Mercurial > repos > jjohnson > drep
changeset 1:7e2debc267eb draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit 3898da7c3685e3deca68c998abd7c7104740f5f3"
| author | jjohnson |
|---|---|
| date | Mon, 06 Jan 2020 15:18:20 -0500 |
| parents | b59ae99e47d4 |
| children | cb2fc9f60381 |
| files | drep_compare.xml drep_dereplicate.xml macros.xml |
| diffstat | 3 files changed, 57 insertions(+), 21 deletions(-) [+] |
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--- a/drep_compare.xml Mon Jan 06 11:11:06 2020 -0500 +++ b/drep_compare.xml Mon Jan 06 15:18:20 2020 -0500 @@ -19,19 +19,10 @@ <expand macro="clustering_options"/> <expand macro="taxonomy_options"/> <expand macro="warning_options"/> + <expand macro="select_outputs"/> </inputs> <outputs> <expand macro="common_outputs" /> -<!-- -outdir/data_tables/Cdb.csv -outdir/data_tables/Mdb.csv -outdir/data_tables/Ndb.csv -outdir/data_tables/Bdb.csv - - <data name="foldChange" format="tabular" label="${tool.name} on ${on_string}: BayesianFoldChangeAnalysis.tsv" from_work_dir="out/BayesianFoldChangeAnalysis.tsv"> - <filter>'bayesian' in experiment and 'ctr' in experiment['bayesian']</filter> - </data> ---> </outputs> <help><![CDATA[ TODO: Fill in help.
--- a/drep_dereplicate.xml Mon Jan 06 11:11:06 2020 -0500 +++ b/drep_dereplicate.xml Mon Jan 06 15:18:20 2020 -0500 @@ -23,12 +23,13 @@ <expand macro="scoring_options"/> <expand macro="taxonomy_options"/> <expand macro="warning_options"/> + <expand macro="select_drep_outputs"/> </inputs> <outputs> - <expand macro="common_outputs" /> <collection name="dereplicated_genomes" type="list" label="dereplicated_genomes"> - <discover_datasets pattern="__designation__" directory="out_drep/dereplicated_genomes" ext='fasta'/> + <discover_datasets pattern="__designation__" directory="outdir/dereplicated_genomes" ext='fasta'/> </collection> + <expand macro="drep_outputs" /> </outputs> <help><![CDATA[ TODO: Fill in help.
--- a/macros.xml Mon Jan 06 11:11:06 2020 -0500 +++ b/macros.xml Mon Jan 06 15:18:20 2020 -0500 @@ -255,18 +255,62 @@ #end if ]]></token> - <xml name="select_outputs"> - </xml> + <xml name="select_outputs"> + <param name="select_outputs" type="select" multiple="true" optional="false" label="Select outputs"> + <option value="log" selected="true">log</option> + <option value="warnings" selected="true">Warnings</option> + <option value="Primary_clustering_dendrogram" selected="true">Primary_clustering_dendrogram.pdf</option> + <option value="Secondary_clustering_dendrograms">Secondary_clustering_dendrograms.pdf</option> + <option value="Secondary_clustering_MDS">Secondary_clustering_MDS.pdf</option> + <option value="Clustering_scatterplots" selected="true">Clustering_scatterplots.pdf</option> + <yield/> + </param> + </xml> + <xml name="select_drep_outputs"> + <expand macro="select_outputs"> + <option value="Cluster_scoring">Cluster_scoring.pdf</option> + <option value="Winning_genomes">Winning_genomes.pdf</option> + <option value="Widb">Widb.csv</option> + <option value="Chdb">Chdb.tsv</option> + </expand> + </xml> <xml name="common_outputs"> - <data name="log" format="txt" label="${tool.name} on ${on_string}: Log" from_work_dir="outdir/log/logger.log"/> - <data name="warnings" format="txt" label="${tool.name} on ${on_string}: Log" from_work_dir="outdir/log/warnings.txt"/> - <data name="Primary_clustering_dendrogram" format="pdf" label="${tool.name} on ${on_string}: Primary_clustering_dendrogram.pdf" from_work_dir="outdir/figures/Primary_clustering_dendrogram.pdf"/> - <data name="Secondary_clustering_dendrograms" format="pdf" label="${tool.name} on ${on_string}: Secondary_clustering_dendrograms.pdf" from_work_dir="outdir/figures/Secondary_clustering_dendrograms.pdf"/> - <data name="Secondary_clustering_MDS" format="pdf" label="${tool.name} on ${on_string}: Secondary_clustering_MDS.pdf" from_work_dir="outdir/figures/Secondary_clustering_MDS.pdf"/> - <data name="Clustering_scatterplots" format="pdf" label="${tool.name} on ${on_string}: Clustering_scatterplots.pdf" from_work_dir="outdir/figures/Clustering_scatterplots.pdf"/> + <data name="log" format="txt" label="${tool.name} on ${on_string}: Log" from_work_dir="outdir/log/logger.log"> + <filter>'log' in select_outputs or not select_outputs</filter> + </data> + <data name="warnings" format="txt" label="${tool.name} on ${on_string}: Warnings" from_work_dir="outdir/log/warnings.txt"> + <filter>'warnings' in select_outputs</filter> + </data> + <data name="Primary_clustering_dendrogram" format="pdf" label="${tool.name} on ${on_string}: Primary_clustering_dendrogram.pdf" from_work_dir="outdir/figures/Primary_clustering_dendrogram.pdf"> + <filter>'Primary_clustering_dendrogram' in select_outputs</filter> + </data> + <data name="Secondary_clustering_dendrograms" format="pdf" label="${tool.name} on ${on_string}: Secondary_clustering_dendrograms.pdf" from_work_dir="outdir/figures/Secondary_clustering_dendrograms.pdf"> + <filter>'Secondary_clustering_dendrograms' in select_outputs</filter> + </data> + <data name="Secondary_clustering_MDS" format="pdf" label="${tool.name} on ${on_string}: Secondary_clustering_MDS.pdf" from_work_dir="outdir/figures/Secondary_clustering_MDS.pdf"> + <filter>'Secondary_clustering_MDS' in select_outputs</filter> + </data> + <data name="Clustering_scatterplots" format="pdf" label="${tool.name} on ${on_string}: Clustering_scatterplots.pdf" from_work_dir="outdir/figures/Clustering_scatterplots.pdf"> + <filter>'Clustering_scatterplots' in select_outputs</filter> + </data> </xml> - <xml name="common_outputs2"> + + + <xml name="drep_outputs"> + <expand macro="common_outputs"/> + <data name="Cluster_scoring" format="pdf" label="${tool.name} on ${on_string}: Cluster_scoring.pdf" from_work_dir="outdir/figures/Cluster_scoring.pdf"> + <filter>'Cluster_scoring' in select_outputs</filter> + </data> + <data name="Winning_genomes" format="pdf" label="${tool.name} on ${on_string}: Winning_genomes.pdf" from_work_dir="outdir/figures/Winning_genomes.pdf"> + <filter>'Winning_genomes' in select_outputs</filter> + </data> + <data name="Widb" format="csv" label="${tool.name} on ${on_string}: Widb.csv" from_work_dir="outdir/data_tables/Widb.csv"> + <filter>'Widb' in select_outputs</filter> + </data> + <data name="Chdb" format="tabular" label="${tool.name} on ${on_string}: Chdb.tsv" from_work_dir="outdir/data/checkM/checkM_outdir/Chdb.tsv"> + <filter>'Chdb' in select_outputs</filter> + </data> </xml> <token name="@GENOMES_HELP@"><![CDATA[