Mercurial > repos > kkonganti > lexmapr2_from_cfsan
changeset 13:bdccef316f65
"planemo upload"
| author | kkonganti |
|---|---|
| date | Thu, 15 Sep 2022 14:11:09 -0400 |
| parents | 530cafac56f9 |
| children | 89998b9b4d46 |
| files | cfsan_lexmapr2.xml lexmapr_run.log o.tsv |
| diffstat | 3 files changed, 8 insertions(+), 10 deletions(-) [+] |
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--- a/cfsan_lexmapr2.xml Thu Sep 15 13:55:38 2022 -0400 +++ b/cfsan_lexmapr2.xml Thu Sep 15 14:11:09 2022 -0400 @@ -13,8 +13,8 @@ </requirements> <version_command>python $__tool_directory__/lexmapr2.py --version</version_command> <command detect_errors="exit_code"><![CDATA[ - echo \$PYTHONPATH 1>&2; mkdir -p lexmapr2-input || exit 1; + ln -sf '/tool/tool-data/cfsan_lexmapr2/0/lexmapr' .; ln -sf '$input' './lexmapr2-input/$input.name'; python $__tool_directory__/lexmapr2.py #if ($embl_ont != ""): @@ -39,7 +39,6 @@ ]]></command> <environment_variables> <environment_variable name="NLTK_DATA">/tool/tool-data/cfsan_lexmapr2/0/nltk_data</environment_variable> - <environment_variable name="PYTHONPATH">/tool/tool-data/cfsan_lexmapr2/0</environment_variable> </environment_variables> <inputs> <param name="input" type="data" format="csv" label="Input CSV"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lexmapr_run.log Thu Sep 15 14:11:09 2022 -0400 @@ -0,0 +1,5 @@ +INFO:root:Run start: 2022-09-15 14:05:40.236514 +INFO:root:Run start: 2022-09-15 14:07:13.815176 +INFO:root:Run start: 2022-09-15 14:08:11.894380 +INFO:root:Database build/confirm: 2022-09-15 14:08:11.908013 +WARNING:root:Did not retrieve URL for https://www.ebi.ac.uk/ols/api/ontologies/foodon/ancestors?id=FOODON:00002703&page=1&size=20 during API search
--- a/o.tsv Thu Sep 15 13:55:38 2022 -0400 +++ b/o.tsv Thu Sep 15 14:11:09 2022 -0400 @@ -1,8 +1,2 @@ -Sample_Id Sample_Desc Processed_Sample Annotated_Sample Matched_Components Match_Status (Macro Level) Match_Status (Micro Level) Sample_Transformations fo_product fo_quality fo_organism ncbi_taxon -small_simple1 Chicken Breast Not annotated chicken breast:FOODON_00002703 Full Term Match [] {} poultry food product:FOODON_00001283|vertebrate animal food product:FOODON_00001092 -small_simple2 Baked Potato Not annotated potato (whole, baked):FOODON_03302196 Full Term Match ['Used Processed Sample', 'Suffix Addition'] {} plant food product:FOODON_00001015 food (baked):FOODON_00002456|food (cooked):FOODON_00001181 -small_simple3 Canned Corn Not annotated corn (canned):FOODON_03302665 Full Term Match [] {} plant food product:FOODON_00001015 -small_simple4 Frozen Yogurt Not annotated frozen yogurt:FOODON_03307445 Full Term Match [] {} dairy food product:FOODON_00001256|vertebrate animal food product:FOODON_00001092 -small_simple5 Apple Pie Not annotated apple pie:FOODON_00002475 Full Term Match [] {} bakery food product:FOODON_00001626|plant food product:FOODON_00001015|prepared food product:FOODON_00001180 -small_simple5 Apple cider apple cider Not annotated apple food product:FOODON_00001611 Component Match ['Inflection (Plural) Treatment: apple', 'Inflection (Plural) Treatment: cider', 'Suffix Addition'] {} plant food product:FOODON_00001015 -small_simple6 Chicken egg chicken egg Not annotated chicken:FOODON_03411457|egg food product:FOODON_00001274 Component Match ['Inflection (Plural) Treatment: chicken', 'Inflection (Plural) Treatment: egg', 'Suffix Addition'] {} poultry food product:FOODON_00001283|vertebrate animal food product:FOODON_00001092 Aves:NCBITaxon_8782 \ No newline at end of file +Sample_Id Sample_Desc Processed_Sample Annotated_Sample Matched_Components Match_Status (Macro Level) Match_Status (Micro Level) Sample_Transformations ncbi_taxon +small_simple1 Chicken Breast Not annotated chicken breast:FOODON_00002703 Full Term Match [] {} \ No newline at end of file