| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/0.9.2 |
| toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/0.9.1 |
| toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/0.8 |
| table_compute |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| pandas | 1.2.4 | package |
| numpy | 1.19.2 | package |
| Additional information about this tool |
## Can only import generated userconfig.py if calling
## script is in the same directory. Soft-linking does
## not satisfy importing, so we copy everything.
cp '$userconf' ./userconfig.py &&
cp '$__tool_directory__/scripts/safety.py' ./safety.py &&
cp '$__tool_directory__/scripts/table_compute.py' ./table_compute.py &&
python ./table_compute.py
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
singtabop|input: small.tsv singtabop|user|select_cols_wanted: 2:4,2,2 singtabop|user|select_rows_wanted: 2:5,3,3 singtabop|user|select_keepdupe: select_cols_keepdupe singtabop|user|mode: select singtabop|use_type: single precision: 2 |
name: value |
small.tsv value |
| Test-2 |
singtabop|input: small.tsv singtabop|user|select_cols_wanted: 2:4,2,2 singtabop|user|select_keepdupe: ['select_cols_keepdupe', 'select_rows_keepdupe'] singtabop|user|mode: select singtabop|use_type: single precision: 2 |
name: value |
small.tsv value |
| Test-3 |
singtabop|input: small.tsv singtabop|user|select_rows_wanted: 2:5,3,3 singtabop|user|select_keepdupe: select_cols_keepdupe singtabop|user|mode: select singtabop|use_type: single precision: 2 |
name: value |
small.tsv value |
| Test-4 |
singtabop|input: small.tsv singtabop|user|axis: 1 singtabop|user|filtersumval_mode|operation: sum singtabop|user|filtersumval_mode|compare_op: gt singtabop|user|filtersumval_mode|against: 50 singtabop|user|filtersumval_mode|use: operation singtabop|user|mode: filtersumval singtabop|use_type: single precision: 2 |
name: value |
small.tsv value |
| Test-5 |
singtabop|input: small.tsv singtabop|user|axis: 0 singtabop|user|filtersumval_mode|operation: sum singtabop|user|filtersumval_mode|compare_op: ne singtabop|user|filtersumval_mode|against: 0 singtabop|user|filtersumval_mode|use: operation singtabop|user|mode: filtersumval singtabop|use_type: single precision: 2 |
name: value |
small.tsv value |
| Test-6 |
singtabop|input: small.tsv singtabop|user|axis: 0 singtabop|user|filtersumval_mode|operation: sum singtabop|user|filtersumval_mode|compare_op: gt singtabop|user|filtersumval_mode|against: 10 singtabop|user|filtersumval_mode|use: operation singtabop|user|mode: filtersumval singtabop|use_type: single precision: 2 |
name: value |
small.tsv value |
| Test-7 |
singtabop|input: small.tsv singtabop|user|axis: 0 singtabop|user|filtersumval_mode|operation: median singtabop|user|filtersumval_mode|compare_op: ge singtabop|user|filtersumval_mode|against: 2 singtabop|user|filtersumval_mode|use: operation singtabop|user|mode: filtersumval singtabop|use_type: single precision: 5 |
name: value |
small.tsv value |
| Test-8 |
singtabop|input: small.tsv singtabop|user|axis: 1 singtabop|user|filtersumval_mode|minmatch: 2 singtabop|user|filtersumval_mode|operation: gt singtabop|user|filtersumval_mode|against: 2 singtabop|user|filtersumval_mode|use: element singtabop|user|mode: filtersumval singtabop|use_type: single precision: 5 |
name: value |
small.tsv value |
| Test-9 |
singtabop|input: small.tsv singtabop|user|axis: 0 singtabop|user|filtersumval_mode|minmatch: 4 singtabop|user|filtersumval_mode|operation: str_ne singtabop|user|filtersumval_mode|against: 0 singtabop|user|filtersumval_mode|use: element singtabop|user|mode: filtersumval singtabop|use_type: single precision: 3 |
name: value |
small.tsv value |
| Test-10 |
singtabop|input: small.tsv singtabop|user|matrixapply_func|vector_op: max singtabop|user|dimension: 1 singtabop|user|mode: matrixapply singtabop|use_type: single out_opts: ['ignore_nas', 'output_headers_row'] precision: 0 |
name: value |
small.tsv value |
| Test-11 |
singtabop|input: small.tsv singtabop|user|element|scale_op: mod singtabop|user|element|scale_value: 5 singtabop|user|element|mode: scale singtabop|user|elem_val|element_op: None singtabop|user|mode: element singtabop|use_type: single precision: 2 |
name: value |
small.tsv value |
| Test-12 |
singtabop|input: small.tsv singtabop|user|matrixapply_func|custom_func: vec.sum()+vec.median() singtabop|user|matrixapply_func|vector_op: custom singtabop|user|dimension: 0 singtabop|user|mode: matrixapply singtabop|use_type: single out_opts: ['ignore_nas', 'output_headers_row'] precision: 2 |
name: value |
small.tsv value |
| Test-13 |
singtabop|input: small.tsv singtabop|user|element|custom_expr: (math.log10(elem)+elem)/elem if (elem < math.inf) else 1.0 singtabop|user|element|mode: custom singtabop|user|elem_val|element_value: 0 singtabop|user|elem_val|element_op: gt singtabop|user|mode: element singtabop|use_type: single |
name: value |
small.tsv value |
| Test-14 |
singtabop|input: mat1.umi.tsv singtabop|user|element|custom_expr: -math.log(1 - elem/4096) * 4096 if elem != 4096 else elem - 0.5 singtabop|user|element|mode: custom singtabop|user|elem_val|element_op: None singtabop|user|mode: element |
name: value |
mat1.umi.tsv value |
| Test-15 |
singtabop|input: mat2.umi.tsv singtabop|user|element|custom_expr: -math.log(1 - elem/4096) * 4096 if elem != 4096 else elem - 0.5 singtabop|user|element|mode: custom singtabop|user|elem_val|element_op: None singtabop|user|mode: element |
name: value |
mat2.umi.tsv value |
| Test-16 |
singtabop|input: small.tsv singtabop|user|general|fulltable_custom_expr: table - table.mean(0) / table.std(0) singtabop|user|general|use: custom singtabop|user|mode: fulltable singtabop|use_type: single |
name: value |
small.tsv value |
| Test-17 |
singtabop|tables_0|input: small.tsv singtabop|tables_1|input: small.tsv singtabop|tables_2|input: small.tsv singtabop|fulltable_custom_expr: (3 * table1) + np.log(table3 + 20) - table2 singtabop|use_type: multiple |
name: value |
small.tsv value |
| Test-18 |
singtabop|input: small.tsv singtabop|user|general|fulltable_custom_expr: table * 2 singtabop|user|general|use: custom singtabop|user|mode: fulltable singtabop|use_type: single |
name: value |
small.tsv value |
| Test-19 |
singtabop|input: small.tsv singtabop|user|general|fulltable_custom_expr: table == 5 singtabop|user|general|use: custom singtabop|user|mode: fulltable singtabop|use_type: single |
name: value |
small.tsv value |
| Test-20 |
singtabop|input: small.tsv singtabop|user|general|fulltable_custom_expr: for n in table: n = n + 1 singtabop|user|general|use: custom singtabop|user|mode: fulltable singtabop|use_type: single |
small.tsv |
|
| Test-21 |
singtabop|input: small.tsv singtabop|user|general|fulltable_custom_expr: table + table[0,0] singtabop|user|general|use: custom singtabop|user|mode: fulltable singtabop|use_type: single |
small.tsv |
|
| Test-22 |
singtabop|input: small.tsv singtabop|user|general|use: transpose singtabop|user|mode: fulltable singtabop|use_type: single out_opts: ['ignore_nas', 'output_headers_col'] |
name: value |
small.tsv value |
| Test-23 |
singtabop|input: small.tsv singtabop|user|general|id_vars: cell1,cell3 singtabop|user|general|value_vars: cell5,cell6 singtabop|user|general|use: melt singtabop|user|mode: fulltable singtabop|use_type: single out_opts: ['ignore_nas', 'output_headers_col'] |
name: value |
small.tsv value |
| Test-24 |
singtabop|input: small.tsv singtabop|user|general|index: cell1 singtabop|user|general|column: cell2 singtabop|user|general|values: cell3,cell7,cell9 singtabop|user|general|use: pivot singtabop|user|mode: fulltable singtabop|use_type: single |
name: value |
small.tsv value |
| Test-25 |
singtabop|input: examples.1.tsv singtabop|col_row_names: ['has_col_names', 'has_row_names'] singtabop|user|select_cols_wanted: 1,1,3 singtabop|user|select_rows_wanted: 1:3,2 singtabop|user|select_keepdupe: ['select_cols_keepdupe', 'select_rows_keepdupe'] singtabop|user|mode: select singtabop|use_type: single |
name: value |
examples.1.tsv value |
| Test-26 |
singtabop|input: examples.2.tsv singtabop|col_row_names: ['has_col_names', 'has_row_names'] singtabop|user|axis: 1 singtabop|user|filtersumval_mode|operation: sum singtabop|user|filtersumval_mode|compare_op: lt singtabop|user|filtersumval_mode|against: 50 singtabop|user|filtersumval_mode|use: operation singtabop|user|mode: filtersumval singtabop|use_type: single |
name: value |
examples.2.tsv value |
| Test-27 |
singtabop|input: examples.3p1.tsv singtabop|col_row_names: ['has_col_names', 'has_row_names'] singtabop|user|element|custom_expr: elem < 10 singtabop|user|element|mode: custom singtabop|user|elem_val|element_op: None singtabop|user|mode: element singtabop|use_type: single |
name: value |
examples.3p1.tsv value |
| Test-28 |
singtabop|input: examples.3p2.tsv singtabop|col_row_names: ['has_col_names', 'has_row_names'] singtabop|user|matrixapply_func|vector_op: sum singtabop|user|dimension: 1 singtabop|user|mode: matrixapply singtabop|use_type: single |
name: value |
examples.3p2.tsv value |
| Test-29 |
singtabop|input: examples.4.tsv singtabop|col_row_names: ['has_col_names', 'has_row_names'] singtabop|user|element|custom_expr: (math.log(elem) / elem) if (elem > 5) else 1 singtabop|user|element|mode: custom singtabop|user|mode: element singtabop|use_type: single |
name: value |
examples.4.tsv value |
| Test-30 |
singtabop|input: examples.5.tsv singtabop|col_row_names: ['has_col_names', 'has_row_names'] singtabop|user|general|fulltable_custom_expr: table - table.mean(0)/table.std(0) singtabop|user|general|use: custom singtabop|user|mode: fulltable singtabop|use_type: single |
name: value |
examples.5.tsv value |
| Test-31 |
singtabop|tables_0|input: examples.6p1.tsv singtabop|tables_0|col_row_names: ['has_col_names', 'has_row_names'] singtabop|tables_1|input: examples.6p2.tsv singtabop|tables_1|col_row_names: ['has_col_names', 'has_row_names'] singtabop|tables_2|input: examples.6p3.tsv singtabop|tables_2|col_row_names: ['has_col_names', 'has_row_names'] singtabop|fulltable_custom_expr: table1 / min(np.max(np.max(table2)), np.max(np.max(table3))) singtabop|use_type: multiple |
name: value |
examples.6p1.tsv examples.6p2.tsv examples.6p3.tsv value |
| Test-32 |
singtabop|input: examples.7.tsv singtabop|col_row_names: ['has_col_names', 'has_row_names'] singtabop|user|general|id_vars: A singtabop|user|general|value_vars: B,C singtabop|user|general|use: melt singtabop|user|mode: fulltable singtabop|use_type: single |
name: value |
examples.7.tsv value |
| Test-33 |
singtabop|input: examples.8.tsv singtabop|col_row_names: ['has_col_names', 'has_row_names'] singtabop|user|general|index: foo singtabop|user|general|column: bar singtabop|user|general|values: baz singtabop|user|general|use: pivot singtabop|user|mode: fulltable singtabop|use_type: single |
name: value |
examples.8.tsv value |
| Test-34 |
singtabop|input: examples.1.tsv singtabop|user|select_cols_wanted: -2:2,1,-1 singtabop|user|select_rows_wanted: 1,3:-3,1 singtabop|user|mode: select singtabop|use_type: single |
name: value |
examples.1.tsv value |
| Test-35 |
singtabop|input: examples.1.tsv singtabop|user|select_cols_wanted: -1,-3,3:-3,2 singtabop|user|select_rows_wanted: 3:-1 singtabop|user|select_keepdupe: singtabop|user|mode: select singtabop|use_type: single |
name: value |
examples.1.tsv value |
| Test-36 |
singtabop|input: skiplines.tsv singtabop|adv|header: 2 singtabop|adv|nrows: 4 singtabop|adv|skip_blank_lines: True singtabop|user|mode: precision singtabop|use_type: single precision: 2 |
name: value |
skiplines.tsv value |
| Test-37 |
singtabop|input: skiplines.tsv singtabop|adv|header: 2 singtabop|adv|skipfooter: 2 singtabop|adv|skip_blank_lines: False singtabop|user|mode: precision singtabop|use_type: single out_opts: precision: 2 |
name: value |
skiplines.tsv value |
| Test-38 |
singtabop|input: examples.1.tsv singtabop|col_row_names: ['has_col_names', 'has_row_names'] singtabop|user|element|replace_value: chr{elem:.0f} singtabop|user|element|mode: replace singtabop|user|elem_val|select_cols_wanted: 2 singtabop|user|elem_val|select_rows_wanted: 2,4 singtabop|user|elem_val|inclusive_selection: True singtabop|user|elem_val|element_op: rowcol singtabop|user|mode: element singtabop|use_type: single |
name: value |
examples.1.tsv value |
| Test-39 |
singtabop|input: examples.1.tsv singtabop|col_row_names: ['has_col_names', 'has_row_names'] singtabop|user|element|replace_value: chr{elem:.0f} singtabop|user|element|mode: replace singtabop|user|elem_val|select_cols_wanted: 2 singtabop|user|elem_val|select_rows_wanted: 2,4 singtabop|user|elem_val|inclusive_selection: False singtabop|user|elem_val|element_op: rowcol singtabop|user|mode: element singtabop|use_type: single |
name: value |
examples.1.tsv value |
| Test-40 |
singtabop|input: examples.1.tsv singtabop|col_row_names: ['has_col_names', 'has_row_names'] singtabop|user|element|replace_value: a'+'b singtabop|user|element|mode: replace singtabop|user|elem_val|element_op: None singtabop|user|mode: element singtabop|use_type: single |
name: value |
examples.1.tsv value |
| Test-41 |
singtabop|input: examples.4.tsv singtabop|col_row_names: ['has_col_names', 'has_row_names'] singtabop|user|element|custom_expr: el'+'em singtabop|user|element|mode: custom singtabop|user|mode: element singtabop|use_type: single |
examples.4.tsv |
|
| Test-42 |
singtabop|input: pivot.tsv singtabop|col_row_names: ['has_col_names', 'has_row_names'] singtabop|user|general|index: Position singtabop|user|general|colfun_map_0|column: Age singtabop|user|general|colfun_map_0|functions_0|aggfunc: mean singtabop|user|general|colfun_map_1|column: Random singtabop|user|general|colfun_map_1|functions_0|aggfunc: mean singtabop|user|general|colfun_map_1|functions_1|aggfunc: std singtabop|user|general|use: pivot singtabop|user|mode: fulltable singtabop|use_type: single |
name: value |
pivot.tsv value |
| Test-43 |
singtabop|input: table1.tsv singtabop|col_row_names: has_col_names singtabop|user|general|index: A singtabop|user|general|column: C singtabop|user|general|values: D singtabop|user|general|aggfunc: max singtabop|user|general|use: pivot singtabop|user|mode: fulltable singtabop|use_type: single |
name: value |
table1.tsv value |