </test>
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142
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143 <!-- test setting a diamond option-->
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144 <test expect_num_outputs="3">
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145 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work -->
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146 <conditional name="ortho_method">
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147 <param name="m" value="diamond" />
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148 <param name="input" value="Nmar_0135.fa" ftype="fasta"/>
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149 <param name="sensmode" value="fast" />
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150 </conditional>
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151 <section name="output_options">
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152 <param name="report_orthologs" value="true"/>
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153 </section>
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154 <expand macro="seed_orthologs_assertion"/>
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155 <expand macro="annotations_assertion"/>
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156 <expand macro="annotations_orthologs_assertion"/>
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157 <expand macro="stdout_assertion">
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158 <has_text text="--sensmode fast"/>
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159 </expand>
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160 </test>
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161 <!-- not enabled as it requires a specific .db file, hard to minimize -->
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162 <!--test>
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163 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/>
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164 <param name="input" value="Nmar_0135.fa" ftype="fasta"/>
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165 <section name="seed_ortho_options">
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166 <conditional name="ortho_method">
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167 <param name="m" value="mmseqs" />
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168 <param name="start_sens" value="4" />
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169 </conditional>
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170 </section>
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171 <param name="report_orthologs" value="true"/>
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172 <param name="no_file_comments" value="true"/>
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173 <output name="seed_orthologs" file="DIA_nlim.emapper.seed_orthologs" ftype="tabular" compare="sim_size"/>
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174 <output name="annotations" file="DIA_nlim.emapper.annotations" ftype="tabular" compare="sim_size"/>
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175 <output name="annotations_orthologs" file="DIA_nlim.emapper.annotations_orthologs" ftype="tabular"/>
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176 </test-->
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177 </tests>
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178 <help><![CDATA[
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179
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180 eggnog-mapper
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181 =============
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182 Overview
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183 --------
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184
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185 ``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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186 Obvious examples include the annotation of novel genomes, transcriptomes or even metagenomic gene catalogs.
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187 The use of orthology predictions for functional annotation is considered more precise than traditional homology searches,
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188 as it avoids transferring annotations from paralogs (duplicate genes with a higher chance of being involved in functional divergence).
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189
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190 EggNOG-mapper is also available as a public online resource: `<http://beta-eggnogdb.embl.de/#/app/emapper>`_.
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191
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192 Outputs
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193 -------
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194
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195 @HELP_SEARCH_OUTPUTS@
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196
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197 @HELP_ANNOTATION_OUTPUTS@
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198
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199
0
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200
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201 **Recommentation for large input data**
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202
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203 EggNOG-mapper consists of two phases
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204
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205 1. finding seed orthologous sequences (compute intensive)
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206 2. expanding annotations (IO intensive)
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207
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208 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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209 both phases are executed within one tool run.
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210
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211 For large input FASTA datasets in can be favourable to split this in two separate
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212 tool runs as follows:
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213
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214 1. Split the FASTA (e.g. 1M seqs per data set)
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215 2. Run the search phase only (set *Annotate seed orthologs* to *No*) on the separate FASTA files.
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216 3. Run the annotation phase (set *Method to search seed orthologs* to *Skip search stage...*)
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217
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218 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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219
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220 Another alternative is to use cached annotations (produced in a run with --md5 enabled).
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221
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222 ]]></help>
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223 <expand macro="citations"/>
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224 </tool>