| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/earlhaminst/t_coffee/t_coffee/13.45.0.4846264 (this tool) |
| toolshed.g2.bx.psu.edu/repos/earlhaminst/t_coffee/t_coffee/11.0.8_1 |
| toolshed.g2.bx.psu.edu/repos/earlhaminst/t_coffee/t_coffee/11.0.8 |
| t_coffee |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| t-coffee | 13.45.0.4846264 | package |
| Additional information about this tool |
#if str($input_type.filter_fasta) == 'yes'
#set $input = 'temp.fasta'
python '$__tool_directory__/filter_by_fasta_ids.py' '$input_type.identifiers' '$input_type.fasta_input' > temp.fasta &&
#end if
#set $method_opt = ''
#if $method01
#set $method_opt += str($method01) + ','
#end if
#if $method02
#set $method_opt += str($method02) + ','
#end if
#if $method03
#set $method_opt += str($method03) + ','
#end if
#if $method_opt
#set $method_opt = '-method ' + $method_opt[:-1]
#end if
#set $output_opt = ''
#if $outputs
#set $outputs_arr = str($outputs).split(',')
#for $o in $outputs_arr
#if $o != 'dnd'
#set $output_opt += $o + ','
#end if
#end for
#else
#set $outputs_arr = []
#end if
#if $output_opt
#set $output_opt = '-output ' + $output_opt[:-1]
#end if
t_coffee '$input' $method_opt $output_opt -n_core \${GALAXY_SLOTS:-1} -run_name t_coffee_out -quiet
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
input_type|input: input.fasta input_type|filter_fasta: no method02: clustalw_msa outputs: fasta_aln |
name: value |
input.fasta value |
| Test-2 |
input_type|fasta_input: input.fasta input_type|identifiers: ids.txt input_type|filter_fasta: yes method02: clustalw_msa outputs: fasta_aln |
name: value |
input.fasta ids.txt value |
| Test-3 |
input_type|input: input.fasta input_type|filter_fasta: no method03: ['clustalw_pair', 't_coffee_pair'] method01: ['sap_pair', 'mustang_pair', 'TMalign_pair'] method02: ['mafft_msa', 'clustalw_msa', 'dialigntx_msa', 'poa_msa', 'probcons_msa', 'muscle_msa', 't_coffee_msa', 'kalign_msa'] outputs: ['clustalw_aln', 'dnd', 'fasta_aln', 'fasta_seq', 'msf_aln', 'phylip', 'pir_aln', 'pir_seq', 'score_ascii', 'score_html'] |
name: value name: value name: value name: value name: value name: value name: value name: value name: value name: value |
input.fasta value |