Pipeline: longer/descriptive flags in tiny-* CommandLineTool specifications

tiny/cwl/tools/tiny-collapse.cwl

@@ -12,15 +12,15 @@ inputs:
     type: File
     inputBinding:
       position: 0
-      prefix: -i
+      prefix: --input-file
     doc: "The optionally gzipped fastq files to collapse"
 
   # Collapsed fasta name
   out_prefix:
     type: string
     inputBinding:
       position: 1
-      prefix: -o
+      prefix: --out-prefix
     doc: "The prefix for output files {prefix}_collapsed.fa and, if
       counts fall below threshold, {prefix}_collapsed_lowcounts.fa"
 
@@ -30,7 +30,7 @@ inputs:
     default: 0
     inputBinding:
       position: 2
-      prefix: -t
+      prefix: --threshold
     doc: "Sequences <= THRESHOLD will be omitted from {prefix}_collapsed.fa
       and will instead be placed in {prefix}_collapsed_lowcounts.fa"
 
@@ -40,7 +40,7 @@ inputs:
     default: false
     inputBinding:
       position: 3
-      prefix: -c
+      prefix: --compress
     doc: "Use gzip compression when writing fasta outputs"
 
   5p_trim:

tiny/cwl/tools/tiny-count.cwl

@@ -21,44 +21,44 @@ inputs:
   paths_file:
     type: File
     inputBinding:
-      prefix: -pf
+      prefix: --paths-file
 
   out_prefix:
     type: string
     inputBinding:
-      prefix: -o
+      prefix: --out-prefix
 
   # Optional inputs
 
   normalize_by_hits:
     type: string?
     inputBinding:
-      prefix: -nh
+      prefix: --normalize-by-hits
 
   decollapse:
     type: boolean?
     inputBinding:
-      prefix: -dc
+      prefix: --decollapse
 
   stepvector:
     type: string?
     inputBinding:
-      prefix: -sv
+      prefix: --stepvector
 
   all_features:
     type: boolean?
     inputBinding:
-      prefix: -a
+      prefix: --all-features
 
   is_pipeline:
     type: boolean?
     inputBinding:
-      prefix: -p
+      prefix: --is-pipeline
 
   diagnostics:
     type: boolean?
     inputBinding:
-      prefix: -d
+      prefix: --report-diags
 
   # The following optional inputs are for staging InitialWorkingDir files for pipeline execution
 

tiny/cwl/tools/tiny-plot.cwl

@@ -11,121 +11,121 @@ inputs:
   raw_counts:
     type: File
     inputBinding:
-      prefix: -rc
+      prefix: --raw-counts
     doc: "Raw, non-normalized feature counts from Counter"
 
   rule_counts:
     type: File
     inputBinding:
-      prefix: -uc
+      prefix: --rule-counts
     doc: "Raw, non-normalized counts by matched rule from Counter"
 
   norm_counts:
     type: File?
     inputBinding:
-      prefix: -nc
+      prefix: --norm-counts
     doc: "Normalized feature counts from DESeq"
 
   dge_tables:
     type: File[]?
     inputBinding:
-      prefix: -dge
+      prefix: --dge-tables
     doc: "Sample comparison tables from DESeq"
 
   summ_stats:
     type: File
     inputBinding:
-      prefix: -ss
+      prefix: --summary-stats
     doc: "The summary stats csv from Counter"
 
   len_dist_tables:
     type: File[]
     inputBinding:
-      prefix: -len
+      prefix: --len-dist
     doc: "5' end nucleotide vs. length matrices from Counter"
 
   dge_pval:
     type: float?
     inputBinding:
-      prefix: -pv
+      prefix: --p-value
     doc: "The p-value to use for DGE scatter plots (default: 0.05)"
 
   style_sheet:
     type: File?
     inputBinding:
-      prefix: -s
+      prefix: --style-sheet
     doc: "A .mplstyle sheet to use instead of tinyrna default styles"
 
   vector_scatter:
     type: boolean?
     inputBinding:
-      prefix: -v
+      prefix: --vector-scatter
     doc: "If provided, scatter plots will have vectorized points (slower)"
 
   len_dist_min:
     type: int?
     inputBinding:
-      prefix: -ldi
+      prefix: --len-dist-min
     doc: "The first length to plot in the range for len_dist plots"
 
   len_dist_max:
     type: int?
     inputBinding:
-      prefix: -lda
+      prefix: --len-dist-max
     doc: "The last length to plot in the range for len_dist plots"
 
   dge_min:
     type: double?
     inputBinding:
-      prefix: -dgi
+      prefix: --dge-min
     doc: "The log2 lower view limit in DGE scatter plots"
 
   dge_max:
     type: double?
     inputBinding:
-      prefix: -dga
+      prefix: --dge-max
     doc: "The log2 upper view limit in DGE scatter plots"
 
   unknown_class_label:
     type: string?
     inputBinding:
-      prefix: -unk
+      prefix: --unknown-class
     doc: \
       'Use this label in class-related plots for counts which were '
       'assigned by rules lacking a "Classify as..." value'
 
   unassigned_class_label:
     type: string?
     inputBinding:
-      prefix: -una
+      prefix: --unassigned-class
     doc: 'Use this label in class-related plots for unassigned counts'
 
   classes_include:
     type: string[]?
     inputBinding:
-      prefix: -ic
+      prefix: --classes-include
     doc: \
       'Only include these classes, if present, in class scatter '
       'plots (applies regardless of P value)'
 
   classes_exclude:
     type: string[]?
     inputBinding:
-      prefix: -ec
+      prefix: --classes-exclude
     doc: \
       'Omit these classes, if present, from class scatter plots '
       '(applies regardless of P value)'
 
   out_prefix:
     type: string?
     inputBinding:
-      prefix: -o
+      prefix: --out-prefix
     doc: "The prefix to use when naming output files (optional)"
 
   plot_requests:
     type: string[]
     inputBinding:
-      prefix: -p
+      prefix: --plots
     doc: "A list of desired plot types to produce"
 
 outputs: