| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/melpetera/batchcorrection/Batch_correction/3.0.0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/melpetera/batchcorrection/Batch_correction/2.0.6 |
| Batch_correction |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| r-batch | 1.1_4 | package |
| r-ade4 | 1.7_8 | package |
| bioconductor-pcamethods | 1.70.0 | package |
| bioconductor-ropls | 1.10.0 | package |
| Additional information about this tool |
#if str($span_condition.method) == 'all_loess_pool':
Rscript $__tool_directory__/batch_correction_all_loess_wrapper.R
dataMatrix "$dataMatrix"
sampleMetadata "$sampleMetadata"
variableMetadata "$variableMetadata"
method "all_loess_pool"
span "${span_condition.span}"
#elif str($span_condition.method) == 'all_loess_sample':
Rscript $__tool_directory__/batch_correction_all_loess_wrapper.R
dataMatrix "$dataMatrix"
sampleMetadata "$sampleMetadata"
variableMetadata "$variableMetadata"
method "all_loess_sample"
span "${span_condition.span}"
#else:
Rscript $__tool_directory__/batch_correction_3Lwrapper.R
analyse "batch_correction"
dataMatrix "$dataMatrix"
sampleMetadata "$sampleMetadata"
variableMetadata "$variableMetadata"
method "${span_condition.method}"
#if str($span_condition.method) == 'linear':
span "none"
#else:
span "${span_condition.span}"
#end if
valnull "${span_condition.valnull}"
ref_factor "${span_condition.ref_factor}"
detail "${span_condition.detail}"
#end if
dataMatrix_out "$dataMatrix_out" variableMetadata_out "$variableMetadata_out"
graph_output "$graph_output" rdata_output "$rdata_output"
batch_col_name "$smcust.batch_col_name"
injection_order_col_name "$smcust.injection_order_col_name"
sample_type_col_name "$smcust.sample_type_col_name"
sample_type_tags "blank=$smcust.sampleTypeTagBlank,pool=$smcust.sampleTypeTagPool,sample=$smcust.sampleTypeTagSample"
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
dataMatrix: input-batchcorrection-dataMatrix.tsv sampleMetadata: input-batchcorrection-sampleMetadata.tsv variableMetadata: input-batchcorrection-variableMetadata.tsv span_condition|span: 1 span_condition|method: all_loess_pool |
name: value |
input-batchcorrection-dataMatrix.tsv input-batchcorrection-sampleMetadata.tsv input-batchcorrection-variableMetadata.tsv value |
| Test-2 |
dataMatrix: input-batchcorrection-dataMatrix.tsv sampleMetadata: input-batchcorrection-sampleMetadata-customSampleType.tsv variableMetadata: input-batchcorrection-variableMetadata.tsv smcust|sample_type_col_name: MySampType smcust|sampleTypeTagPool: lot smcust|sampleTypeTagBlank: blanc smcust|sampleTypeTagSample: echant span_condition|span: 1 span_condition|method: loess |
name: value |
input-batchcorrection-dataMatrix.tsv input-batchcorrection-sampleMetadata-customSampleType.tsv input-batchcorrection-variableMetadata.tsv value |