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Specifying multiple deferred datasets for an input parameter is not handled correctly #19324

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richard-burhans opened this issue Dec 13, 2024 · 0 comments
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@richard-burhans
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richard-burhans commented Dec 13, 2024

Describe the bug
The following tool has an input parameter that takes multiple datasets. When multiple datasets are selected as the input, it works as expected. If multiple deferred datasets are selected as input, only a single deferred dataset is passed to the tool.

I did not test using a mix of regular and deferred datasets.

<tool id="bug" name="Bug" version="1.0+galaxy0" profile="21.05">
    <description>with deferred datasets</description>
    <requirements>
        <requirement type="package" version="5">bash</requirement>
    </requirements>
    <command detect_errors="aggressive"><![CDATA[
    touch cmd.txt cfg.txt &&
    #for $file in $rnaseq
        echo $file >> cmd.txt &&
    #end for
    cat $bug_config >> cfg.txt
    ]]></command>
    <configfiles>
        <configfile name="bug_config"><![CDATA[
        #for $file in $rnaseq
$file
        #end for
        ]]></configfile>
    </configfiles>
    <inputs>
        <param name="rnaseq" type="data" format="fastqsanger,fastqsanger.gz" multiple="true" label="Select multiple RNA-seq fastqsanger inputs from the current history"/>
    </inputs>
    <outputs>
        <data name="cmd_output" format="txt" label="Bug command on ${on_string}" from_work_dir="cmd.txt"/>
        <data name="cfg_output" format="txt" label="Bug config on ${on_string}" from_work_dir="cfg.txt"/>
    </outputs>
    <help><![CDATA[
::

  for copy-paste:
  https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/sample_data/Dermatophagoides_farinae_small/SRR8506572_1.gz
  https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/sample_data/Dermatophagoides_farinae_small/SRR8506572_2.gz
  https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/sample_data/Dermatophagoides_farinae_small/SRR9005248_1.gz
  https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/sample_data/Dermatophagoides_farinae_small/SRR9005248_2.gz


    ]]></help>
</tool>

Galaxy Version and/or server at which you observed the bug
Galaxy Version: 24.1
Commit: 3c82972

Browser and Operating System
Operating System: Linux
Browser: Chrome

To Reproduce
bug

Expected behavior
All deferred datasets selected as in input should be made available to the tool.

@mvdbeek mvdbeek self-assigned this Dec 17, 2024
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