Mercurial > repos > iuc > pcdl_get_conc_attribute
diff pcdl_get_conc_attribute.xml @ 0:f7f40cc1cfce draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
| author | iuc |
|---|---|
| date | Mon, 04 Aug 2025 18:55:11 +0000 |
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| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pcdl_get_conc_attribute.xml Mon Aug 04 18:55:11 2025 +0000 @@ -0,0 +1,69 @@ +<tool id="pcdl_get_conc_attribute" name="pcdl_get_conc_attribute" version="3.0.1+galaxy0" profile="21.05"> + <macros> + <import>pcdl_macros.xml</import> + </macros> + <requirements> + <expand macro="requirement"/> + </requirements> + <command><![CDATA[ + #import re + mkdir output_pc && + #for $file in $path: + #set $filename = re.sub('[^\w\-\.\s]', '_', str($file.element_identifier)) + ln -s '$file' output_pc/$filename && + #end for + + pcdl_get_conc_attribute 'output_pc' $entropy + --verbose $verbose + --drop $drop + --keep $keep + --allvalues $allvalues + ]]></command> + <inputs> + <section name="essential" title="essential:" expanded="true"> + <expand macro="path"/> + <expand macro="entropy"/> + <expand macro="drop"/> + <expand macro="keep"/> + <expand macro="allvalues"/> + </section> + <section name="advanced" title="advanced:" expanded="false"> + <expand macro="verbose"/> + </section> + </inputs> + <outputs> + <collection name="conc_attribute_json" type="list"> + <discover_datasets pattern="(?P<designation>timeseries_conc_attribute_.+)\.json" format="json" directory="output_pc" visible="false"/> + </collection> + </outputs> + <tests> + <test expect_num_outputs="1"> + <section name="essential"> + <param name="path"> + <expand macro="output"/> + </param> + </section> + <section name="advanced"> + <param name="verbose" value="true"/> + </section> + <output_collection name="conc_attribute_json" count="1"> + <element name="timeseries_conc_attribute_minmax"> + <assert_contents> + <has_text text="{""/> + <has_text text="": ["/> + <has_text text="], ""/> + <has_text text="]}"/> + </assert_contents> + </element> + </output_collection> + </test> + </tests> + <help><![CDATA[ +Function to detect informative substrate concentration variables in a time series. This function detects even variables which have less than the minimal state count in each time step, but different values from time step to time step. The output is a json file with an entry of all non-coordinate column names that, at least in one of the time steps or in between time steps, reach the given minimal value count. Key is the column name, mapped is a list of all values (bool, str, and, if allvalues is True, int and float) or a list with minimum and maximum values (int, float). + +Homepage: https://github.com/elmbeech/physicelldataloader + ]]></help> + <citations> + <expand macro="citation"/> + </citations> +</tool>