Fix duplicated options

[bernt-matthias]

There are many tools that have select parameters with duplicated values or names, which probably needs to be fixes. It would be interesting to see if there are valid cases among those.

In addition there are a few cases that mix defining options with 'option' children elements, a 'options' element or the 'dynamic_options' attribute .. here we need to verify if this actually works, e.g. with a test. If so we need to adapt the linter.

Here is the list of tools that currently suffer from this (please put your name / link to the PR next to the tool if you are working on this):

• tool_collections/bamtools/bamtools_filter/bamtools-filter.xml
  • bam_property_selector has multiple options with the same text content
• tools/augustus/augustus.xml Add explicit tar dependency for Augustus and Augustus Train #4813
  • organism has multiple options with the same text content
  • organism has multiple options with the same value
• tools/bcftools/bcftools_view.xml
  • types has multiple options with the same text content
  • exclude_types has multiple options with the same text content
• tools/bedtools/groupbyBed.xml
  • operation has multiple options with the same text content
  • operation has multiple options with the same value
• tools/busco/busco.xml
  • augustus_species has multiple options with the same text content
  • augustus_species has multiple options with the same value
• tools/colibread/discosnp_RAD.xml
  • coverage_options has multiple options with the same text content
• tools/colibread/discosnp_pp.xml
  • coverage_options has multiple options with the same text content
• tools/deseq2/deseq2.xml DESeq2: update dependencies #4188
  • output_selector has multiple options with the same text content
• tools/emboss_5/emboss_twofeat.xml emboss implement missing parameters #4734
  • overlap has multiple options with the same text content
• tools/enasearch/enasearch_search_data.xml
  • sortfields has multiple options with the same text content
  • sortfields has multiple options with the same text content
  • sortfields has multiple options with the same text content
  • sortfields options have to be defined by either 'option' children elements, a 'options' element or the 'dynamic_options' attribute.
  • sortfields has multiple options with the same text content
  • sortfields has multiple options with the same text content
  • sortfields has multiple options with the same text content
  • sortfields has multiple options with the same text content
  • sortfields has multiple options with the same text content
  • sortfields has multiple options with the same text content
  • sortfields has multiple options with the same text content
  • field has multiple options with the same text content
  • sortfields has multiple options with the same text content
  • field has multiple options with the same text content
  • sortfields has multiple options with the same text content
  • field has multiple options with the same text content
  • sortfields has multiple options with the same text content
  • field options have to be defined by either 'option' children elements, a 'options' element or the 'dynamic_options' attribute.
  • sortfields options have to be defined by either 'option' children elements, a 'options' element or the 'dynamic_options' attribute.
  • field has multiple options with the same text content
  • sortfields has multiple options with the same text content
  • field has multiple options with the same text content
  • sortfields has multiple options with the same text content
  • field has multiple options with the same text content
  • sortfields has multiple options with the same text content
  • field has multiple options with the same text content
  • sortfields has multiple options with the same text content
  • field has multiple options with the same text content
  • sortfields has multiple options with the same text content
  • field has multiple options with the same text content
  • sortfields has multiple options with the same text content
  • field has multiple options with the same text content
  • sortfields has multiple options with the same text content
• tools/freec/control_freec.xml
  • sex has multiple options with the same text content
  • sex has multiple options with the same text content
  • sex has multiple options with the same text content
• tools/gffread/gffread.xml
  • source has multiple options with the same text content
• tools/goenrichment/goenrichment.xml
  • correction has multiple options with the same text content
  • cutoff has multiple options with the same text content
  • graph has multiple options with the same text content
• tools/graphembed/graphembed.xml
  • cmap_name has multiple options with the same text content
• tools/gwastools/manhattan_plot.xml
  • thinning has multiple options with the same text content
• tools/hicexplorer/hicDetectLoops.xml
  • expected has multiple options with the same value
• tools/hicexplorer/hicPlotMatrix.xml
  • pca_type has multiple options with the same text content
• tools/hisat2/hisat2.xml
  • rg_labels has multiple options with the same text content
• tools/iedb_api/iedb_api.xml
  • seqsrc has multiple options with the same text content
• tools/jellyfish/jellyfish.xml
  • command has multiple options with the same text content
  • format_select has multiple options with the same text content
• tools/maker/maker.xml Maker: add an option to warn users about license #4390
  • augustus_species has multiple options with the same text content
  • augustus_species has multiple options with the same value
• tools/mothur/get.communitytype.xml
  • calc has multiple options with the same text content
  • calc has multiple options with the same value
  • calc has multiple options with the same text content
  • calc has multiple options with the same value
• tools/mothur/dist.shared.xml
  • calc has multiple options with the same text content
  • calc has multiple options with the same value
• tools/mothur/summary.shared.xml
  • calc has multiple options with the same text content
  • calc has multiple options with the same value
• tools/mothur/collect.shared.xml
  • calc has multiple options with the same text content
  • calc has multiple options with the same value
• [] tools/mothur/tree.shared.xml
  • calc has multiple options with the same text content
  • calc has multiple options with the same value
• tools/picard/picard_ValidateSamFile.xml
  • ignore has multiple options with the same text content
• tools/plink/plink.xml
  • func has multiple options with the same text content
  • ex_func has multiple options with the same text content
  • thinning has multiple options with the same text content
  • hwe has multiple options with the same text content
  • filter has multiple options with the same text content
  • set has multiple options with the same text content
  • cluster has multiple options with the same text content
  • mds_scaling has multiple options with the same text content
  • assoc has multiple options with the same text content
  • adjust has multiple options with the same text content
  • logistic has multiple options with the same text content
  • output_genome has multiple options with the same text content
• tools/poretools/poretools_qualpos.xml
  • extension has multiple options with the same text content
  • extension has multiple options with the same value
• tools/pretext/pretext_snapshot.xml
  • outformat has multiple options with the same text content
• tools/pygenometracks/pyGenomeTracks.xml
  • track_file_style_selector has multiple options with the same value
  • colormap has multiple options with the same text content
  • colormap has multiple options with the same value
  • colormap has multiple options with the same value
• tools/rgrnastar/rg_rnaStarSolo.xml
  • soloStrand has multiple options with the same text content
• tools/shasta/shasta.xml
  • config_select has multiple options with the same text content
  • consensus_caller_select has multiple options with the same text content
• tools/snpfreqplot/snpfreqplot.xml
  • color has multiple options with the same text content
  • method has multiple options with the same text content
• tools/umi_tools/umi-tools_whitelist.xml
  • extract_method has multiple options with the same text content
  • method has multiple options with the same text content
  • knee_method has multiple options with the same text content
• tools/umi_tools/umi-tools_extract.xml
  • extract_method has multiple options with the same text content
• tools/vsearch/search.xml
  • userfields has multiple options with the same text content
• tools/vsearch/alignment.xml
  • userfields has multiple options with the same text content

[tuncK]

As if this problem does not exist for Deseq2 anymore, or?

tools-iuc/tools/deseq2/deseq2.xml

Line 215 in f422a5a

<section name="output_options" title="Output options">

[bernt-matthias]

indeed