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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
Expected behavior
All deferred datasets selected as in input should be made available to the tool.
The text was updated successfully, but these errors were encountered:
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.
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
Expected behavior
All deferred datasets selected as in input should be made available to the tool.
The text was updated successfully, but these errors were encountered: