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Merged
bernt-matthias merged 11 commits into from
Oct 9, 2025
Merged

Add regex switch expression tool #7314

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0285823
Initial commit
npinter Sep 29, 2025
edf2b1e
Change test input name
npinter Sep 29, 2025
915c1e0
Fix linting
npinter Sep 29, 2025
c220d1f
Push
npinter Sep 29, 2025
4199ec9
Fix linting
npinter Sep 29, 2025
7851c28
Fix linting
npinter Oct 2, 2025
e2e5097
Fix linting
npinter Oct 2, 2025
767e9f5
Fix tests
npinter Oct 6, 2025
2da8ced
Update repository URLs to main branch
npinter Oct 8, 2025
e4dfb0c
Refactor regex matching logic and add link for regex syntax to help
npinter Oct 8, 2025
64f78fe
Test
npinter Oct 9, 2025
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10 changes: 10 additions & 0 deletions tools/regex_switch/.shed.yml
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categories:
- Text Manipulation
description: Regex switch
long_description: |
Regex switch outputs a boolean from regex on element identifier.
name: regex_switch
owner: iuc
remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/regex_switch
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homepage_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/regex_switch
type: unrestricted
77 changes: 77 additions & 0 deletions tools/regex_switch/regex_switch.xml
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<tool name="Regex switch" id="regex_switch" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="expression">
<description>boolean from regex on element identifier</description>
<macros>
<token name="@TOOL_VERSION@">1.0.0</token>
<token name="@VERSION_SUFFIX@">0</token>
</macros>
<expression type="ecma5.1"><![CDATA[{
var name = $job.input.name;
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var pat = $job.pattern;
var matched = false;

try {
if (pat !== "") {
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@bernt-matthias bernt-matthias Oct 7, 2025

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Should we add a empty_field validator instead to the param?

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@npinter npinter Oct 8, 2025

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Thanks! Added!

var re = new RegExp(pat);
matched = re.test(name);
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}
} catch (e) {
return { "__error_message": "Invalid regular expression: " + (e && e.message ? e.message : String(e)) };
}

return { "matched": matched, "unmatched": !matched };
}]]></expression>
<inputs>
<param name="input" type="data" format="data"
label="Dataset" />
<param name="pattern" sanitize="false" type="text" label="Regex pattern"
help="Example: \.csv$">
<sanitizer>
<valid>
<add preset="string.printable"/>
<add value="\"/>
<add value="$"/>
</valid>
</sanitizer>
</param>
</inputs>
<outputs>
<output type="boolean" name="matched" from="matched" label="Match result"/>
<output type="boolean" name="unmatched" from="unmatched" label="Unmatched result"/>
</outputs>
<tests>
<test expect_num_outputs="2">
<param name="input" value="sample.csv"/>
<param name="pattern" value="\.csv$"/>
<output name="matched">
<assert_contents>
<has_line line="true"/>
</assert_contents>
</output>
<output name="unmatched">
<assert_contents>
<has_line line="false"/>
</assert_contents>
</output>
</test>
<test expect_num_outputs="2">
<param name="input" value="table.tsv"/>
<param name="pattern" value="\.csv$"/>
<output name="matched">
<assert_contents>
<has_line line="false"/>
</assert_contents>
</output>
<output name="unmatched">
<assert_contents>
<has_line line="true"/>
</assert_contents>
</output>
</test>
</tests>
<help><![CDATA[
**Regex switch**

Matches a regular expression against an element name. It emits two booleans:
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@bernt-matthias bernt-matthias Sep 29, 2025

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Guess "element name" needs better explanation. I guess you assume that the tool is mapped over a collection.

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@npinter npinter Sep 30, 2025

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It's the name of the dict element (job["input"]["name"]) of cwl (?), which looks like that:

    "engineConfig": [],
    "job": {
        "input": {
            "file_ext": "tabular",
            "file_size": 14,
            "name": "table.tsv",
            "metadata": {
                "dbkey": "?",
                "data_lines": 2,
                "comment_lines": 0,
                "columns": 2,
                "column_types": [
                    "int",
                    "int"
                ],
                "column_names": [],
                "delimiter": "__tc__"
            },
            "src": {
                "src": "hda",
                "id": 4
            }
        },
        "pattern": "\.csv$"
    },
    "context": null,
    "outdir": null,
    "tmpdir": null,

Not sure if this name comes either of the element identifier or the element name (I guessed the latter).

`matched` (the match result) and `unmatched` (its negation). Connect either to a step's **Conditionally skip step?** input.
]]></help>
</tool>
2 changes: 2 additions & 0 deletions tools/regex_switch/test-data/sample.csv
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col1,col2
1,2
2 changes: 2 additions & 0 deletions tools/regex_switch/test-data/table.tsv
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col1 col2
1 2
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