Fix invalid datatypes

[bernt-matthias]

IUC has quite some tools using datatypes that are not known to Galaxy:

for i in $(grep 'format="' . --include "*xml" -r | sed "s/'/\"/g" | sed 's/.*format="\([^"]*\)".*/\1/' | sed 's/,/\n/g' | sort -u) 
do
if ! grep -q "\"$i\"" ~/projects/galaxy/lib/galaxy/config/sample/datatypes_conf.xml.sample;
then
echo "- $i" && grep "format=\"$i" . --include "*xml" -r -l | sort -u | sed 's/^/  - /'
fi
done | grep -E -v "\.gz|\.bz2"

Would be cool to extend planemo lint checking for valid datatypes, but I could not find datatypes.conf (or the sample) in any of the galaxy-* packages. Comments for this are very welcome.

• [ ] allegro_haplo allegro_linkage
  • ./tools/allegro/allegro.xml ..(ideas for missing datatypes may be here: https://github.com/galaxyproject/tools-iuc/pull/1488)
• [ ] aln
  • ./tools/art/art_454.xml
  • ./tools/art/art_illumina.xml
• [ ] antigenic https://github.com/galaxyproject/tools-iuc/pull/4734
  • ./tools/emboss_5/emboss_antigenic.xml
• [ ] BAM
  • ./tools/deepvariant/deepvariant.xml https://github.com/galaxyproject/tools-iuc/pull/5811
• [ ] biom
  • ./tools/humann/humann.xml
  • ./tools/metagenomeseq/metagenomeseq_normalization.xml
  • ./tools/metaphlan/metaphlan.xml
  • ./tools/mothur/biom.info.xml
  • ./tools/mothur/make.biom.xml
  • ./tools/mothur/make.shared.xml
  • ./tools/picrust/categorize_by_function.xml
  • ./tools/picrust/compare_biom.xml
  • ./tools/picrust/macros.xml
  • ./tools/picrust/metagenome_contributions.xml
  • ./tools/picrust/normalize_by_copy_number.xml
  • ./tools/picrust/predict_metagenomes.xml
  • ./tools/qiime/qiime_add_on/collapse_samples.xml
  • ./tools/qiime/qiime_add_on/make_otu_table.xml
  • ./tools/qiime/qiime_core/filter_fasta.xml
  • ./tools/qiime/qiime_core/filter_otus_from_otu_table.xml
  • ./tools/qiime/qiime_core/filter_samples_from_otu_table.xml
  • ./tools/qiime/qiime_core/filter_taxa_from_otu_table.xml
  • ./tools/qiime/qiime_core/make_otu_heatmap.xml
  • ./tools/qiime/qiime_core/pick_closed_reference_otus.xml
  • ./tools/qiime/qiime_core/pick_open_reference_otus.xml
  • ./tools/qiime/qiime_core/summarize_taxa_through_plots.xml
• [ ] blast
  • ./tools/blastxml_to_gapped_gff3/blastxml_to_gapped_gff3.xml
  • ./tools/kobas/kobas_macros.xml
  • ./tools/last/maf-convert.xml
• [ ] dict
  • ./tools/last/maf-convert.xml
• [ ] dot
  • ./tools/roary/roary.xml
• [ ] emf
  • ./tools/hicexplorer/macros.xml
• [ ] Fasta
  • ./tools/basil/basil.xml
  • ./tools/porechop/porechop.xml
• [ ] linkage_recomb
  • ./tools/allegro/allegro.xml
  • ./tools/swift/swift.xml
• [x] lod https://github.com/galaxyproject/tools-iuc/pull/4037
  • ./tools/merlin/merlin.xml
• [ ] nw
  • ./tools/newick_utils/newick_display.xml
• [ ] nwk
  • ./tools/newick_utils/newick_display.xml
• [ ] oddcomp
  • ./tools/emboss_5/emboss_oddcomp.xml
• [ ] phy
  • ./tools/breseq/breseq.xml
  • ./tools/fasttree/fasttree.xml
  • ./tools/graphlan/graphlan_annotate.xml
  • ./tools/gubbins/gubbins.xml
  • ./tools/msaboot/msaboot.xml
  • ./tools/phyml/phyml.xml
  • ./tools/rapidnj/rapidnj.xml
• [ ] ps
  • ./tools/ggplot2/macros.xml
  • ./tools/graphlan/graphlan.xml
  • ./tools/mitos/mitos2.xml https://github.com/galaxyproject/tools-iuc/pull/5152
  • ./tools/mitos/mitos.xml https://github.com/galaxyproject/tools-iuc/pull/5152
• [x] psl
  • ./tools/ucsc_blat/blat.xml https://github.com/galaxyproject/tools-iuc/pull/4928
• [x] scool https://github.com/galaxyproject/tools-iuc/pull/4060
  • ./tools/schicexplorer/macros.xml
  • ./tools/schicexplorer/scHicAdjustMatrix.xml
  • ./tools/schicexplorer/scHicConsensusMatrices.xml
  • ./tools/schicexplorer/scHicCorrectMatrices.xml
  • ./tools/schicexplorer/scHicMergeMatrixBins.xml
  • ./tools/schicexplorer/scHicMergeToSCool.xml
  • ./tools/schicexplorer/scHicNormalize.xml
  • ./tools/schicexplorer/scHicQualityControl.xml
• [ ] seqmatchall
  • ./tools/emboss_5/emboss_seqmatchall.xml
• [ ] text
  • ./tools/augustus/augustus.xml
  • ./tools/biom_format/biom_subset_table.xml https://github.com/galaxyproject/tools-iuc/pull/4027
  • ./tools/biom_format/biom_summarize_table.xml https://github.com/galaxyproject/tools-iuc/pull/5545
  • ~./tools/emboss_5/emboss_textsearch.xml~ textsearch is a valid datatype
  • ./tools/enasearch/enasearch_search_data.xml
  • ./tools/hivclustering/hivclustering.xml
  • ./tools/ncbi_entrez_eutils/ https://github.com/galaxyproject/tools-iuc/pull/4048
  • ./tools/sra-tools/sra_macros.xml https://github.com/galaxyproject/tools-iuc/pull/5546
  • ./tools/tetyper/tetyper.xml
  • ./tools/ucsc_blat/blat.xml https://github.com/galaxyproject/tools-iuc/pull/4928

[bernt-matthias]

Would be cool to extend planemo lint checking for valid datatypes

This might come automatically (but via planemo test) by https://github.com/galaxyproject/galaxy/pull/12073

[bernt-matthias]

Would be cool to extend planemo lint checking for valid datatypes

This might come automatically (but via planemo test) by galaxyproject/galaxy#12073

True for inputs that are covered by tests. But not for uncovered inputs and all outputs. So linting for this would be cool.