Fix test parameters that are not defined in the inputs

[bernt-matthias]

There are many cases where test parameters are used that are not defined in the inputs.

I guess most cases are easy to solve, but may require a bit of research:

• check if the parameter was there in the past and was removed, then we can also remove the test parameter
• check the underlying tools if there is such a parameter and maybe add it to the inputs (ie. it was forgotten to be implemented in the tool)
• ...

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):

• [x] tool_collections/cufflinks/cuffdiff/cuffdiff_wrapper.xml https://github.com/galaxyproject/tools-iuc/pull/4202
  • do_normalization
• [x] tool_collections/vcflib/vcfcheck/vcfcheck.xml https://github.com/galaxyproject/tools-iuc/pull/4201
  • failure_selection
• [x] tool_collections/fastx_toolkit/fastx_clipper/fastx_clipper.xml https://github.com/galaxyproject/tools-iuc/pull/4200
  • maxmismatches
• [x] tool_collections/kraken/kraken-translate.xml https://github.com/galaxyproject/tools-iuc/pull/4199
  • mpa-format
• [x] tool_collections/bamtools/bamtools_split/bamtools_split.xml https://github.com/galaxyproject/tools-iuc/pull/4198
  • output_type
• [x] tool_collections/samtools/ https://github.com/galaxyproject/tools-iuc/pull/4197
  • samtools_merge/samtools_merge.xml bed
  • samtools_markdup/samtools_markdup.xml mode_selector
  • samtools_markdup/samtools_markdup.xml fails
• [x] tools/merlin/merlin.xml https://github.com/galaxyproject/tools-iuc/pull/4203
  • random
• [x] tools/bioext/bealign.xml https://github.com/galaxyproject/tools-iuc/pull/4204
  • add_background
  • background_source
• [ ] tools/mothur/consensus.seqs.xml
  • labels
• [ ] tools/mothur/list.otulabels.xml
  • infile
• [ ] tools/mothur/classify.otu.xml
  • sum
• [ ] tools/mothur/seq.error.xml
  • output_sel
• [ ] tools/mothur/get.coremicrobiome.xml
  • group
• [x] tools/berokka/berokka.xml https://github.com/galaxyproject/tools-iuc/pull/4205
  • filter_select
• [x] tools/chira/chira_map.xml https://github.com/galaxyproject/tools-iuc/pull/4206
  • unmapped
• [ ] tools/metaspades/metaspades.xml
  • sc
  • careful
• [x] tools/masigpro/masigpro.xml https://github.com/galaxyproject/tools-iuc/pull/4207
  • replicates_selector
• [x] tools/cutadapt/cutadapt.xml https://github.com/galaxyproject/tools-iuc/pull/4195
  • output_filtering
  • read_modification
• [x] tools/hyphy/ https://github.com/galaxyproject/tools-iuc/pull/4246
  • branches
  • posterior
  • multiple_hits
• [ ] tools/porechop/porechop.xml
  • extra_middle_trim_good_size
  • extra_middle_trim_bad_size
• [ ] tools/schicexplorer/scHicAdjustMatrix.xml
  • clusterMethod_selector
• [ ] tools/cutesv/cutesv.xml
  • seq_method
• [ ] tools/lofreq/lofreq_alnqual.xml
  • recompute
• [ ] tools/sniffles/sniffles.xml
  • output_format
• [ ] tools/picard/picard_MergeBamAlignment.xml https://github.com/galaxyproject/tools-iuc/pull/5151 https://github.com/galaxyproject/tools-iuc/pull/5103
  • orientation
• [ ] tools/picard/picard_CollectAlignmentSummaryMetrics.xml https://github.com/galaxyproject/tools-iuc/pull/5151 https://github.com/galaxyproject/tools-iuc/pull/5103
  • sorted
  • adaptors
• [ ] tools/picard/picard_SamToFastq.xml https://github.com/galaxyproject/tools-iuc/pull/5151 https://github.com/galaxyproject/tools-iuc/pull/5103
  • output_per_rg
• [x] tools/bcftools/bcftools_view.xml https://github.com/galaxyproject/tools-iuc/pull/4728
  • regions
• [ ] tools/poretools/poretools_times.xml
  • types
  • detailed
• [ ] tools/poretools/poretools_winner.xml
  • types
• [ ] tools/poretools/poretools_tabular.xml
  • types
  • detailed
• [ ] tools/lastz/lastz.xml
  • traceback
  • word
• [ ] tools/emboss_5/emboss_sirna.xml https://github.com/galaxyproject/tools-iuc/pull/4734
  • mismatchpercent
• [ ] tools/macs2/macs2_callpeak.xml
  • lower
  • upper
• [ ] tools/iqtree/iqtree.xml
  • b https://github.com/galaxyproject/tools-iuc/pull/4724
• [ ] tools/bedtools/mergeBed.xml https://github.com/galaxyproject/tools-iuc/pull/4219
  • strandedness
  • report_number
• [ ] tools/hivclustering/hivclustering.xml
  • json
• [ ] tools/tb-profiler/tb_profiler_profile.xml
  • call_whole_genome
• [ ] tools/samblaster/samblaster.xml
  • discordandFile
• [ ] tools/salsa2/salsa2.xml
  • length
  • enzyme
• [x] tools/hicexplorer/hicPlotSVL.xml https://github.com/galaxyproject/tools-iuc/pull/4670
  • color
• [ ] tools/gatk4/gatk4_Mutect2.xml
  • seqdict_source
• [x] tools/rseqc/geneBody_coverage2.xml https://github.com/galaxyproject/tools-iuc/pull/4235
  • rscript_output
• [ ] tools/sonneityping/parse_mykrobe_predict.xml
  • optional.alleles
• [ ] tools/umi_tools/umi-tools_extract.xml
  • quality_encoding
• [ ] tools/usher/usher.xml
  • retain_input_branch
• [ ] tools/qiime/qiime_core/multiple_join_paired_ends.xml
  • barcode_indicator
• [ ] tools/qiime/qiime_core/pick_closed_reference_otus.xml
  • input_fps
• [x] tools/bwa_mem2/bwa-mem2.xml https://github.com/galaxyproject/tools-iuc/pull/4220
  • index_a
• [x] tools/crossmap/crossmap_bam.xml https://github.com/galaxyproject/tools-iuc/pull/4221
  • include_fails
• [ ] tools/intermine_galaxy_exchange/intermine_galaxy_exchange.xml
  • forganism_column
• [x] tools/mummer4 https://github.com/galaxyproject/tools-iuc/pull/4209
  • dnadiff.xml input_type
  • mummer.xml options
• [x] tools/diamond/diamond.xml https://github.com/galaxyproject/tools-iuc/pull/4210
  • comp-based-stat
• [x] tools/orthofinder/orthofinder_only_groups.xml https://github.com/galaxyproject/tools-iuc/pull/4222
  • inflation
• [x] tools/codeml/codeml.xml https://github.com/galaxyproject/tools-iuc/pull/4216
  • adv.fix_omega
  • adv.omega
  • adv.fix_omega
  • adv.omega
  • adv.fix_omega
  • adv.omega
• [x] tools/transit/transit_resampling.xml https://github.com/galaxyproject/tools-iuc/pull/4223
  • burnin
• [x] tools/bandage/bandage_info.xml https://github.com/galaxyproject/tools-iuc/pull/4217
  • select_mode
• [x] tools/trinity/align_and_estimate_abundance.xml https://github.com/galaxyproject/tools-iuc/pull/4218
  • gene_to_trans
• [x] tools/funannotate/funannotate_compare.xml https://github.com/galaxyproject/tools-iuc/pull/4211
  • outputs
• [x] tools/repeatmodeler/repeatmodeler.xml https://github.com/galaxyproject/tools-iuc/pull/4214
  • name
  • pa
• [x] tools/genebed_maf_to_fasta/genebed_maf_to_fasta.xml https://github.com/galaxyproject/tools-iuc/pull/4215
  • maf_identifier
• [x] tools/bwameth/bwameth.xml https://github.com/galaxyproject/tools-iuc/pull/4213
  • referenceSource
• [ ] tools/hansel/bio_hansel.xml
  • type_of_scheme https://github.com/galaxyproject/tools-iuc/pull/6416
• [ ] tools/colibread/
  • input_type https://github.com/galaxyproject/tools-iuc/pull/6417
• [ ] tools/colibread/discosnp_RAD.xml
  • b https://github.com/galaxyproject/tools-iuc/pull/6417
• [ ] tools/bracken/est-abundance.xml
  • bracken_database
• [x] tools/stacks2/stacks_shortreads.xml https://github.com/galaxyproject/tools-iuc/pull/4194
  • add_log

[gallardoalba]

In the case of SALSA2, I think that only this lines should be removed https://github.com/galaxyproject/tools-iuc/blob/master/tools/salsa2/salsa2.xml#L92 https://github.com/galaxyproject/tools-iuc/blob/master/tools/salsa2/salsa2.xml#L85

[gallardoalba]

In the case of USHER, the parameter of this test should be replaced by retain_input_branch_length, but the rest is fine https://github.com/galaxyproject/tools-iuc/blob/master/tools/usher/usher.xml#L302

[bernt-matthias]

but the rest is fine

Which rest do you mean?

[gallardoalba]

but the rest is fine

Which rest do you mean?

I mean, the correct name of this parameter is retain_input_branch_lengths; only this test should be modified.