Small problems in workflows

I installed all the tools on a clean galaxy instance based on all the workflows (`workflow-to-tools` + `shed-tools install`) + installed all the workflows itself and went trough all them manually, revealing following issues:

contributing | create-new-tutorial | Find Exons with the highest number of SNPs (or other features) | example-workflow.ga
-- | -- | -- | --

Step 4: Group\
No value found for 'Operation 1 > Replace non numeric data'.\
Step 5: Group\
No value found for 'Operation 1 > Replace non numeric data'.

epigenetics | estrogen-receptor-binding-site-identification | Identification of the binding sites of the Estrogen receptor - chip-seq | chip_seq.ga
-- | -- | -- | --

Step 13: plotFingerprint\
At least 1 datasets are required. Using default: ''.\
Step 21: multiBamSummary\
At least 2 datasets are required. Using default: ''.\
Step 22: computeMatrix\
At least 1 datasets are required. Using default: ''.\
Step 23: computeMatrix\
At least 1 datasets are required. Using default: ''.

epigenetics | methylation-seq | workflow-methylation-seq | methylation-seq.ga
-- | -- | -- | --

Step 19: computeMatrix\
At least 1 datasets are required. Using default: ''.\
Step 21: computeMatrix\
At least 1 datasets are required. Using default: ''.

proteomics | database-handling | Database Handling Tutorial Workflow2 including Mycoplasma | wf_database-handling_mycoplasma.ga
-- | -- | -- | --

Step 3: Protein Database Downloader\
An invalid option was selected for taxon, u'2148', please verify. Using default: '9606'.\
Step 4: Protein Database Downloader\
An invalid option was selected for taxon, u'2094', please verify. Using default: '9606'.\
Step 5: Protein Database Downloader\
An invalid option was selected for taxon, u'2115', please verify. Using default: '9606'.\
Step 6: Protein Database Downloader\
An invalid option was selected for taxon, u'2098', please verify. Using default: '9606'.\
Step 7: Protein Database Downloader\
An invalid option was selected for taxon, u'2100', please verify. Using default: '9606'.\
Step 8: Protein Database Downloader\
An invalid option was selected for taxon, u'2121', please verify. Using default: '9606'.

proteomics | protein-id-sg-ps | ProteinID_SG_PS_Tutorial_WF_datasetCollection | wf_proteinID_SG_PS_multipleFiles.ga
-- | -- | -- | --

Step 6: Peptide Shaker\
No value found for 'The species type to use for the gene annotation'. Using default: 'no_species_type'.

proteomics | protein-id-sg-ps | Peptide and Protein ID Tutorial | wf_proteinID_SG_PS.ga
-- | -- | -- | --

Step 6: Peptide Shaker\
No value found for 'The species type to use for the gene annotation'. Using default: 'no_species_type'.

proteomics | protein-id-oms | Peptide and Protein ID via OMS using two search engines | workflow_two-search-engines.ga
-- | -- | -- | --

Step 7: IDMerger\
No value found for 'Input files separated by blanks'. Using default: ''.

statistics | age-prediction-with-ml | age_prediction_rna_seq (imported from uploaded file) | age-prediction-rna.ga
-- | -- | -- | --

Step 4: Parallel Coordinates Plot\
No value found for 'All the dimensions in categorized datatype:'. Using default: 'True'.

transcriptomics | scrna-scanpy-pbmc3k | Clustering 3K PBMCs with Scanpy | main_workflow.ga
-- | -- | -- | --

Step 5: Import Anndata and loom\
No value found for 'obs_names'. Using default: 'CellID'.\
No value found for 'Annotated data matrix'. Using default: ''.\
No value found for 'Is the data matrix to read sparse?'. Using default: 'True'.\
No value found for 'var_names'. Using default: 'Gene'.\
No value found for 'Cleanup?'. Using default: 'False'.\
No value found for 'X_name'. Using default: 'spliced'.\
No value found for 'hd5 format to be created'. Using default: 'anndata'.\
No value found for 'Format for the annotated data matrix'. Using default: 'loom'.

transcriptomics | de-novo | transcriptomics-denovo-workflow | transcriptomics-denovo-workflow.ga
-- | -- | -- | --

Step 44: DESeq2\
No value found for '(Optional) provide a tabular file with additional batch factors to include in the model.'. Using default: ''.

visualisation | circos | asdf | main_workflow.ga
-- | -- | -- | --

Step 3: Circos\
No value found for 'Reverse these Chromosomes'.\
No value found for 'Skip first label'. Using default: 'False'.\
No value found for 'Convert bands from BED format to circos karyotype band format'. Using default: 'True'.\
No value found for 'Skip last label'. Using default: 'False'.\
No value found for 'Cytogenetic Bands'. Using default: ''.\
No value found for 'Limit/Filter Chromosomes'.\
No value found for 'Ideogram Color Scheme'. Using default: 'paired-12-qual'.

I don't know which need to be solved, and how we could to this the fastest?

Start by reproducing the workflow-to-tools and shed-tools install process on a clean Galaxy instance, then inspect the listed .ga files and their reported steps. Compare each warning with the corresponding workflow and tool configuration to determine which entries are actionable. Done means the affected workflows are corrected or each warning is explicitly triaged and documented.

Written by the indexing model from the issue text.