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Commit message:
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/blob/main/tools/saqc/ commit 271a95aef4cbe6b85a3c5dae1db005bfacf4084b |
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added:
macros.xml saqc.xml test-data/config.txt test-data/data.csv test-data/maint.csv test-data/out.csv |
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| diff -r 000000000000 -r 55bbea0cdc60 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Jan 13 16:27:12 2025 +0000 |
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| @@ -0,0 +1,18 @@ +<macros> + +<xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">saqc</requirement> + </requirements> +</xml> + +<token name="@TOOL_VERSION@">2.4.1</token> +<token name="@VERSION_SUFFIX@">0</token> + +<xml name="citations"> + <citations> + <citation type="doi">https://doi.org/10.1016/j.envsoft.2023.105809</citation> + </citations> +</xml> + +</macros> \ No newline at end of file |
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| diff -r 000000000000 -r 55bbea0cdc60 saqc.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/saqc.xml Mon Jan 13 16:27:12 2025 +0000 |
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| @@ -0,0 +1,57 @@ +<tool name="SaQC" id="saqc" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01"> + <description>quality control for time series</description> + <creator> + <organization name="Helmholtz Centre for Environmental Research - UFZ, Research Data Management" + url ="https://www.ufz.de/index.php?en=45348"/> + </creator> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <version_command><![CDATA[python -c 'import saqc; print(saqc.__version__)']]></version_command> + <command detect_errors="exit_code"><![CDATA[ + ln -s '$config' config.csv && + #for $i, $d in enumerate($data) + ln -s '$d' '${i}.csv' && + #end for + saqc -c config.csv + #for $i, $d in enumerate($data) + -d '${i}.csv' + #end for + -o output.csv + ]]></command> + <inputs> + <param label="Input Table(s)" + argument="--data" + type="data" + format="csv" + multiple="true" + optional="false" + /> + <param label="Configuration" + argument="--config" + type="data" + format="txt" + optional="false"/> + </inputs> + <outputs> + <data name="output" + format="csv" + from_work_dir="output.csv" + hidden="false"/> + </outputs> + <tests> + <test> + <!-- https://rdm-software.pages.ufz.de/saqc/cookbooks/MultivariateFlagging.html --> + <param name="data" value="data.csv,maint.csv" ftype="csv"/> + <param name="config" value="config.txt" ftype="txt"/> + <output name="output" value="out.csv" ftype="csv"/> + </test> + </tests> + <help><![CDATA[ + This tool runs the SaQC quality control pipeline specified by a config file on the input data. + Just upload your data and a config file, and the tool will run the SaQC pipeline on the data. +]]></help> + <expand macro="citations"/> +</tool> + |
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| diff -r 000000000000 -r 55bbea0cdc60 test-data/config.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/config.txt Mon Jan 13 16:27:12 2025 +0000 |
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| @@ -0,0 +1,21 @@ +varname ; test +#-----------------------;------------------------------------------- +# Data Preparation +sac254_raw ; flagManual(mdata='maint', method='closed') +level_raw ; flagRange(min=0) +water_temp_raw ; flagRange(min=-1) +sac254_raw ; flagRange(min=0, max=60) +level_raw ; align(freq='15min') +water_temp_raw ; align(freq='15min') +sac254_raw ; align(freq='15min') +# Drift Correcture +sac254_raw ; correctDrift(target='sac254_corr', maintenance_field='maint', model='exponential') +# Multivariate Flagging Procedure +level_z ; transform(field=['level_raw'], func=zScore(x), freq='20D') +water_z ; transform(field=['water_temp_raw'], func=zScore(x), freq='20D') +sac_z ; transform(field=['sac254_raw'], func=zScore(x), freq='20D') +kNN_scores ; assignKNNScore(field=['level_z', 'water_z', 'sac_z'], freq='20D') +kNN_scores ; flagByStray(freq='20D') +level_raw ; transferFlags(field=['kNN_scores'], label='STRAY') +sac254_corr ; transferFlags(field=['kNN_scores'], label='STRAY') +water_temp_raw ; transferFlags(field=['kNN_scores'], label='STRAY') \ No newline at end of file |
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| diff -r 000000000000 -r 55bbea0cdc60 test-data/data.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/data.csv Mon Jan 13 16:27:12 2025 +0000 |
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| b'@@ -0,0 +1,2642 @@\n+Timestamp,sac254_raw,level_raw,water_temp_raw\n+2016-11-07 09:02:00,22.3512,95.23,7.99\n+2016-11-07 09:17:00,21.7262,95.22,7.99\n+2016-11-07 09:32:00,22.8363,95.2125,7.99\n+2016-11-07 09:47:00,20.975,95.2275,8.01\n+2016-11-07 10:02:00,22.255,95.2275,8.0\n+2016-11-07 10:17:00,21.7237,95.275,7.97\n+2016-11-07 10:32:00,20.595,95.3025,7.96\n+2016-11-07 10:47:00,21.9638,95.275,7.97\n+2016-11-07 11:02:00,22.7438,95.2075,8.0\n+2016-11-07 11:17:00,22.79,95.1425,8.01\n+2016-11-07 11:32:00,23.2213,95.07,8.01\n+2016-11-07 11:47:00,23.415,95.01,8.02\n+2016-11-07 12:02:00,19.9137,94.995,8.0\n+2016-11-07 12:17:00,23.9962,94.98,7.93\n+2016-11-07 12:32:00,22.3962,95.05,7.83\n+2016-11-07 12:47:00,21.28,95.1425,7.78\n+2016-11-07 13:02:00,22.6912,95.295,7.75\n+2016-11-07 13:17:00,23.0287,95.4825,7.73\n+2016-11-07 13:32:00,22.9812,95.715,7.72\n+2016-11-07 13:47:00,23.0287,96.0175,7.65\n+2016-11-07 14:02:00,21.8675,96.355,7.54\n+2016-11-07 14:17:00,23.4675,96.715,7.47\n+2016-11-07 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19:47:00,24.1925,106.5,2.41\n+2016-12-04 20:02:00,24.7887,106.485,2.4\n+2016-12-04 20:17:00,23.6087,106.427,2.4\n+2016-12-04 20:32:00,22.9337,106.298,2.39\n+2016-12-04 20:47:00,23.9925,106.158,2.38\n+2016-12-04 21:02:00,24.6888,106.015,2.36\n+2016-12-04 21:17:00,23.9412,105.902,2.35\n+2016-12-04 21:32:00,24.2937,105.867,2.34\n+2016-12-04 21:47:00,23.7975,105.86,2.33\n\\ No newline at end of file\n' |
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| diff -r 000000000000 -r 55bbea0cdc60 test-data/maint.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/maint.csv Mon Jan 13 16:27:12 2025 +0000 |
| b |
| @@ -0,0 +1,37 @@ +Timestamp,maint +2016-01-10 11:15:00,2016-01-10 12:15:00 +2016-01-12 14:40:00,2016-01-12 15:30:00 +2016-02-10 13:40:00,2016-02-10 14:40:00 +2016-02-24 16:40:00,2016-02-24 17:30:00 +2016-03-08 09:30:00,2016-03-08 10:30:00 +2016-03-15 12:00:00,2016-03-15 16:30:00 +2016-03-21 11:00:00,2016-03-21 14:00:00 +2016-04-05 07:00:00,2016-04-05 07:55:00 +2016-05-02 15:30:00,2016-05-02 16:30:00 +2016-05-03 15:25:00,2016-05-03 16:35:00 +2016-05-31 07:00:00,2016-05-31 08:25:00 +2016-06-02 13:00:00,2016-06-02 15:50:00 +2016-06-28 07:30:00,2016-06-28 08:45:00 +2016-06-28 09:30:00,2016-06-28 10:30:00 +2016-07-25 08:45:00,2016-07-25 10:00:00 +2016-08-22 08:15:00,2016-08-22 09:20:00 +2016-09-20 07:00:00,2016-09-20 09:15:00 +2016-10-25 08:15:00,2016-10-25 09:50:00 +2016-11-08 09:40:00,2016-11-08 11:50:00 +2016-11-14 09:35:00,2016-11-14 10:40:00 +2016-12-13 15:05:00,2016-12-13 16:50:00 +2017-01-10 08:05:00,2017-01-10 09:15:00 +2017-02-06 09:20:00,2017-02-06 11:00:00 +2017-03-07 08:40:00,2017-03-07 09:40:00 +2017-04-05 07:50:00,2017-04-05 09:20:00 +2017-04-12 07:30:00,2017-04-12 09:45:00 +2017-05-02 13:20:00,2017-05-02 13:30:00 +2017-05-30 07:20:00,2017-05-30 08:30:00 +2017-06-14 08:25:00,2017-06-14 09:30:00 +2017-06-27 07:30:00,2017-06-27 08:40:00 +2017-07-24 08:00:00,2017-07-24 09:00:00 +2017-09-20 14:00:00,2017-09-20 14:35:00 +2017-10-17 08:55:00,2017-10-17 10:20:00 +2017-11-14 15:30:00,2017-11-14 16:20:00 +2017-11-27 09:10:00,2017-11-27 10:10:00 +2017-12-12 14:10:00,2017-12-12 14:50:00 |
| b |
| diff -r 000000000000 -r 55bbea0cdc60 test-data/out.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.csv Mon Jan 13 16:27:12 2025 +0000 |
| b |
| b'@@ -0,0 +1,2684 @@\n+,kNN_scores,kNN_scores,level_raw,level_raw,level_z,level_z,maint,maint,sac254_corr,sac254_corr,sac254_raw,sac254_raw,sac_z,sac_z,water_temp_raw,water_temp_raw,water_z,water_z\n+,data,flags,data,flags,data,flags,data,flags,data,flags,data,flags,data,flags,data,flags,data,flags\n+Timestamp,,,,,,,,,,,,,,,,,,\n+2016-01-10 11:15:00,nan,nan,nan,nan,nan,nan,2016-01-10 12:15:00,UNFLAGGED,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan\n+2016-01-12 14:40:00,nan,nan,nan,nan,nan,nan,2016-01-12 15:30:00,UNFLAGGED,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan\n+2016-02-10 13:40:00,nan,nan,nan,nan,nan,nan,2016-02-10 14:40:00,UNFLAGGED,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan\n+2016-02-24 16:40:00,nan,nan,nan,nan,nan,nan,2016-02-24 17:30:00,UNFLAGGED,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan\n+2016-03-08 09:30:00,nan,nan,nan,nan,nan,nan,2016-03-08 10:30:00,UNFLAGGED,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan\n+2016-03-15 12:00:00,nan,nan,nan,nan,nan,nan,2016-03-15 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