Mercurial > repos > diodupima > data_manager_coast_taxonomic_filters
changeset 13:70d5b154b91f draft
"planemo upload commit 8f9b7580dc80c99bc735ea899819ff1d109de311-dirty"
| author | diodupima |
|---|---|
| date | Thu, 15 Jul 2021 11:36:17 +0000 |
| parents | 061d0b316b13 |
| children | b2fb92399590 |
| files | README.rst high_order2species.sh ho2s.py txids_dm.xml |
| diffstat | 4 files changed, 10 insertions(+), 27 deletions(-) [+] |
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--- a/README.rst Thu Jul 08 12:10:21 2021 +0000 +++ b/README.rst Thu Jul 15 11:36:17 2021 +0000 @@ -1,4 +1,5 @@ -# COAST's Taxonomic Filters - Data Manager +COAST's Taxonomic Filters - Data Manager +________________________________________ This data manager helps an admin provide the galaxy instance users with pre-cached taxonomic filters. This helps increase the speed of the queries against larger databases.
--- a/high_order2species.sh Thu Jul 08 12:10:21 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,15 +0,0 @@ -#!/bin/bash - -CURRENT_DATE=`date +"%Y.%m.%d_%H.%M.%S"` -high_order=$1 -name=$2 -directory=$PWD - -# Get the data -wget -c ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz -tar -zxvf taxdump.tar.gz - -# Removed indentation so it only has 1 collumn -taxonkit list --ids $high_order --data-dir $directory \ - | taxonkit filter --equal-to Species --lower-than Species --save-predictable-norank --data-dir $directory \ - > ${name}.txids
--- a/ho2s.py Thu Jul 08 12:10:21 2021 +0000 +++ b/ho2s.py Thu Jul 15 11:36:17 2021 +0000 @@ -34,9 +34,8 @@ subprocess.call( f"taxonkit list --ids {taxid} --data-dir {target_directory}" f"| taxonkit filter --equal-to Species --lower-than Species --save-predictable-norank --data-dir {target_directory}" - f"> {data_id}.txids", - shell=True, - cwd=target_directory + f"> {os.path.join(target_directory, data_id)}.txids", + shell=True ) data_table_entry = {
--- a/txids_dm.xml Thu Jul 08 12:10:21 2021 +0000 +++ b/txids_dm.xml Thu Jul 15 11:36:17 2021 +0000 @@ -4,21 +4,19 @@ <requirements> <requirement type="package" version="0.8">taxonkit</requirement> </requirements> - <command interpreter="python">ho2s.py --file "${out_file}" --tool_data_table_name "coast_taxonomic_filters"</command> + <command>python3 ho2s.py --file "${out_file}" --tool_data_table_name "coast_taxonomic_filters"</command> <inputs> - <param name="taxid" type="integer" value="" optional="False" label="TAXID for the desired top node" help="Root Taxonomy node."/> - <param name="node_name" type="text" value="" optional="False" label="The name you want for the node" help="Label for the filter."/> + <param name="taxid" optional="False" value="" type="integer" label="TAXID for the desired top node" help="Root Taxonomy node."/> + <param name="node_name" optional="False" value="" type="text" label="The name you want for the node" help="Label for the filter."/> </inputs> <outputs> <data name="out_file" format="data_manager_json"/> </outputs> <tests> <test> - <test> - <param name="taxid" value="10239"/> - <param name="node_name" value="Virus"/> - <output name="out_file" file="out_file.json"/> - </test> + <param name="taxid" value="10239"/> + <param name="node_name" value="Virus"/> + <output name="out_file"/> </test> </tests> <help>