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Unused tool parameters #1185

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bernt-matthias opened this issue Jan 24, 2022 · 0 comments
Open
23 tasks

Unused tool parameters #1185

bernt-matthias opened this issue Jan 24, 2022 · 0 comments

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@bernt-matthias
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bernt-matthias commented Jan 24, 2022 •
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With galaxyproject/galaxy#12724 planemo lint may error on input parameters that are not used:

  • chemicaltoolbox/openbabel/ob_filter.xml
    • hbd_min
    • hbd_max
    • hba_min
    • hba_max
    • psa_min
    • psa_max
    • rotbonds_min
    • rotbonds_max
    • molwt_min
    • molwt_max
    • logp_min
    • logp_max
    • mr_min
    • mr_max
    • atoms_min
    • atoms_max
  • tools/antismash/antismash.xml
    • pfam2go
  • tools/flye/flye.xml
    • keep_haplotypes
  • tools/graphclust/graphclust.xml
    • nspdk_D
    • nspdk_ensf
    • nspdk_knn_center
    • nspdk_ensf
    • nspdk_ensf
    • nspdk_ensf
  • tools/image_processing/imagej2/imagej2_bunwarpj_elastic_transform.xml
    .. WARNING: XXX Param input [source_out_datatype] only found in output actions, better use extended metadata. (line 35) [/tool/inputs/param[4]]
  • tools/image_processing/imagej2/imagej2_bunwarpj_raw_transform.xml
    .. WARNING: XXX Param input [source_out_datatype] only found in output actions, better use extended metadata. (line 35) [/tool/inputs/param[4]]
  • tools/numeric_clustering/numeric_clustering.xml
    • n_clusters
    • init
    • n_init
    • max_iter
    • tol
    • precompute_distances
    • random_state
    • copy_x
    • eps
    • min_samples
    • metric
    • algorithm
    • leaf_size
    • threshold
    • branching_factor
    • n_clusters
    • damping
    • max_iter
    • convergence_iter
    • copy
    • affinity
    • bandwidth
    • bin_seeding
    • min_bin_freq
    • cluster_all
    • n_clusters
    • affinity
    • n_components
    • linkage
    • n_clusters
    • eigen_solver
    • random_state
    • n_init
    • gamma
    • affinity
    • n_neighbors
    • assign_labels
    • degree
    • coef0
    • n_clusters
    • init
    • n_init
    • max_iter
    • tol
    • random_state
    • batch_size
    • max_no_improvement
    • init_size
    • reassignment_ratio
  • tools/rest_tool/rest_tool.xml
    • input_type_search
    • search_name
    • xref_compound_select
    • xref_compound_select
  • tools/rna_tools/cofold/cofold.xml
    • noPS
  • tools/rna_tools/infernal/cmsearch.xml
    • noali
    • verbose
  • tools/rna_tools/infernal/cmalign.xml
    • g
  • tools/rna_tools/locarna/locarna_pairwise_p.xml Bump locarna to latest 1.x #1263
    • alifold_consensus_dp
    • consensus_structure
    • lonely_pairs
  • tools/rna_tools/locarna/locarna_exparnap.xml Bump locarna to latest 1.x #1263
    • rnafold_temperature
    • max_uil_length_ratio
    • max_bpil_length_ratio
  • tools/rna_tools/miRDeep2/miRDeep2_quantifier/quantifier.xml
    • skipPrecursMapping
  • tools/rna_tools/vienna_rna/rnasubopt.xml
    • circ
  • tools/rna_tools/vienna_rna/rnainverse.xml
    • temperature
    • dangling
  • tools/rna_tools/vienna_rna/rnaplfold.xml
    • plex_output
  • tools/rna_tools/vienna_rna/rnafold.xml
    • auto_id
    • id_prefix
    • id_digits
    • id_start
  • tools/rna_tools/vienna_rna/rnaduplex.xml
    • sorted
  • tools/rna_tools/vienna_rna/rnacofold.xml
    • c
  • tools/salmon/salmonquant.xml
    • phash
  • tools/salmon/alevin.xml
    • phash
    • minScoreFraction
  • tools/tgsgapcloser/tgsgapcloser.xml
    • r_round
    • p_round
@bernt-matthias bernt-matthias mentioned this issue Jan 24, 2022
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bernt-matthias added a commit to bernt-matthias/galaxytools that referenced this issue Nov 16, 2022
@bernt-matthias
add missing parameters to command
1f5ad29 
or remove non existent parameters from inputs

xref bgruening#1185
bernt-matthias added a commit to bernt-matthias/galaxytools that referenced this issue Nov 17, 2022
@bernt-matthias
add missing parameters to command
1e473c2 
or remove non existent parameters from inputs

xref bgruening#1185
bernt-matthias added a commit to bernt-matthias/galaxytools that referenced this issue Nov 23, 2022
@bernt-matthias
add missing parameters to command
5a2a8b9 
or remove non existent parameters from inputs

xref bgruening#1185
bgruening pushed a commit that referenced this issue Nov 23, 2022
@bernt-matthias
Bump locarna to latest 1.x (#1263)
d4d3f01 
* bump locarna to 1.9.2.3

- remove deprecated `--width` argument from `command`
- remove redundant `name` attributes
- add missing dashes to `argument` attributes
- make boolean attributes lowercase

* standardize labels and extend tests

- add expect_num_outputs
- standardize output labels

* add missing parameters to command

or remove non existent parameters from inputs

xref #1185

* add r requirement and workaround gxy bug

- r is needed in reiability profile tool
- make ouput options values unique as workaround for galaxyproject/galaxy#14998
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