| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/cooc_pubmut/cooc_pubmut/0.9.1+galaxy0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/cooc_pubmut/cooc_pubmut/0.9+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/cooc_pubmut/cooc_pubmut/0.2+galaxy0 |
| cooc_pubmut |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| cojac | 0.9.1 | package |
| pandoc | 3.1.3 | package |
| gmp | 6.2.1 | package |
| Additional information about this tool |
#if $annotations.availability == 'full':
#set $voc_config = $annotations.voc_source
#if $voc_config.choice == 'custom'
mkdir -p voc &&
#for $input_file in $voc_config.collection
ln -s '$input_file' 'voc/$input_file.element_identifier' &&
#end for
#else
DB_PATH="\$(dirname "\$(dirname "\$(which cojac)")")/share/cojac/voc" &&
ln -s "\$DB_PATH" voc &&
#end if
#end if
cojac cooc-pubmut
#if $annotations.availability == 'full':
-m voc/
#end if
#if $annotations.availability != 'none':
-a '$annotations.in_amp'
#end if
#if $cooc_data.ext == 'json':
-j '$cooc_data'
#else
-y '$cooc_data'
#end if
-q
#if $out_opts.format == 'tsv':
-o cooc-table.tsv
#else:
-o cooc-table.csv
#if $out_opts.format == 'html':
&& pandoc cooc-table.csv -o cooc-table.html
#end if
#end if
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
cooc_data: cooc-test111.json annotations|in_amp: amplicons111.yaml |
name: value |
cooc-test111.json amplicons111.yaml value |
| Test-2 |
cooc_data: cooc-test111.json annotations|in_amp: amplicons111.yaml out_opts|format: csv |
name: value |
cooc-test111.json amplicons111.yaml value |
| Test-3 |
cooc_data: cooc-test111.json annotations|in_amp: amplicons111.yaml out_opts|format: html |
name: value |
cooc-test111.json amplicons111.yaml value |