| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/nanocompore_sampcomp/nanocompore_sampcomp/1.0.0rc3.post2+galaxy1 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/nanocompore_sampcomp/nanocompore_sampcomp/1.0.0rc3.post2+galaxy0 |
| nanocompore_sampcomp |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| nanocompore | 1.0.0rc3.post2 | package |
| tar | 1.32 | package |
| Additional information about this tool |
## initialize
## requires a minimum of 3 threads
threads=\$((3 > \${GALAXY_SLOTS:-3} ? 3 : \${GALAXY_SLOTS:-3})) &&
## same name pattern required
#for $i, $current in enumerate($file1_rep)
ln -s '$current.file' 'sample_1_${i}.tsv' &&
ln -s '$current.index' 'sample_1_${i}.tsv.idx' &&
#end for
#for $i, $current in enumerate($file2_rep)
ln -s '$current.file' 'sample_2_${i}.tsv' &&
ln -s '$current.index' 'sample_2_${i}.tsv.idx' &&
#end for
## symlink fasta file because a .fai file is created
ln -s '$fasta' reference.fa &&
## run
nanocompore sampcomp
## required
--label1 '$label1'
#set files1 = ','.join(['sample_1_' + str(item) + '.tsv' for item in range(len($file1_rep))])
--file_list1 '$files1'
--label2 '$label2'
#set files2 = ','.join(['sample_2_' + str(item) + '.tsv' for item in range(len($file2_rep))])
--file_list2 '$files2'
--fasta reference.fa
## optional
#if $ap.bed
--bed '$ap.bed'
#end if
--max_invalid_kmers_freq $ap.max_invalid_kmers_freq
--min_coverage $ap.min_coverage
--min_ref_length $ap.min_ref_length
--comparison_methods '$ap.comparison_methods'
--sequence_context $ap.sequence_context
--sequence_context_weights '$ap.sequence_context_weights'
--pvalue_thr $ap.pvalue_thr
$ap.logit
$ap.allow_warnings
--outpath 'results'
--nthreads \$threads
--log_level debug
&& tar -cf 'results/db.tar' 'results/out_SampComp.db.bak' 'results/out_SampComp.db.dir' 'results/out_SampComp.db.dat'
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
file1_rep_0|file: sample1.tsv file1_rep_0|index: sample1.tsv.idx file2_rep_0|file: sample2.tsv file2_rep_0|index: sample2.tsv.idx fasta: reference.fa |
name: value name: value name: value |
sample1.tsv sample1.tsv.idx sample2.tsv sample2.tsv.idx reference.fa value |
| Test-2 |
label1: C1 file1_rep_0|file: sample1.tsv file1_rep_0|index: sample1.tsv.idx label2: C2 file2_rep_0|file: sample2.tsv file2_rep_0|index: sample2.tsv.idx fasta: reference.fa ap|max_invalid_kmers_freq: 0.2 ap|min_coverage: 31 ap|min_ref_length: 101 ap|comparison_methods: ['GMM', 'KS', 'TT', 'MW'] ap|sequence_context: 1 ap|sequence_context_weights: harmonic ap|pvalue_thr: 0.06 ap|logit: True ap|allow_warnings: True ap|out: ['results', 'shift', 'db', 'log'] |
name: value name: value name: value name: value |
sample1.tsv sample1.tsv.idx sample2.tsv sample2.tsv.idx reference.fa value |