| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/migmap/migmap/1.0.3+galaxy2 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/migmap/migmap/1.0.3+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/iuc/migmap/migmap/1.0.3 |
| toolshed.g2.bx.psu.edu/repos/iuc/migmap/migmap/1.0.2.2 |
| toolshed.g2.bx.psu.edu/repos/iuc/migmap/migmap/1.0.2.1 |
| migmap |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| migmap | 1.0.3 | package |
| Additional information about this tool |
export IGBLAST_PATH=\$(dirname \$(which igblastn)) &&
mkdir -p temp_db/igblast &&
ln -s "\${IGBLAST_PATH}/../share/igblast/bin/" ./temp_db/igblast &&
ln -s "\${IGBLAST_PATH}/../share/igblast/internal_data/" ./temp_db/igblast &&
ln -s "\${IGBLAST_PATH}/../share/igblast/optional_file/" ./temp_db/igblast &&
#if $input.is_of_type('fasta') :
ln -s '$input' in.fa &&
#else if $input.is_of_type('fasta.gz') :
ln -s '$input' in.fa.gz &&
#else if $input.is_of_type('fastq') :
ln -s '$input' in.fq &&
#else if $input.is_of_type('fastq.gz') :
ln -s '$input' in.fq.gz
#end if
migmap
$allow_incomplete
$allow_no_cdr3
$allow_noncanonical
$allow_noncoding
$all_alleles
$by_read
#if str($qual_threshold):
-q $qual_threshold
#end if
-p "\${GALAXY_SLOTS:-4}"
--data-dir ./temp_db/igblast/
-S $species
-R $receptor_list
#if $input.is_of_type('fasta'):
in.fa
#else
in.fq
#end if
'$output'
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
input: test_stop_codon.fa allow_incomplete: True all_alleles: True allow_no_cdr3: True allow_noncanonical: True allow_noncoding: True by_read: True |
name: value |
test_stop_codon.fa value |
| Test-2 |
input: test_stop_codon.fq.gz allow_incomplete: True all_alleles: True allow_no_cdr3: True allow_noncanonical: True allow_noncoding: True by_read: True |
name: value |
test_stop_codon.fq.gz value |
| Test-3 |
input: test_out_of_frame.fa allow_noncoding: True by_read: True |
name: value |
test_out_of_frame.fa value |