| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_contigs/mothur_make_contigs/1.39.5.1 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_contigs/mothur_make_contigs/1.39.5.0 |
| toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_contigs/mothur_make_contigs/1.36.1.0 |
| mothur_make_contigs |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| mothur | 1.39.5 | package |
| Additional information about this tool |
set -o pipefail; export TERM=vt100;
## Symlinks creation or On the fly creation of a combo file
#if $input_type.type == 'list_collection'
#for $pair in $input_type.list_paired_collection:
ln -s ${pair.forward} `basename ${pair.forward}` &&
ln -s ${pair.reverse} `basename ${pair.reverse}` &&
echo -e "${pair.name}\t`basename ${pair.forward}`\t`basename ${pair.reverse}`" >> combo_fastq.dat &&
#end for
#elif $input_type.type == 'simple_collection'
ln -s '$input_type.paired_collection.forward' ffastq.dat &&
ln -s '$input_type.paired_collection.reverse' rfastq.dat &&
#else
ln -s '$input_type.forward_fastq' ffastq.dat &&
ln -s '$input_type.reverse_fastq' rfastq.dat &&
#end if
#if $oligo.add == "yes":
ln -s '$oligo.oligos' oligo.oligos.dat &&
ln -s '$oligo.findex' oligo.findex.dat &&
ln -s '$oligo.rindex' oligo.rindex.dat &&
#end if
echo 'make.contigs(
#if $input_type.type == 'list_collection':
file=combo_fastq.dat,
#else:
ffastq=ffastq.dat,
rfastq=rfastq.dat,
#end if
align=$align,
#if $oligo.add == "yes":
oligos=oligo.oligos.dat,
bdiffs=$oligo.bdiffs,
pdiffs=$oligo.pdiffs,
tdiffs=$oligo.tdiffs,
#if $oligo.findex:
findex=oligo.findex.dat,
#end if
#if $oligo.rindex:
rindex=oligo.rindex.dat,
#end if
#end if
match=$match,
mismatch=$mismatch,
gapopen=$gapopen,
gapextend=$gapextend,
rename=$rename,
processors='\${GALAXY_SLOTS:-8}'
)'
| sed 's/ //g' ## mothur trips over whitespace
| mothur
| tee mothur.out.log
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
input_type|forward_fastq: Mock_S280_L001_R1_001_small.fastq input_type|reverse_fastq: Mock_S280_L001_R2_001_small.fastq input_type|type: regular rename: False savelog: True |
name: value name: value name: value name: value |
Mock_S280_L001_R1_001_small.fastq Mock_S280_L001_R2_001_small.fastq value |
| Test-2 |
input_type|paired_collection: paired collection input_type|type: simple_collection rename: False savelog: True |
name: value name: value name: value name: value |
Mock_S280_L001_R1_001_small.fastq Mock_S280_L001_R2_001_small.fastq value |
| Test-3 |
input_type|paired_collection: paired collection input_type|type: simple_collection align: gotoh match: 2 mismatch: -2 gapopen: -3 gapextend: -2 rename: False savelog: True |
name: value name: value name: value name: value |
Mock_S280_L001_R1_001_small.fastq Mock_S280_L001_R2_001_small.fastq value |
| Test-4 |
input_type|paired_collection: paired collection input_type|type: simple_collection rename: True savelog: True |
name: value name: value name: value name: value |
Mock_S280_L001_R1_001_small.fastq Mock_S280_L001_R2_001_small.fastq value |
| Test-5 |
input_type|list_paired_collection: list:paired collection input_type|type: list_collection rename: False savelog: True |
name: value name: value name: value name: value name: value |
Mock_S280_L001_R1_001_small.fastq Mock_S280_L001_R2_001_small.fastq test_forward.fastq test_reverse.fastq value |