annotate test-data/biosample.tsv @ 5:10866c1f8e06 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 7f7605c2c8d8e92f3369dfdc290e5d8d06fa409a

#This is a tab-delimited file. Additional Documentation can be found at http://www.mothur.org/wiki/MIMarks_Data_Packages.
#Please fill all the required fields indicated with '*'
#Unknown or inapplicable fields can be assigned 'missing' value.
#You may add extra custom fields to this template. Make sure all the fields are separated by tabs.
#You may remove any fields not required (marked with '*'). Make sure all the fields are separated by tabs.
#You can edit this template using Microsoft Excel or any other editor. But while saving the file please make sure to save them as 'TAB-DELIMITED' TEXT FILE.
#MIMARKS.survey.miscellaneous.4.0
#{sample name}	{description of sample}	{sample title}	{description of library_construction_protocol}	{http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=408169&lvl=3&keep=1&srchmode=1&unlock}	{Date of sampling, in "DD-Mmm-YYYY", "Mmm-YYYY" or "YYYY" format (eg., 30-Oct-1990, Oct-1990 or 1990) or ISO 8601 standard "YYYY-mm-dd", "YYYY-mm" or "YYYY-mm-ddThh:mm:ss" (eg., 1990-10-30, 1990-10 or 1990-10-30T14:41:36)}	{descriptor of the broad ecological context of a sample. Examples include: desert, taiga, deciduous woodland, or coral reef. EnvO (v 2013-06-14) terms can be found via the link: www.environmentontology.org/Browse-EnvO}	{descriptor of the local environment. Examples include: harbor, cliff, or lake. EnvO (v 2013-06-14) terms can be found via the link: www.environmentontology.org/Browse-EnvO}	{material that was displaced by the sample, or material in which a sample was embedded, prior to the sampling event. Examples include: air, soil, or water. EnvO (v 2013-06-14) terms can be found via the link: www.environmentontology.org/Browse-EnvO}	{Geographical origin of the sample; use the appropriate name from this list http://www.insdc.org/documents/country-qualifier-vocabulary. Use a colon to separate the country or ocean from more detailed information about the location, eg "Canada: Vancouver" or "Germany: halfway down Zugspitze, Alps"}	{The geographical coordinates of the location where the sample was collected. Specify as degrees latitude and longitude in format "d[d.dddd] N|S d[dd.dddd] W|E", eg, 38.98 N 77.11 W}	{alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate}	{The altitude of the sample is the vertical distance between Earth's surface above Sea Level and the sampled position in the air.}	{concentration of ammonium}	{amount of biomass; should include the name for the part of biomass measured, e.g. microbial, total. can include multiple measurements}	{concentration of bromide}	{concentration of calcium}	{list of chemical compounds administered to the host or site where sampling occurred, and when (e.g. antibiotics, N fertilizer, air filter); can include multiple compounds. For Chemical Entities of Biological Interest ontology (CHEBI) (v1.72), please see http://bioportal.bioontology.org/visualize/44603}	{concentration of chloride}	{concentration of chlorophyll}	{density of sample}	{Depth is defined as the vertical distance below surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectivly. Depth can be reported as an interval for subsurface samples.}	{concentration of diether lipids; can include multiple types of diether lipids}	{concentration of dissolved carbon dioxide}	{concentration of dissolved hydrogen}	{dissolved inorganic carbon concentration}	{dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2}	{concentration of dissolved oxygen}	{The elevation of the sampling site as measured by the vertical distance from mean sea level.}	{any other measurement performed or parameter collected, that is not listed here}	{concentration of nitrate}	{concentration of nitrite}	{concentration of nitrogen (total)}	{concentration of organic carbon}	{concentration of organic matter}	{concentration of organic nitrogen}	{total count of any organism per gram or volume of sample,should include name of organism followed by count; can include multiple organism counts}	{oxygenation status of sample}	{type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with time that perturbation occurred; can include multiple perturbation types}	{pH measurement}	{concentration of phosphate}	{concentration of phospholipid fatty acids; can include multiple values}	{concentration of potassium}	{pressure to which the sample is subject, in atmospheres}	{Aerobic or anaerobic}	{salinity measurement}	{Method or device employed for collecting sample}	{Processing applied to the sample during or after isolation}	{Amount or size of sample (volume, mass or area) that was collected}	{none}	{none}	{none}	{volume (mL) or weight (g) of sample processed for DNA extraction}	{concentration of silicate}	{sodium concentration}	{unique identifier assigned to a material sample used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples.}	{concentration of sulfate}	{concentration of sulfide}	{temperature of the sample at time of sampling}	{measurement of magnitude and direction of flow within a fluid}
#{text}	{text}	{text}	{text}	{controlled vacabulary}	{{timestamp}}	{{term}}	{{term}}	{{term}}	{{term}:{term}:{text}}	{{float} {float}}	{{float} {unit}}	{{float} m}	{{float} {unit}}	{{text};{float} {unit}}	{{float} {unit}}	{{float} {unit}}	{{term}; {timestamp}}	{{float} {unit}}	{{float} {unit}}	{{float} {unit}}	{{float} m}	{{text};{float} {unit}}	{{float} {unit}}	{{float} {unit}}	{{float} {unit}}	{{float} {unit}}	{{float} {unit}}	{{float} {unit}}	{{text};{float} {unit}}	{{float} {unit}}	{{float} {unit}}	{{float} {unit}}	{{float} {unit}}	{{float} {unit}}	{{float} {unit}}	{{text};{float} {unit}}	{['', 'aerobic', 'anaerobic']}	{{text};{interval}}	{{float} {unit}}	{{float} {unit}}	{{text};{float} {unit}}	{{float} {unit}}	{{float} {unit}}	{['', 'aerobe', 'anaerobe', 'facultative', 'microaerophilic', 'microanaerobe', 'obligate aerobe', 'obligate anaerobe']}	{{float} {unit}}	{{text}}	{{text|term}}	{{float} {unit}}	{{none}}	{{none}}	{{none}}	{{float} {unit}}	{{float} {unit}}	{{float} {unit}}	{{text}}	{{float} {unit}}	{{float} {unit}}	{{float} {unit}}	{{float} {unit}}
*sample_name	*description	*sample_title	*seq_methods	*organism	*collection_date	*env_biome	*env_feature	*env_material	*geo_loc_name	*lat_lon	alkalinity	altitude	ammonium	biomass	bromide	calcium	chem_administration	chloride	chlorophyll	density	depth	diether_lipids	diss_carb_dioxide	diss_hydrogen	diss_inorg_carb	diss_org_nitro	diss_oxygen	elev	misc_param	nitrate	nitrite	nitro	org_carb	org_matter	org_nitro	organism_count	oxy_stat_samp	perturbation	ph	phosphate	phosplipid_fatt_acid	potassium	pressure	rel_to_oxygen	salinity	samp_collect_device	samp_mat_process	samp_size	samp_store_dur	samp_store_loc	samp_store_temp	samp_vol_we_dna_ext	silicate	sodium	source_material_id	sulfate	sulfide	temp	water_current