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annotate test-data/biosample.tsv @ 0:45af9683de29 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author iuc
date Fri, 19 May 2017 05:42:13 -0400
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45af9683de29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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1 #This is a tab-delimited file. Additional Documentation can be found at http://www.mothur.org/wiki/MIMarks_Data_Packages.
45af9683de29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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2 #Please fill all the required fields indicated with '*'
45af9683de29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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3 #Unknown or inapplicable fields can be assigned 'missing' value.
45af9683de29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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4 #You may add extra custom fields to this template. Make sure all the fields are separated by tabs.
45af9683de29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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5 #You may remove any fields not required (marked with '*'). Make sure all the fields are separated by tabs.
45af9683de29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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6 #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.
45af9683de29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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7 #MIMARKS.survey.miscellaneous.4.0
45af9683de29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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8 #{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}
45af9683de29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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9 #{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}}
45af9683de29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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10 *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