Mercurial > repos > oinizan > frogs
changeset 3:3d3268f0aa77 draft
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit e71bbd90cf4706a353de17d3296d7203f906d4a0"
| author | oinizan |
|---|---|
| date | Thu, 08 Apr 2021 09:02:33 +0000 |
| parents | ea386220db3c |
| children | 8d88c426e94c |
| files | FROGS_data_manager/data_manager/FROGS_data_manager.xml all.lint.log shedSave.yml |
| diffstat | 3 files changed, 38 insertions(+), 577 deletions(-) [+] |
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--- a/FROGS_data_manager/data_manager/FROGS_data_manager.xml Thu Apr 08 07:29:32 2021 +0000 +++ b/FROGS_data_manager/data_manager/FROGS_data_manager.xml Thu Apr 08 09:02:33 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="FROGS_data_manager" name="FROGS Data manager" version="3.2.1" tool_type="manage_data"> +<tool id="FROGS_data_manager" name="FROGS Data manager" version="3.2.2" tool_type="manage_data"> <requirements> </requirements> <stdio> @@ -25,23 +25,41 @@ <param name="db" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Download all databases"/> <when value="true"/> <when value="false"> - <param name="date" value="0" type="text" label="Only more recent database than this date will be downloaded" help="Please enter a date at the following format: YYYYMMDD, leave 0 for no date"> + <param name="date" value="0" type="text" label="Download only most recent databases" help="Select databases uploaded later than this date. Please enter a date at the following format: YYYYMMDD, else leave 0."> <validator type="regex" message="Please enter a date at the following format: YYYYMMDD, leave 0 for no date">0|[1-2]{1}[0-9]{3}[0-1]{1}[0-9]{1}([0-2]{1}[0-9]{1}|3[0-1]{1})</validator> </param> - <param name="amplicons" type="text" label='Select database to download by amplicons, put an amplicons list separated by "," ' help='example: "COI,ITS,16S" or "23S"'/> - <param name="bases" type="text" label='Select database to download by base, put a bases list separated by "," ' help='example: "SILVA,PR2,MIDAS" or "BOLD"'/> - <param name="filters" type="text" label='Select database to download by filters, put a filters list separated by "," ' help='example: "Pintail100,Fungi"'/> + <param name="amplicons" type="text" label='Select amplicon specific databases' help='Write amplicons names separated by ","; example: "COI,ITS,16S" or "23S"'/> + <param name="bases" type="text" label='Select database by name' help='Write base names separated by ","; example: "SILVA,PR2,MIDAS" or "BOLD"'/> + <param name="filters" type="text" label='Select database on filter name' help='Write filter names separated by ",";example: "Pintail100,Fungi"'/> </when> </conditional> - <param name="only_last_versions" type="boolean" checked="true" label="Download only the last version of each database"/> + <param name="only_last_versions" type="boolean" checked="true" label="Download only the last version of selected database"/> </inputs> <outputs> <data name="output" format="data_manager_json"/> </outputs> <help> + .. image:: static/images/FROGS_logo.png + :height: 144 + :width: 110 + FROGS datamanager allows to download preformated databases for FROGS Affiliation OTU tool. All databases are available at http://genoweb.toulouse.inra.fr/frogs_databanks/assignation/. - This tools is based on the `FROGS_databases.tsv.txt <http://genoweb.toulouse.inra.fr/frogs_databanks/assignation/FROGS_databases.tsv.txt>`_, that we update each time a new database is formatted.</help> + This tools is based on the `FROGS_databases.tsv.txt <http://genoweb.toulouse.inra.fr/frogs_databanks/assignation/FROGS_databases.tsv.txt>`_, that we update each time a new database is formatted. + + .. image:: static/images/FROGS_db.png + :height: 157 + :width: 961 + + You may download all databases, but you may (should) filter whished database on different criteria: + + - on a date, to download only last formated databases + - on an amplicon type + - on a base name + - eventually on a filtered name, this may be the case for example, for 16S SILVA database, for which we provide reference sequence with pintail score above a threshold + + Last option allow you to download only last version of previously selected databases, indeed we provide reference database since 2016 with for example, around 1 version of SILVA per year. + </help> </tool> \ No newline at end of file
--- a/all.lint.log Thu Apr 08 07:29:32 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,570 +0,0 @@ -Linting tool /home/maria/workspace/FROGS-wrappers_dev/affiliation_filters.xml -Failed linting -Applying linter tests... CHECK -.. CHECK: 2 test(s) found. -Applying linter output... CHECK -.. INFO: 5 outputs found. -Applying linter inputs... CHECK -.. INFO: Found 11 input parameters. -Applying linter help... CHECK -.. CHECK: Tool contains help section. -.. CHECK: Help contains valid reStructuredText. -Applying linter general... CHECK -.. CHECK: Tool defines a version [3.2]. -.. CHECK: Tool defines a name [FROGS Affiliation Filters]. -.. CHECK: Tool defines an id [FROGS_affiliation_filters]. -.. CHECK: Tool targets 16.01 Galaxy profile. -Applying linter command... CHECK -.. INFO: Tool contains a command. -Applying linter citations... WARNING -.. WARNING: No citations found, consider adding citations to your tool. -Applying linter tool_xsd... CHECK -.. INFO: File validates against XML schema. -Linting tool /home/maria/workspace/FROGS-wrappers_dev/affiliation_OTU.xml -Applying linter tests... CHECK -.. CHECK: 2 test(s) found. -Applying linter output... CHECK -.. INFO: 2 outputs found. -Applying linter inputs... CHECK -.. INFO: Found 5 input parameters. -Applying linter help... CHECK -.. CHECK: Tool contains help section. -.. CHECK: Help contains valid reStructuredText. -Applying linter general... CHECK -.. CHECK: Tool defines a version [3.2]. -.. CHECK: Tool defines a name [FROGS Affiliation OTU]. -.. CHECK: Tool defines an id [FROGS_affiliation_OTU]. -.. CHECK: Tool targets 16.01 Galaxy profile. -Applying linter command... CHECK -.. INFO: Tool contains a command. -Applying linter citations... CHECK -.. CHECK: Found 1 likely valid citations. -Applying linter tool_xsd... CHECK -.. INFO: File validates against XML schema. -Linting tool /home/maria/workspace/FROGS-wrappers_dev/affiliation_postprocess.xml -Applying linter tests... CHECK -.. CHECK: 1 test(s) found. -Applying linter output... CHECK -.. INFO: 3 outputs found. -Applying linter inputs... CHECK -.. INFO: Found 6 input parameters. -Applying linter help... CHECK -.. CHECK: Tool contains help section. -.. CHECK: Help contains valid reStructuredText. -Applying linter general... CHECK -.. CHECK: Tool defines a version [3.2]. -.. CHECK: Tool defines a name [FROGS Affiliation postprocess]. -.. CHECK: Tool defines an id [FROGS_affiliation_postprocess]. -.. CHECK: Tool targets 16.01 Galaxy profile. -Applying linter command... CHECK -.. INFO: Tool contains a command. -Applying linter citations... CHECK -.. CHECK: Found 1 likely valid citations. -Applying linter tool_xsd... CHECK -.. INFO: File validates against XML schema. -Linting tool /home/maria/workspace/FROGS-wrappers_dev/affiliations_stat.xml -Applying linter tests... CHECK -.. CHECK: 1 test(s) found. -Applying linter output... CHECK -.. INFO: 1 outputs found. -Applying linter inputs... CHECK -.. INFO: Found 8 input parameters. -Applying linter help... CHECK -.. CHECK: Tool contains help section. -.. CHECK: Help contains valid reStructuredText. -Applying linter general... CHECK -.. CHECK: Tool defines a version [3.2]. -.. CHECK: Tool defines a name [FROGS Affiliations stat]. -.. CHECK: Tool defines an id [FROGS_affiliations_stat]. -.. CHECK: Tool targets 16.01 Galaxy profile. -Applying linter command... CHECK -.. INFO: Tool contains a command. -Applying linter citations... CHECK -.. CHECK: Found 1 likely valid citations. -Applying linter tool_xsd... CHECK -.. INFO: File validates against XML schema. -Linting tool /home/maria/workspace/FROGS-wrappers_dev/biom_to_stdBiom.xml -Applying linter tests... CHECK -.. CHECK: 1 test(s) found. -Applying linter output... CHECK -.. INFO: 2 outputs found. -Applying linter inputs... CHECK -.. INFO: Found 1 input parameters. -Applying linter help... CHECK -.. CHECK: Tool contains help section. -.. CHECK: Help contains valid reStructuredText. -Applying linter general... CHECK -.. CHECK: Tool defines a version [3.2]. -.. CHECK: Tool defines a name [FROGS BIOM to std BIOM]. -.. CHECK: Tool defines an id [FROGS_biom_to_stdBiom]. -.. CHECK: Tool targets 16.01 Galaxy profile. -Applying linter command... CHECK -.. INFO: Tool contains a command. -Applying linter citations... CHECK -.. CHECK: Found 1 likely valid citations. -Applying linter tool_xsd... CHECK -.. INFO: File validates against XML schema. -Linting tool /home/maria/workspace/FROGS-wrappers_dev/biom_to_tsv.xml -Applying linter tests... CHECK -.. CHECK: 1 test(s) found. -Applying linter output... CHECK -.. INFO: 2 outputs found. -Applying linter inputs... CHECK -.. INFO: Found 3 input parameters. -Applying linter help... CHECK -.. CHECK: Tool contains help section. -.. CHECK: Help contains valid reStructuredText. -Applying linter general... CHECK -.. CHECK: Tool defines a version [3.2]. -.. CHECK: Tool defines a name [FROGS BIOM to TSV]. -.. CHECK: Tool defines an id [FROGS_biom_to_tsv]. -.. CHECK: Tool targets 16.01 Galaxy profile. -Applying linter command... CHECK -.. INFO: Tool contains a command. -Applying linter citations... CHECK -.. CHECK: Found 1 likely valid citations. -Applying linter tool_xsd... CHECK -.. INFO: File validates against XML schema. -Linting tool /home/maria/workspace/FROGS-wrappers_dev/clustering.xml -Applying linter tests... CHECK -.. CHECK: 2 test(s) found. -Applying linter output... CHECK -.. INFO: 3 outputs found. -Applying linter inputs... CHECK -.. INFO: Found 7 input parameters. -Applying linter help... CHECK -.. CHECK: Tool contains help section. -.. CHECK: Help contains valid reStructuredText. -Applying linter general... CHECK -.. CHECK: Tool defines a version [3.2]. -.. CHECK: Tool defines a name [FROGS Clustering swarm]. -.. CHECK: Tool defines an id [FROGS_clustering]. -.. CHECK: Tool targets 16.01 Galaxy profile. -Applying linter command... CHECK -.. INFO: Tool contains a command. -Applying linter citations... CHECK -.. CHECK: Found 1 likely valid citations. -Applying linter tool_xsd... CHECK -.. INFO: File validates against XML schema. -Linting tool /home/maria/workspace/FROGS-wrappers_dev/clusters_stat.xml -Applying linter tests... CHECK -.. CHECK: 1 test(s) found. -Applying linter output... CHECK -.. INFO: 1 outputs found. -Applying linter inputs... CHECK -.. INFO: Found 1 input parameters. -Applying linter help... CHECK -.. CHECK: Tool contains help section. -.. CHECK: Help contains valid reStructuredText. -Applying linter general... CHECK -.. CHECK: Tool defines a version [3.2]. -.. CHECK: Tool defines a name [FROGS Clusters stat]. -.. CHECK: Tool defines an id [FROGS_clusters_stat]. -.. CHECK: Tool targets 16.01 Galaxy profile. -Applying linter command... CHECK -.. INFO: Tool contains a command. -Applying linter citations... CHECK -.. CHECK: Found 1 likely valid citations. -Applying linter tool_xsd... CHECK -.. INFO: File validates against XML schema. -Linting tool /home/maria/workspace/FROGS-wrappers_dev/demultiplex.xml -Applying linter tests... CHECK -.. CHECK: 1 test(s) found. -Applying linter output... CHECK -.. INFO: 3 outputs found. -Applying linter inputs... CHECK -.. INFO: Found 7 input parameters. -Applying linter help... CHECK -.. CHECK: Tool contains help section. -.. CHECK: Help contains valid reStructuredText. -Applying linter general... CHECK -.. CHECK: Tool defines a version [3.2]. -.. CHECK: Tool defines a name [FROGS Demultiplex reads]. -.. CHECK: Tool defines an id [FROGS_demultiplex]. -.. CHECK: Tool targets 16.01 Galaxy profile. -Applying linter command... CHECK -.. INFO: Tool contains a command. -Applying linter citations... CHECK -.. CHECK: Found 1 likely valid citations. -Applying linter tool_xsd... CHECK -.. INFO: File validates against XML schema. -Linting tool /home/maria/workspace/FROGS-wrappers_dev/deseq2_preprocess.xml -Applying linter tests... CHECK -.. CHECK: 1 test(s) found. -Applying linter output... CHECK -.. INFO: 1 outputs found. -Applying linter inputs... CHECK -.. INFO: Found 5 input parameters. -Applying linter help... CHECK -.. CHECK: Tool contains help section. -.. CHECK: Help contains valid reStructuredText. -Applying linter general... CHECK -.. CHECK: Tool defines a version [3.2]. -.. CHECK: Tool defines a name [FROGSSTAT DESeq2 Preprocess]. -.. CHECK: Tool defines an id [FROGSSTAT_DESeq2_Preprocess]. -.. CHECK: Tool targets 16.01 Galaxy profile. -Applying linter command... CHECK -.. INFO: Tool contains a command. -Applying linter citations... CHECK -.. CHECK: Found 1 likely valid citations. -Applying linter tool_xsd... CHECK -.. INFO: File validates against XML schema. -Linting tool /home/maria/workspace/FROGS-wrappers_dev/deseq2_visualizationSave.xml -Failed linting -Applying linter tests... FAIL -.. ERROR: Found output tag with unknown name [output_html], valid names [['html']] -.. CHECK: 1 test(s) found. -Applying linter output... CHECK -.. INFO: 1 outputs found. -Applying linter inputs... CHECK -.. INFO: Found 7 input parameters. -Applying linter help... CHECK -.. CHECK: Tool contains help section. -.. CHECK: Help contains valid reStructuredText. -Applying linter general... CHECK -.. CHECK: Tool defines a version [3.2]. -.. CHECK: Tool defines a name [FROGSTAT Deseq2 Visualization]. -.. CHECK: Tool defines an id [FROGSSTAT_DESeq2_Visualization]. -.. CHECK: Tool targets 16.01 Galaxy profile. -Applying linter command... CHECK -.. INFO: Tool contains a command. -Applying linter citations... CHECK -.. CHECK: Found 1 likely valid citations. -Applying linter tool_xsd... CHECK -.. INFO: File validates against XML schema. -Linting tool /home/maria/workspace/FROGS-wrappers_dev/deseq2_visualization.xml -Applying linter tests... CHECK -.. CHECK: 1 test(s) found. -Applying linter output... CHECK -.. INFO: 1 outputs found. -Applying linter inputs... CHECK -.. INFO: Found 7 input parameters. -Applying linter help... CHECK -.. CHECK: Tool contains help section. -.. CHECK: Help contains valid reStructuredText. -Applying linter general... CHECK -.. CHECK: Tool defines a version [3.2]. -.. CHECK: Tool defines a name [FROGSTAT Deseq2 Visualization]. -.. CHECK: Tool defines an id [FROGSSTAT_DESeq2_Visualization]. -.. CHECK: Tool targets 16.01 Galaxy profile. -Applying linter command... CHECK -.. INFO: Tool contains a command. -Applying linter citations... CHECK -.. CHECK: Found 1 likely valid citations. -Applying linter tool_xsd... CHECK -.. INFO: File validates against XML schema. -Linting tool /home/maria/workspace/FROGS-wrappers_dev/itsx.xml -Applying linter tests... CHECK -.. CHECK: 1 test(s) found. -Applying linter output... CHECK -.. INFO: 4 outputs found. -Applying linter inputs... CHECK -.. INFO: Found 4 input parameters. -Applying linter help... CHECK -.. CHECK: Tool contains help section. -.. CHECK: Help contains valid reStructuredText. -Applying linter general... CHECK -.. CHECK: Tool defines a version [3.2]. -.. CHECK: Tool defines a name [FROGS ITSx]. -.. CHECK: Tool defines an id [FROGS_itsx]. -.. CHECK: Tool targets 16.01 Galaxy profile. -Applying linter command... CHECK -.. INFO: Tool contains a command. -Applying linter citations... CHECK -.. CHECK: Found 1 likely valid citations. -Applying linter tool_xsd... CHECK -.. INFO: File validates against XML schema. -Linting tool /home/maria/workspace/FROGS-wrappers_dev/normalisation.xml -Applying linter tests... CHECK -.. CHECK: 1 test(s) found. -Applying linter output... CHECK -.. INFO: 3 outputs found. -Applying linter inputs... CHECK -.. INFO: Found 3 input parameters. -Applying linter help... CHECK -.. CHECK: Tool contains help section. -.. CHECK: Help contains valid reStructuredText. -Applying linter general... CHECK -.. CHECK: Tool defines a version [3.2]. -.. CHECK: Tool defines a name [FROGS Abundance normalisation]. -.. CHECK: Tool defines an id [FROGS_normalisation]. -.. CHECK: Tool targets 16.01 Galaxy profile. -Applying linter command... CHECK -.. INFO: Tool contains a command. -Applying linter citations... CHECK -.. CHECK: Found 1 likely valid citations. -Applying linter tool_xsd... CHECK -.. INFO: File validates against XML schema. -Linting tool /home/maria/workspace/FROGS-wrappers_dev/otu_filters.xml -Applying linter tests... CHECK -.. CHECK: 1 test(s) found. -Applying linter output... CHECK -.. INFO: 4 outputs found. -Applying linter inputs... CHECK -.. INFO: Found 10 input parameters. -Applying linter help... CHECK -.. CHECK: Tool contains help section. -.. CHECK: Help contains valid reStructuredText. -Applying linter general... CHECK -.. CHECK: Tool defines a version [3.2]. -.. CHECK: Tool defines a name [FROGS OTU Filters]. -.. CHECK: Tool defines an id [FROGS_OTU_filters]. -.. CHECK: Tool targets 16.01 Galaxy profile. -Applying linter command... CHECK -.. INFO: Tool contains a command. -Applying linter citations... CHECK -.. CHECK: Found 1 likely valid citations. -Applying linter tool_xsd... CHECK -.. INFO: File validates against XML schema. -Linting tool /home/maria/workspace/FROGS-wrappers_dev/preprocess.xml -Applying linter tests... CHECK -.. CHECK: 2 test(s) found. -Applying linter output... CHECK -.. INFO: 3 outputs found. -Applying linter inputs... CHECK -.. INFO: Found 35 input parameters. -Applying linter help... CHECK -.. CHECK: Tool contains help section. -.. CHECK: Help contains valid reStructuredText. -Applying linter general... CHECK -.. CHECK: Tool defines a version [3.2]. -.. CHECK: Tool defines a name [FROGS Pre-process]. -.. CHECK: Tool defines an id [FROGS_preprocess]. -.. CHECK: Tool targets 16.01 Galaxy profile. -Applying linter command... CHECK -.. INFO: Tool contains a command. -Applying linter citations... CHECK -.. CHECK: Found 1 likely valid citations. -Applying linter tool_xsd... CHECK -.. INFO: File validates against XML schema. -Linting tool /home/maria/workspace/FROGS-wrappers_dev/r_alpha_diversity.xml -Applying linter tests... CHECK -.. CHECK: 1 test(s) found. -Applying linter output... CHECK -.. INFO: 2 outputs found. -Applying linter inputs... CHECK -.. INFO: Found 3 input parameters. -Applying linter help... CHECK -.. CHECK: Tool contains help section. -.. CHECK: Help contains valid reStructuredText. -Applying linter general... CHECK -.. CHECK: Tool defines a version [3.2]. -.. CHECK: Tool defines a name [FROGSSTAT Phyloseq Alpha Diversity]. -.. CHECK: Tool defines an id [FROGSSTAT_Phyloseq_Alpha_Diversity]. -.. CHECK: Tool targets 16.01 Galaxy profile. -Applying linter command... CHECK -.. INFO: Tool contains a command. -Applying linter citations... CHECK -.. CHECK: Found 1 likely valid citations. -Applying linter tool_xsd... CHECK -.. INFO: File validates against XML schema. -Linting tool /home/maria/workspace/FROGS-wrappers_dev/r_beta_diversity.xml -Applying linter tests... CHECK -.. CHECK: 1 test(s) found. -Applying linter output... CHECK -.. INFO: 1 outputs found. -Applying linter inputs... CHECK -.. INFO: Found 4 input parameters. -Applying linter help... CHECK -.. CHECK: Tool contains help section. -.. CHECK: Help contains valid reStructuredText. -Applying linter general... CHECK -.. CHECK: Tool defines a version [3.2]. -.. CHECK: Tool defines a name [FROGSSTAT Phyloseq Beta Diversity]. -.. CHECK: Tool defines an id [FROGSSTAT_Phyloseq_Beta_Diversity]. -.. CHECK: Tool targets 16.01 Galaxy profile. -Applying linter command... CHECK -.. INFO: Tool contains a command. -Applying linter citations... CHECK -.. CHECK: Found 1 likely valid citations. -Applying linter tool_xsd... CHECK -.. INFO: File validates against XML schema. -Linting tool /home/maria/workspace/FROGS-wrappers_dev/r_clustering.xml -Applying linter tests... CHECK -.. CHECK: 1 test(s) found. -Applying linter output... CHECK -.. INFO: 1 outputs found. -Applying linter inputs... CHECK -.. INFO: Found 3 input parameters. -Applying linter help... CHECK -.. CHECK: Tool contains help section. -.. CHECK: Help contains valid reStructuredText. -Applying linter general... CHECK -.. CHECK: Tool defines a version [3.2]. -.. CHECK: Tool defines a name [FROGSSTAT Phyloseq Sample Clustering]. -.. CHECK: Tool defines an id [FROGSSTAT_Phyloseq_Sample_Clustering]. -.. CHECK: Tool targets 16.01 Galaxy profile. -Applying linter command... CHECK -.. INFO: Tool contains a command. -Applying linter citations... CHECK -.. CHECK: Found 1 likely valid citations. -Applying linter tool_xsd... CHECK -.. INFO: File validates against XML schema. -Linting tool /home/maria/workspace/FROGS-wrappers_dev/r_composition.xml -Applying linter tests... CHECK -.. CHECK: 1 test(s) found. -Applying linter output... CHECK -.. INFO: 1 outputs found. -Applying linter inputs... CHECK -.. INFO: Found 6 input parameters. -Applying linter help... CHECK -.. CHECK: Tool contains help section. -.. CHECK: Help contains valid reStructuredText. -Applying linter general... CHECK -.. CHECK: Tool defines a version [3.2]. -.. CHECK: Tool defines a name [FROGSSTAT Phyloseq Composition Visualisation]. -.. CHECK: Tool defines an id [FROGSSTAT_Phyloseq_Composition_Visualisation]. -.. CHECK: Tool targets 16.01 Galaxy profile. -Applying linter command... CHECK -.. INFO: Tool contains a command. -Applying linter citations... CHECK -.. CHECK: Found 1 likely valid citations. -Applying linter tool_xsd... CHECK -.. INFO: File validates against XML schema. -Linting tool /home/maria/workspace/FROGS-wrappers_dev/remove_chimera.xml -Applying linter tests... CHECK -.. CHECK: 1 test(s) found. -Applying linter output... CHECK -.. INFO: 4 outputs found. -Applying linter inputs... CHECK -.. INFO: Found 4 input parameters. -Applying linter help... CHECK -.. CHECK: Tool contains help section. -.. CHECK: Help contains valid reStructuredText. -Applying linter general... CHECK -.. CHECK: Tool defines a version [3.2]. -.. CHECK: Tool defines a name [FROGS Remove chimera]. -.. CHECK: Tool defines an id [FROGS_remove_chimera]. -.. CHECK: Tool targets 16.01 Galaxy profile. -Applying linter command... CHECK -.. INFO: Tool contains a command. -Applying linter citations... CHECK -.. CHECK: Found 1 likely valid citations. -Applying linter tool_xsd... CHECK -.. INFO: File validates against XML schema. -Linting tool /home/maria/workspace/FROGS-wrappers_dev/r_import_data.xml -Applying linter tests... CHECK -.. CHECK: 1 test(s) found. -Applying linter output... CHECK -.. INFO: 2 outputs found. -Applying linter inputs... CHECK -.. INFO: Found 5 input parameters. -Applying linter help... CHECK -.. CHECK: Tool contains help section. -.. CHECK: Help contains valid reStructuredText. -Applying linter general... CHECK -.. CHECK: Tool defines a version [3.2]. -.. CHECK: Tool defines a name [FROGSSTAT Phyloseq Import Data]. -.. CHECK: Tool defines an id [FROGSSTAT_Phyloseq_Import_Data]. -.. CHECK: Tool targets 16.01 Galaxy profile. -Applying linter command... CHECK -.. INFO: Tool contains a command. -Applying linter citations... CHECK -.. CHECK: Found 1 likely valid citations. -Applying linter tool_xsd... CHECK -.. INFO: File validates against XML schema. -Linting tool /home/maria/workspace/FROGS-wrappers_dev/r_manova.xml -Applying linter tests... CHECK -.. CHECK: 1 test(s) found. -Applying linter output... CHECK -.. INFO: 1 outputs found. -Applying linter inputs... CHECK -.. INFO: Found 3 input parameters. -Applying linter help... CHECK -.. CHECK: Tool contains help section. -.. CHECK: Help contains valid reStructuredText. -Applying linter general... CHECK -.. CHECK: Tool defines a version [3.2]. -.. CHECK: Tool defines a name [FROGSSTAT Phyloseq Multivariate Analysis Of Variance]. -.. CHECK: Tool defines an id [FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance]. -.. CHECK: Tool targets 16.01 Galaxy profile. -Applying linter command... CHECK -.. INFO: Tool contains a command. -Applying linter citations... CHECK -.. CHECK: Found 1 likely valid citations. -Applying linter tool_xsd... CHECK -.. INFO: File validates against XML schema. -Linting tool /home/maria/workspace/FROGS-wrappers_dev/r_structure.xml -Applying linter tests... CHECK -.. CHECK: 1 test(s) found. -Applying linter output... CHECK -.. INFO: 1 outputs found. -Applying linter inputs... CHECK -.. INFO: Found 4 input parameters. -Applying linter help... CHECK -.. CHECK: Tool contains help section. -.. CHECK: Help contains valid reStructuredText. -Applying linter general... CHECK -.. CHECK: Tool defines a version [3.2]. -.. CHECK: Tool defines a name [FROGSSTAT Phyloseq Structure Visualisation]. -.. CHECK: Tool defines an id [FROGSSTAT_Phyloseq_Structure_Visualisation]. -.. CHECK: Tool targets 16.01 Galaxy profile. -Applying linter command... CHECK -.. INFO: Tool contains a command. -Applying linter citations... CHECK -.. CHECK: Found 1 likely valid citations. -Applying linter tool_xsd... CHECK -.. INFO: File validates against XML schema. -Linting tool /home/maria/workspace/FROGS-wrappers_dev/test.xml -Applying linter tests... CHECK -.. CHECK: 1 test(s) found. -Applying linter output... CHECK -.. INFO: 2 outputs found. -Applying linter inputs... CHECK -.. INFO: Found 2 input parameters. -Applying linter help... CHECK -.. CHECK: Tool contains help section. -.. CHECK: Help contains valid reStructuredText. -Applying linter general... CHECK -.. CHECK: Tool defines a version [3.2]. -.. CHECK: Tool defines a name [FROGS Tree]. -.. CHECK: Tool defines an id [FROGS_Tree]. -.. CHECK: Tool targets 16.01 Galaxy profile. -Applying linter command... CHECK -.. INFO: Tool contains a command. -Applying linter citations... CHECK -.. CHECK: Found 1 likely valid citations. -Applying linter tool_xsd... CHECK -.. INFO: File validates against XML schema. -Linting tool /home/maria/workspace/FROGS-wrappers_dev/tree.xml -Applying linter tests... CHECK -.. CHECK: 1 test(s) found. -Applying linter output... CHECK -.. INFO: 2 outputs found. -Applying linter inputs... CHECK -.. INFO: Found 2 input parameters. -Applying linter help... CHECK -.. CHECK: Tool contains help section. -.. CHECK: Help contains valid reStructuredText. -Applying linter general... CHECK -.. CHECK: Tool defines a version [3.2]. -.. CHECK: Tool defines a name [FROGS Tree]. -.. CHECK: Tool defines an id [FROGS_Tree]. -.. CHECK: Tool targets 16.01 Galaxy profile. -Applying linter command... CHECK -.. INFO: Tool contains a command. -Applying linter citations... CHECK -.. CHECK: Found 1 likely valid citations. -Applying linter tool_xsd... CHECK -.. INFO: File validates against XML schema. -Linting tool /home/maria/workspace/FROGS-wrappers_dev/tsv_to_biom.xml -Applying linter tests... CHECK -.. CHECK: 1 test(s) found. -Applying linter output... CHECK -.. INFO: 2 outputs found. -Applying linter inputs... CHECK -.. INFO: Found 3 input parameters. -Applying linter help... CHECK -.. CHECK: Tool contains help section. -.. CHECK: Help contains valid reStructuredText. -Applying linter general... CHECK -.. CHECK: Tool defines a version [3.2]. -.. CHECK: Tool defines a name [FROGS TSV_to_BIOM]. -.. CHECK: Tool defines an id [FROGS_tsv_to_biom]. -.. CHECK: Tool targets 16.01 Galaxy profile. -Applying linter command... CHECK -.. INFO: Tool contains a command. -Applying linter citations... CHECK -.. CHECK: Found 1 likely valid citations. -Applying linter tool_xsd... CHECK -.. INFO: File validates against XML schema.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/shedSave.yml Thu Apr 08 09:02:33 2021 +0000 @@ -0,0 +1,13 @@ +categories: +- Metagenomics +description: Suite for metabarcoding analysis +long_description: | + This is FROGS version 3.2.2 Galaxy Wrappers + FROGS: Find Rapidly OTUs through Galaxy Solution + FROGS is a workflow designed to produce an OTU count matrix from high depth sequencing amplicon data. + Adviced : + reorder integrated_tool_panel.xml as indicated here : https://github.com/geraldinepascal/FROGS-wrappers#simplest-way +name: frogs +owner: oinizan #TestToolshed +homepage_url: https://github.com/geraldinepascal/FROGS-wrappers +remote_repository_url: https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2