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Added expression tool to ease parameter sweeps of recetox-aplcms on Galaxy #624

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Added expression tool to ease parameter sweeps of recetox-aplcms on Galaxy #624

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a9b86c1
recetox-aplcms: parse parameter line tool
hechth Dec 4, 2024
0d8ffd5
added edam operations and topics
hechth Dec 4, 2024
5a574a1
added additional validation logic
hechth Dec 4, 2024
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185 changes: 185 additions & 0 deletions tools/recetox_aplcms/recetox_aplcms_parse_parameters.xml
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<tool id="recetox_aplcms_parse_parameters" name="recetox-aplcms - parse parameters" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT" tool_type="expression">
<description>tool to parse parameters from a csv row for parameter searches, to be used in workflows only.</description>

<macros>
<token name="@TOOL_VERSION@">0.1.0</token>
<token name="@VERSION_SUFFIX@">0</token>
</macros>

<edam_operations>
<edam_operation>operation_1812</edam_operation>
</edam_operations>

<edam_topics>
<edam_topic>topic_3316</edam_topic>
<edam_topic>topic_3071</edam_topic>
</edam_topics>

<expression type="ecma5.1"><![CDATA[{
// Expected column names
var expectedColumnNames = [
"min_run",
"sigma_lower",
"sigma_higher",
"min_sd",
"max_sd",
"mz_tol",
"weighting",
"min_pres",
"group_threshold"
];

// Validate column names
var columnNames = $job.row.metadata.column_names;
if (columnNames.length !== expectedColumnNames.length) {
throw new Error("Column count does not match expected count.");
}
for (var i = 0; i < columnNames.length; i++) {
if (columnNames[i] !== expectedColumnNames[i]) {
throw new Error("Column names do not match expected names.");
}
}

// Read the input CSV file
var data = $job.row.contents;

// Split the data into lines
var lines = data.trim().split('\n');

// Get the header and the first data row
var header = lines[0].split(',');
var row = lines[1].split(',');

// Create a dictionary with column names as keys and row values as values
var result = {};
for (var i = 0; i < header.length; i++) {
result[header[i]] = row[i];
}

// Validate that the float parameters are valid float values
var floatParams = ["min_run", "sigma_lower", "sigma_higher", "min_sd", "max_sd", "mz_tol", "min_pres", "group_threshold"];
for (var i = 0; i < floatParams.length; i++) {
var param = floatParams[i];
if (isNaN(parseFloat(result[param]))) {
throw new Error("Parameter " + param + " does not contain a valid float value.");
}
}

var weighting;
if (result['weighting'] == 'true') {
weighting = true;
} else {
weighting = false;
}

return {
'min_run': parseFloat(result['min_run']),
'sigma_lower': parseFloat(result['sigma_lower']),
'sigma_higher': parseFloat(result['sigma_higher']),
'min_sd': parseFloat(result['min_sd']),
'max_sd': parseFloat(result['max_sd']),
'mz_tol': parseFloat(result['mz_tol']),
'weighting': weighting,
'min_pres': parseFloat(result['min_pres']),
'group_threshold': parseFloat(result['group_threshold'])
};
}]]></expression>

<inputs>
<param argument="--row" type="data" format="csv" label="Row of a CSV with the parameters, with header." help="Header has to be: [min_run,sigma_lower,sigma_higher,min_sd,max_sd,mz_tol,weighting,min_pres,group_threshold
]" load_contents="64000"/>
</inputs>
<outputs>
<output name="min_run" type="float" label="min_run of ${on_string}" from="min_run" />
<output name="sigma_lower" type="float" label="sigma_lower of ${on_string}" from="sigma_lower" />
<output name="sigma_higher" type="float" label="sigma_higher of ${on_string}" from="sigma_higher" />
<output name="min_sd" type="float" label="min_sd of ${on_string}" from="min_sd" />
<output name="max_sd" type="float" label="max_sd of ${on_string}" from="max_sd" />
<output name="mz_tol" type="float" label="mz_tol of ${on_string}" from="mz_tol" />
<output name="weighting" type="boolean" label="weighting of ${on_string}" from="weighting" />
<output name="min_pres" type="float" label="min_pres of ${on_string}" from="min_pres" />
<output name="group_threshold" type="float" label="group_threshold of ${on_string}" from="group_threshold" />
</outputs>
<tests>
<!-- Hint: You can use [ctrl+alt+t] after defining the inputs/outputs to auto-scaffold some basic test cases. -->

<test>
<!--TODO: auto-generated test case. Please fill in the required values-->
<param name="row" value="parse_parameters/test.csv"/>
<output name="min_run">
<assert_contents>
<has_text text="3.1"/>
</assert_contents>
</output>
<output name="sigma_lower">
<assert_contents>
<has_text text="0.5"/>
</assert_contents>
</output>
<output name="sigma_higher">
<assert_contents>
<has_text text="1.5"/>
</assert_contents>
</output>
<output name="min_sd">
<assert_contents>
<has_text text="0.1"/>
</assert_contents>
</output>
<output name="max_sd">
<assert_contents>
<has_text text="0.9"/>
</assert_contents>
</output>
<output name="mz_tol">
<assert_contents>
<has_text text="0.01"/>
</assert_contents>
</output>
<output name="weighting">
<assert_contents>
<has_text text="true"/>
</assert_contents>
</output>
<output name="min_pres">
<assert_contents>
<has_text text="0.8"/>
</assert_contents>
</output>
<output name="group_threshold">
<assert_contents>
<has_text text="0.7"/>
</assert_contents>
</output>
</test>
</tests>
<help><![CDATA[

.. class:: infomark

**What it does**

This tool parses parameters from a CSV row for parameter searches. It splits the CSV file into separate files for each column, excluding the header. This tool is intended to be used in workflows only.

Usage
.....

**Input**

- **Row of a CSV with the parameters, with header**: The input CSV file containing the parameters. The header row should contain the column names.

**Output**

- **min_run**: The minimum run value extracted from the specified column.
- **sigma_lower**: The sigma lower value extracted from the specified column.
- **sigma_higher**: The sigma higher value extracted from the specified column.
- **min_sd**: The minimum standard deviation value extracted from the specified column.
- **max_sd**: The maximum standard deviation value extracted from the specified column.
- **mz_tol**: The mz tolerance value extracted from the specified column.
- **weighting**: The weighting value extracted from the specified column.
- **min_pres**: The minimum presence value extracted from the specified column.
- **group_threshold**: The group threshold value extracted from the specified column.
]]></help>
<citations>
</citations>
</tool>
2 changes: 2 additions & 0 deletions tools/recetox_aplcms/test-data/parse_parameters/test.csv
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min_run,sigma_lower,sigma_higher,min_sd,max_sd,mz_tol,weighting,min_pres,group_threshold
3.1,0.5,1.5,0.1,0.9,0.01,true,0.8,0.7
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