| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/interval2maf/Interval2Maf1/1.0.1+galaxy1 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/interval2maf/Interval2Maf1/1.0.1+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/interval2maf/Interval2Maf1/1.0.1 |
| Interval2Maf1 |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| bx-python | 0.8.9 | package |
| galaxy-data | 22.1.1 | package |
| Additional information about this tool |
#if $maf_source_type.maf_source == "cached"
#set $tab = '\t'
echo "$maf_source_type.mafType.fields.name${tab}$maf_source_type.mafType.fields.value${tab}$maf_source_type.mafType.fields.indexed_for${tab}$maf_source_type.mafType.fields.exists_in_maf${tab}$maf_source_type.mafType.fields.path" >> ./maf_indexes.loc &&
#end if
python '$__tool_directory__/interval2maf.py'
--dbkey=${input1.dbkey}
--chromCol=${input1.metadata.chromCol}
--startCol=${input1.metadata.startCol}
--endCol=${input1.metadata.endCol}
--strandCol=${input1.metadata.strandCol}
--interval_file='$input1'
--output_file='$out_file1'
--species=$maf_source_type.species
--split_blocks_by_species=$split_blocks_by_species_selector.split_blocks_by_species
#if $maf_source_type.maf_source == "user"
--mafFile='$maf_source_type.mafFile'
--mafIndex='$maf_source_type.mafFile.metadata.maf_index'
#else
--mafType='$maf_source_type.mafType'
--mafIndexFile='./maf_indexes.loc'
#end if
#if $split_blocks_by_species_selector.split_blocks_by_species == "split_blocks_by_species"
--remove_all_gap_columns=$split_blocks_by_species_selector.remove_all_gap_columns
#end if
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
input1: interval2maf-in.bed maf_source_type|mafFile: interval2maf-in1.maf maf_source_type|species: ['hg38', 'mm10', 'eulFla1'] maf_source_type|maf_source: user split_blocks_by_species_selector|split_blocks_by_species: dont_split_blocks_by_species |
name: value |
interval2maf-in.bed interval2maf-in1.maf value |
| Test-2 |
input1: interval2maf-in.bed maf_source_type|mafType: TEST maf_source_type|species: ['hg38', 'mm10', 'eulFla1'] maf_source_type|maf_source: cached split_blocks_by_species_selector|split_blocks_by_species: dont_split_blocks_by_species |
name: value |
interval2maf-in.bed value |
| Test-3 |
input1: interval2maf-in.bed maf_source_type|mafType: TEST maf_source_type|species: ['hg38', 'mm10', 'eulFla1'] maf_source_type|maf_source: cached split_blocks_by_species_selector|split_blocks_by_species: dont_split_blocks_by_species |
name: value |
interval2maf-in.bed value |