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view eggnog_mapper_annotate.xml @ 14:d9c3016f7283 draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 192779247c3385704ebd98a2cc47a210fb1f4d0c
author | galaxyp |
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date | Thu, 07 Sep 2023 18:51:23 +0000 (18 months ago) |
parents | 844fa988236b |
children |
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<tool id="eggnog_mapper_annotate" name="eggNOG Mapper" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>annotation phase</description> <macros> <import>eggnog_macros.xml</import> </macros> <expand macro="requirements"/> <expand macro="version_command"/> <command detect_errors="aggressive"><![CDATA[ @MERGE_ANNOTATIONS@ emapper.py @DB_TOKEN@ -m no_search @ORTHO_SEARCH_TOKEN@ @ANNOTATION_TOKEN@ $output_options.no_file_comments $output_options.report_orthologs $output_options.md5 --output='results' --cpu "\${GALAXY_SLOTS:-1}" --scratch_dir \${TEMP:-\$_GALAXY_JOB_TMP_DIR} --temp_dir \${TEMP:-\$_GALAXY_JOB_TMP_DIR} ]]></command> <inputs> <expand macro="db_macro"/> <expand macro="ortho_annotate_macro"/> <section name="annotation_options" title="Annotation options"> <expand macro="annotation_options_macro"/> </section> <expand macro="output_options_annotate_macro"/> </inputs> <outputs> <expand macro="annotation_output_macro"/> <expand macro="annotation_orthologs_output_macro"/> </outputs> <tests> <!-- test producing annotations form seed orthologs --> <test expect_num_outputs="1"> <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work --> <param name="annotate_hits_table" value="DIA_nlim.emapper.seed_orthologs" ftype="tabular"> <!-- this has no effect at the moment since column_names can not be set in uploads <metadata name="column_names" value="@SEED_ORTHOLOG_COLUMNS@"/> --> </param> <conditional name="annotation_options"> </conditional> <section name="output_options"> <param name="report_orthologs" value="false"/> <param name="no_file_comments" value="true"/> </section> <expand macro="annotations_assertion"/> <expand macro="stdout_assertion"/> </test> <!-- test using chached annotations from previous run --> <test expect_num_outputs="2"> <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work --> <conditional name="ortho_method"> <param name="m" value="cache"/> <param name="input" value="Nmar_0135.fa" ftype="fasta"/> <param name="cache" value="DIA_nlim.emapper.annotations_cached" ftype="tabular"/> </conditional> <section name="output_options"> <param name="report_orthologs" value="true"/> <param name="no_file_comments" value="true"/> <param name="md5" value="true"/> </section> <expand macro="annotations_assertion" columns="22" add_metadata_columm_names=",md5" add_column_names="	md5" add_column_re="\t[\d\w]+"/> <output name="no_annotations" ftype="fasta"> <assert_contents> <has_n_lines n="0"/> </assert_contents> </output> <expand macro="stdout_assertion"/> </test> <!-- test setting tax scope--> <test expect_num_outputs="2"> <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work --> <param name="annotate_hits_table" value="DIA_nlim.emapper.seed_orthologs" ftype="tabular"> <!-- this has no effect at the moment since column_names can not be set in uploads <metadata name="column_names" value="@SEED_ORTHOLOG_COLUMNS@"/> --> </param> <section name="annotation_options"> <param name="tax_scope" value="651137" /> </section> <section name="output_options"> <param name="report_orthologs" value="true"/> <param name="no_file_comments" value="true"/> </section> <expand macro="annotations_assertion"/> <expand macro="annotations_orthologs_assertion"/> <expand macro="stdout_assertion"> <has_text text="--tax_scope=651137"/> </expand> </test> </tests> <help>< Another alternative is to use cached annotations (produced in a run with --md5 enabled). ]]></help> <expand macro="citations"/> </tool>