| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/earlhaminst/apoc/apoc/1.0+galaxy1 (this tool) |
| toolshed.g2.bx.psu.edu/repos/earlhaminst/apoc/apoc/1.0 |
| apoc |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| apoc | 1b16 | package |
| coreutils | 8.31 | package |
| Additional information about this tool |
#if $templates_source.template_source_select == 'list'
#for $i, $s in enumerate( $templates_source.template )
echo '${s.input.file_name}' >> templates_path &&
#end for#
paste -d "\t" templates_path '$templates_source.lt' | awk '{print $1"\t"$3}' > templates_list &&
#end if#
#if $query_source.query_source_select == 'list'
#for $i, $s in enumerate( $query_source.query )
echo '${s.input.file_name}' >> queries_path &&
#end for#
paste -d "\t" queries_path '$query_source.lq' | awk '{print $1"\t"$3}' > queries_list &&
#end if#
apoc
-fa $fa
-pvol $pvol
-plen $plen
$alignment_option.sod
-v $alignment_option.v
-m $scoring_option.m
#if str($scoring_option.L)
-L $scoring_option.L
#end if
$scoring_option.a
$scoring_option.b
$scoring_option.c
#if $templates_source.template_source_select == 'list'
-lt templates_list
#else
#if $templates_source.pt
-pt '$templates_source.pt'
#end if
'$templates_source.pdbfile1'
#end if
#if $query_source.query_source_select == 'list'
-lq queries_list
#else
#if $query_source.pq
-pq '$query_source.pq'
#end if
'$query_source.pdbfile2'
#end if
> $output_apoc
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
templates_source|pdbfile1: apoc/1ha3A.pdb templates_source|template_source_select: pdbfile query_source|pdbfile2: apoc/3ec1A.pdb query_source|query_source_select: pdbfile |
name: value |
apoc/1ha3A.pdb apoc/3ec1A.pdb value |
| Test-2 |
templates_source|lt: apoc/templ.lst templates_source|template_0|input: apoc/1ha3A.pdb templates_source|template_1|input: apoc/3ec1A.pdb templates_source|template_2|input: apoc/1yr8A.pdb templates_source|template_source_select: list query_source|pdbfile2: apoc/1yr8A.pdb query_source|query_source_select: pdbfile |
name: value |
apoc/templ.lst apoc/1ha3A.pdb apoc/3ec1A.pdb apoc/1yr8A.pdb value |
| Test-3 |
templates_source|lt: apoc/templ.lst templates_source|template_0|input: apoc/1ha3A.pdb templates_source|template_1|input: apoc/3ec1A.pdb templates_source|template_2|input: apoc/1yr8A.pdb templates_source|template_source_select: list query_source|pdbfile2: apoc/1ha3A.pdb query_source|pq: 1ha3_GDP_A_406 query_source|query_source_select: pdbfile |
name: value |
apoc/templ.lst apoc/1ha3A.pdb apoc/3ec1A.pdb apoc/1yr8A.pdb value |
| Test-4 |
templates_source|lt: apoc/templ.lst templates_source|template_0|input: apoc/1ha3A.pdb templates_source|template_1|input: apoc/3ec1A.pdb templates_source|template_2|input: apoc/1yr8A.pdb templates_source|template_source_select: list query_source|lq: apoc/query.lst query_source|query_0|input: apoc/3ec1A.pdb query_source|query_source_select: list |
name: value |
apoc/templ.lst apoc/1ha3A.pdb apoc/3ec1A.pdb apoc/1yr8A.pdb apoc/query.lst value |