| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/obi_stat/obi_stat/1.2.13 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/obi_stat/obi_stat/1.2.11 |
| toolshed.g2.bx.psu.edu/repos/iuc/obi_stat/obi_stat/1.0.010 |
| obi_stat |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| obitools | 1.2.13 | package |
| Additional information about this tool |
#if $input.ext.endswith(".gz")
gunzip -c '$input' > input &&
#else
ln -s '$input' input &&
#end if
obistat
--without-progress-bar
#for $attribute in $catattributes
#if str( $attribute.options_attributespe.options_attributespe_selector) == "key"
-c '$attribute.options_attributespe.options_catattribute_selector'
#end if
#if str( $attribute.options_attributespe.options_attributespe_selector) == "python"
-c '${attribute.options_attributespe.attribute}'
#end if
#end for
#if str( $options_attribute.options_attributebe_selector) == "yes"
#if str( $options_attribute.options_attribute_selector) == "min"
-m '$options_attribute.options_uniq_selector'
#end if
#if str( $options_attribute.options_attribute_selector) == "max"
-M '$options_attribute.options_uniq_selector'
#end if
#if str( $options_attribute.options_attribute_selector) == "mean"
-a '$options_attribute.options_uniq_selector'
#end if
#if str( $options_attribute.options_attribute_selector) == "variance"
-v '$options_attribute.options_uniq_selector'
#end if
#if str( $options_attribute.options_attribute_selector) == "std"
-s '$options_attribute.options_uniq_selector'
#end if
#end if
#if $input_format_options.options_inputtype
$input_format_options.options_inputtype
#else
#if $input.ext.startswith("fasta")
--fasta
#else if $input.ext.startswith("fastqsolexa")
## input file is in fastq nucleic format produced by solexa sequencer
--solexa
#else
## input file is in sanger fastq nucleic format (standard fastq)
--sanger
#end if
#end if
#if $input_format_options.options_seqtype
$input_format_options.options_seqtype
#end if
input > '$output'
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
input: output_obiannotate.fasta catattributes_0|options_attributespe|options_catattribute_selector: count catattributes_0|options_attributespe|options_attributespe_selector: key catattributes_1|options_attributespe|options_catattribute_selector: merged catattributes_1|options_attributespe|options_attributespe_selector: key options_attribute|options_attribute_selector: min options_attribute|options_uniq_selector: seq_length options_attribute|options_attributebe_selector: yes |
name: value |
output_obiannotate.fasta value |
| Test-2 |
input: output_obiannotate.fasta.gz catattributes_0|options_attributespe|options_catattribute_selector: count catattributes_0|options_attributespe|options_attributespe_selector: key catattributes_1|options_attributespe|options_catattribute_selector: merged catattributes_1|options_attributespe|options_attributespe_selector: key options_attribute|options_attribute_selector: min options_attribute|options_uniq_selector: seq_length options_attribute|options_attributebe_selector: yes |
name: value |
output_obiannotate.fasta.gz value |