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comparison eggnog_mapper_annotate.xml @ 15:02439eb2b37d 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 0e3cff872b53efe21cbf4905ed0b072337192001
author galaxyp
date Mon, 19 Jan 2026 22:22:55 +0000
parents 844fa988236b
children
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equal deleted inserted replaced
14:d9c3016f7283 15:02439eb2b37d
1 <tool id="eggnog_mapper_annotate" name="eggNOG Mapper" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> 1 <tool id="eggnog_mapper_annotate" name="eggNOG Mapper" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>annotation phase</description> 2 <description>annotation phase</description>
3 <macros> 3 <macros>
4 <import>eggnog_macros.xml</import> 4 <import>eggnog_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="biotools"/>
6 <expand macro="requirements"/> 7 <expand macro="requirements"/>
7 <expand macro="version_command"/> 8 <expand macro="version_command"/>
8 <command detect_errors="aggressive"><![CDATA[ 9 <command detect_errors="aggressive"><![CDATA[
9 @MERGE_ANNOTATIONS@ 10 @MERGE_ANNOTATIONS@
10 11
38 </outputs> 39 </outputs>
39 <tests> 40 <tests>
40 <!-- test producing annotations form seed orthologs --> 41 <!-- test producing annotations form seed orthologs -->
41 <test expect_num_outputs="1"> 42 <test expect_num_outputs="1">
42 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work --> 43 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work -->
43 <param name="annotate_hits_table" value="DIA_nlim.emapper.seed_orthologs" ftype="tabular"> 44 <conditional name="ortho_method">
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@"/> --> 45 <param name="annotate_hits_table" value="DIA_nlim.emapper.seed_orthologs" ftype="tabular">
45 </param> 46 <!-- this has no effect at the moment since column_names can not be set in uploads <metadata name="column_names" value="@SEED_ORTHOLOG_COLUMNS@"/> -->
47 </param>
48 </conditional>
46 <conditional name="annotation_options"> 49 <conditional name="annotation_options">
47 </conditional> 50 </conditional>
48 <section name="output_options"> 51 <section name="output_options">
49 <param name="report_orthologs" value="false"/> 52 <param name="report_orthologs" value="false"/>
50 <param name="no_file_comments" value="true"/> 53 <param name="no_file_comments" value="true"/>
76 </test> 79 </test>
77 80
78 <!-- test setting tax scope--> 81 <!-- test setting tax scope-->
79 <test expect_num_outputs="2"> 82 <test expect_num_outputs="2">
80 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work --> 83 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work -->
81 <param name="annotate_hits_table" value="DIA_nlim.emapper.seed_orthologs" ftype="tabular"> 84 <conditional name="ortho_method">
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@"/> --> 85 <param name="annotate_hits_table" value="DIA_nlim.emapper.seed_orthologs" ftype="tabular">
83 </param> 86 <!-- this has no effect at the moment since column_names can not be set in uploads <metadata name="column_names" value="@SEED_ORTHOLOG_COLUMNS@"/> -->
87 </param>
88 </conditional>
84 <section name="annotation_options"> 89 <section name="annotation_options">
85 <param name="tax_scope" value="651137" /> 90 <param name="tax_scope" value="651137" />
86 </section> 91 </section>
87 <section name="output_options"> 92 <section name="output_options">
88 <param name="report_orthologs" value="true"/> 93 <param name="report_orthologs" value="true"/>