Repository revision
2:cd489cbd4d1c

Repository 'dimspy_sample_filter'
hg clone https://toolshed.g2.bx.psu.edu/repos/computational-metabolomics/dimspy_sample_filter

Sample Filter tool metadata
Miscellaneous
Remove peaks that fail to appear in x-out-of-n (biological) samples
dimspy_sample_filter
toolshed.g2.bx.psu.edu/repos/computational-metabolomics/dimspy_sample_filter/dimspy_sample_filter/2.0.0+galaxy0
2.0.0+galaxy0
None
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/computational-metabolomics/dimspy_sample_filter/dimspy_sample_filter/2.0.0+galaxy0 (this tool)
toolshed.g2.bx.psu.edu/repos/computational-metabolomics/dimspy_sample_filter/dimspy_sample_filter/1.4.0+galaxy0
dimspy_sample_filter
Requirements (dependencies defined in the <requirements> tag set)
name version type
dimspy 2.0.0 package
Additional information about this tool
dimspy sample-filter
        --input '$hdf5_file_in'
        --output '$hdf5_file_out'
        --min-fraction $min_fraction
        ${within}
        #if $rsd_threshold
            --rsd-threshold $rsd_threshold
        #end if
        #if $qc_label
            --qc-label '$qc_label'
        #end if
        #if $hdf5_to_txt.standard
            &&
            
        dimspy hdf5-pm-to-txt
        --input '$hdf5_file_out'
        --output '$matrix_file_out'
        --delimiter $delimiter
        --attribute_name $hdf5_to_txt.matrix_attr
        --representation-samples $hdf5_to_txt.representation_samples
    
        #end if
        #if $hdf5_to_txt.comprehensive
            &&
            
        dimspy hdf5-pm-to-txt
        --input '$hdf5_file_out'
        --output '$matrix_comprehensive_file_out'
        --delimiter $delimiter
        --comprehensive
        --attribute_name $hdf5_to_txt.matrix_attr
        --representation-samples $hdf5_to_txt.representation_samples
    
        #end if
    
    
None
False
Functional tests
name inputs outputs required files
Test-1 hdf5_file_in: pm_as_bf.h5
within: False
min_fraction: 0.5
rsd_threshold:
qc_label:
delimiter: tab
hdf5_to_txt|standard: True
hdf5_to_txt|comprehensive: True
hdf5_to_txt|representation_samples: rows
hdf5_to_txt|matrix_attr: intensity
name: value
name: value
name: value
pm_as_bf.h5
value
Test-2 hdf5_file_in: pm_as_bf.h5
within: False
min_fraction: 0.5
rsd_threshold:
qc_label:
delimiter: tab
hdf5_to_txt|standard: True
hdf5_to_txt|comprehensive: True
hdf5_to_txt|representation_samples: columns
hdf5_to_txt|matrix_attr: mz
name: value
name: value
name: value
pm_as_bf.h5
value
Test-3 hdf5_file_in: pm_as_bf.h5
within: True
min_fraction: 0.5
rsd_threshold:
qc_label:
delimiter: tab
hdf5_to_txt|standard: True
hdf5_to_txt|comprehensive: True
hdf5_to_txt|representation_samples: rows
hdf5_to_txt|matrix_attr: intensity
name: value
name: value
name: value
pm_as_bf.h5
value