Miscellaneous |
Version lineage of this tool (guids ordered most recent to oldest) |
toolshed.g2.bx.psu.edu/repos/iuc/stacks2_cstacks/stacks2_cstacks/2.55+galaxy4 (this tool) |
toolshed.g2.bx.psu.edu/repos/iuc/stacks2_cstacks/stacks2_cstacks/2.55+galaxy3 |
toolshed.g2.bx.psu.edu/repos/iuc/stacks2_cstacks/stacks2_cstacks/2.55+galaxy2 |
toolshed.g2.bx.psu.edu/repos/iuc/stacks2_cstacks/stacks2_cstacks/2.55+galaxy1 |
toolshed.g2.bx.psu.edu/repos/iuc/stacks2_cstacks/stacks2_cstacks/2.55+galaxy0 |
toolshed.g2.bx.psu.edu/repos/iuc/stacks2_cstacks/stacks2_cstacks/2.53+galaxy0 |
toolshed.g2.bx.psu.edu/repos/iuc/stacks2_cstacks/stacks2_cstacks/2.4+galaxy1 |
toolshed.g2.bx.psu.edu/repos/iuc/stacks2_cstacks/stacks2_cstacks/2.4+galaxy0 |
stacks2_cstacks |
Requirements (dependencies defined in the <requirements> tag set) |
name | version | type |
stacks | 2.55 | package |
python | 3.7 | package |
findutils | 4.6.0 | package |
Additional information about this tool |
#import re trap ">&2 cat '$output_log'" err exit && mkdir stacks_inputs stacks_outputs && #set $samples = [] #for $input_file in $input_stacks #set $filename = str($input_file.element_identifier) #if not filename.endswith('.tsv') #set $filename = $filename + ".tsv" #end if #if re.search('^(?!catalog).+\.(tags|alleles|snps)\.tsv$', $filename) ln -s '${input_file}' 'stacks_inputs/$filename' && #if $filename.endswith('.tags.tsv') $samples.append($filename[:-9]) #end if #end if #end for cstacks -p \${GALAXY_SLOTS:-1} #if $popmap -P stacks_inputs -M '$popmap' #else #for $sample in $samples -s 'stacks_inputs/$sample' #end for -o stacks_outputs #end if -n $n ## -c not implemented in Galaxy (appending can be done in Galaxy) #if $gapped.use_gapped == "yes" --max_gaps $gapped.max_gaps --min_aln_len $gapped.min_aln_len #else --disable-gapped #end if ## Advanced Options #if $k_len: --k_len $k_len #end if $report_mmatches #if $output_log 2> '$output_log' #end if #if $popmap ## When using a popmap, cstacks writes to the input dir && mv stacks_inputs/catalog.*.tsv stacks_outputs/ #end if
Functional tests |
name | inputs | outputs | required files |
Test-1 |
input_stacks: list collection popmap: denovo_map/popmap_cstacks.tsv add_log: True |
name: value |
ustacks/PopA_01.alleles.tsv ustacks/PopA_01.snps.tsv ustacks/PopA_01.tags.tsv ustacks/PopA_02.alleles.tsv ustacks/PopA_02.snps.tsv ustacks/PopA_02.tags.tsv denovo_map/popmap_cstacks.tsv value |
Test-2 |
input_stacks: list collection add_log: True |
name: value |
ustacks/PopA_01.alleles.tsv ustacks/PopA_01.snps.tsv ustacks/PopA_01.tags.tsv ustacks/PopA_02.alleles.tsv ustacks/PopA_02.snps.tsv ustacks/PopA_02.tags.tsv value |
Test-3 |
input_stacks: list collection n: 2 k_len: 23 report_mmatches: True add_log: False |
ustacks/PopA_01.alleles.tsv ustacks/PopA_01.snps.tsv ustacks/PopA_01.tags.tsv ustacks/PopA_02.alleles.tsv ustacks/PopA_02.snps.tsv ustacks/PopA_02.tags.tsv |