| Previous changeset 10:bcb4895b8b55 (2022-06-07) Next changeset 12:9d1fbff733cf (2022-07-19) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 75035b2919ce95fa8d3b785d86c7c7c9da531db2 |
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modified:
eggnog_macros.xml eggnog_mapper.xml test-data/DIA_nlim.emapper.annotations_orthologs test-data/scoped.emapper.annotations_orthologs |
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| diff -r bcb4895b8b55 -r 5a30ae278db0 eggnog_macros.xml --- a/eggnog_macros.xml Tue Jun 07 14:56:44 2022 +0000 +++ b/eggnog_macros.xml Mon Jun 20 12:49:52 2022 +0000 |
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| @@ -1,6 +1,7 @@ <?xml version="1.0"?> <macros> - <token name="@VERSION@">2.1.6</token> + <token name="@TOOL_VERSION@">2.1.8</token> + <token name="@VERSION_SUFFIX@">2.1.8</token> <token name="@EGGNOG_DB_VERSION@">5.0.2</token> <!-- # DB versionning was super confusing for eggnog-mapper 2.0.x: @@ -18,7 +19,7 @@ </xml> <xml name="requirements"> <requirements> - <requirement type="package" version="@VERSION@">eggnog-mapper</requirement> + <requirement type="package" version="@TOOL_VERSION@">eggnog-mapper</requirement> </requirements> </xml> <xml name="version_command"> @@ -63,4 +64,10 @@ </output> </test> </xml> + <xml name="stdout_assertion"> + <assert_stdout> + <has_line line="# emapper-@TOOL_VERSION@"/> + <has_line line="FINISHED"/> + </assert_stdout> + </xml> </macros> |
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| diff -r bcb4895b8b55 -r 5a30ae278db0 eggnog_mapper.xml --- a/eggnog_mapper.xml Tue Jun 07 14:56:44 2022 +0000 +++ b/eggnog_mapper.xml Mon Jun 20 12:49:52 2022 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="eggnog_mapper" name="eggNOG Mapper" version="@VERSION@+galaxy2"> +<tool id="eggnog_mapper" name="eggNOG Mapper" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>functional sequence annotation by orthology</description> <macros> <import>eggnog_macros.xml</import> @@ -319,14 +319,15 @@ </data> </outputs> <tests> - <test> + <test expect_num_outputs="1"> <param name="input" value="Nmar_0135.fa" ftype="fasta"/> <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <param name="no_annot" value="true"/> <param name="no_file_comments" value="true"/> <output name="seed_orthologs" file="DIA_nlim.emapper.seed_orthologs" ftype="tabular" compare="sim_size"/> + <expand macro="stdout_assertion"/> </test> - <test> + <test expect_num_outputs="3"> <param name="input" value="Nmar_0135.fa" ftype="fasta"/> <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work --> <param name="report_orthologs" value="true"/> @@ -334,8 +335,9 @@ <output name="seed_orthologs" file="DIA_nlim.emapper.seed_orthologs" ftype="tabular" compare="sim_size"/> <output name="annotations" file="DIA_nlim.emapper.annotations" ftype="tabular" compare="sim_size"/> <output name="annotations_orthologs" file="DIA_nlim.emapper.annotations_orthologs" ftype="tabular"/> + <expand macro="stdout_assertion"/> </test> - <test> + <test expect_num_outputs="3"> <param name="input" value="Nmar_0135.fa" ftype="fasta"/> <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work --> <param name="report_orthologs" value="true"/> @@ -346,8 +348,9 @@ <output name="seed_orthologs" file="scoped.emapper.seed_orthologs" ftype="tabular" compare="sim_size"/> <output name="annotations" file="scoped.emapper.annotations" ftype="tabular" compare="sim_size"/> <output name="annotations_orthologs" file="scoped.emapper.annotations_orthologs" ftype="tabular"/> + <expand macro="stdout_assertion"/> </test> - <test> + <test expect_num_outputs="3"> <param name="input" value="Nmar_0135.fa" ftype="fasta"/> <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work --> <section name="seed_ortho_options"> @@ -361,6 +364,7 @@ <output name="seed_orthologs" file="DIA_nlim.emapper.seed_orthologs" ftype="tabular" compare="sim_size"/> <output name="annotations" file="DIA_nlim.emapper.annotations" ftype="tabular" compare="sim_size"/> <output name="annotations_orthologs" file="DIA_nlim.emapper.annotations_orthologs" ftype="tabular"/> + <expand macro="stdout_assertion"/> </test> <!-- not enabled as it requires a specific .db file, hard to minimize --> <!--test> |
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| diff -r bcb4895b8b55 -r 5a30ae278db0 test-data/DIA_nlim.emapper.annotations_orthologs --- a/test-data/DIA_nlim.emapper.annotations_orthologs Tue Jun 07 14:56:44 2022 +0000 +++ b/test-data/DIA_nlim.emapper.annotations_orthologs Mon Jun 20 12:49:52 2022 +0000 |
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| @@ -1,3 +1,3 @@ #query orth_type species orthologs Nmar_0135 one2one Marine Group I thaumarchaeote SCGC AB-629-I23(1131266) *ARWQ01000003_gene1537 -Nmar_0135 one2one Nitrosopumilus maritimus SCM1(436308) *Nmar_0135 +Nmar_0135 seed Nitrosopumilus maritimus SCM1(436308) *Nmar_0135 |
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| diff -r bcb4895b8b55 -r 5a30ae278db0 test-data/scoped.emapper.annotations_orthologs --- a/test-data/scoped.emapper.annotations_orthologs Tue Jun 07 14:56:44 2022 +0000 +++ b/test-data/scoped.emapper.annotations_orthologs Mon Jun 20 12:49:52 2022 +0000 |
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| @@ -1,3 +1,3 @@ #query orth_type species orthologs Nmar_0135 one2one Marine Group I thaumarchaeote SCGC AB-629-I23(1131266) *ARWQ01000003_gene1537 -Nmar_0135 one2one Nitrosopumilus maritimus SCM1(436308) *Nmar_0135 +Nmar_0135 seed Nitrosopumilus maritimus SCM1(436308) *Nmar_0135 |