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EGA test fixes #3648

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EGA test fixes #3648

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cb47c45
EGA test fixes
bernt-matthias May 3, 2021
f1c2884
do not download to output variable directly
bernt-matthias May 12, 2021
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20 changes: 11 additions & 9 deletions tools/pyega3/pyega3.xml
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
<tool id="pyega3" name="EGA Download Client" version="@VERSION@+galaxy0" profile="19.09" >
<tool id="pyega3" name="EGA Download Client" version="@VERSION@+galaxy1" profile="20.01" >
<macros>
<token name="@VERSION@">3.4.0</token>
</macros>
Expand Down Expand Up @@ -30,7 +30,9 @@
--end $action.range.end
#end if
#end if
--saveto '$downloaded_file'
## do not download to `$downloaded_file`
## since a .md5 file will be stored next to it
--saveto downloaded_file
#end if
]]></command>
<configfiles>
Expand Down Expand Up @@ -62,7 +64,7 @@
<when value="list_datasets"/>
<when value="download_file">
<param name="file_id" type="text" optional="false" label="EGA File Accession Identifier" help="Identifier starting with 'EGAF'. For example: EGAF00001753735">
<validator type="regex" message="EGA Accession ID must be a string of numbers prefixed by 'EGAD' (datasets) or 'EGAF' (files)">EGAF[0-9]+</validator>
<validator type="regex" message="EGA Accession ID must be a string of numbers prefixed or 'EGAF' (files)">EGAF[0-9]+</validator>
</param>
<section name="range" title="Request a specific Genomic range?" expanded="false">
<param argument="--reference-name" type="text" optional="true" label="Reference Sequence Name" help="For example 'chr1', '1', or 'chrX'. If unspecified, all data is returned." />
Expand All @@ -79,7 +81,7 @@
<data name="dataset_file_list" format="txt" from_work_dir="pyega3_output.log" label="${tool.name}: dataset file list">
<filter> action['action_type'] == 'list_dataset_files' </filter>
</data>
<data name="downloaded_file" auto_format="true" label="${tool.name}: ${action.file_id} ${action.range.reference_name} ${action.range.start} ${action.range.end}">
<data name="downloaded_file" auto_format="true" from_work_dir="downloaded_file" label="${tool.name}: ${action.file_id} ${action.range.reference_name} ${action.range.start} ${action.range.end}">
<filter> action['action_type'] == 'download_file' </filter>
</data>
</outputs>
Expand All @@ -106,15 +108,15 @@
</test>
<test expect_num_outputs="1"> <!-- download a single file -->
<param name="action_type" value="download_file"/>
<param name="file_id" value="EGAF00001775036"/>
<output name="downloaded_file" md5="3b89b96387db5199fef6ba613f70e27c"/>
<param name="file_id" value="EGAF00001770106"/>
<output name="downloaded_file" md5="ce073afcbc07afa343f2d4e4d07efeda"/>
</test>
<test expect_num_outputs="1"> <!-- download a single file, with genomic range specified -->
<param name="action_type" value="download_file"/>
<param name="file_id" value="EGAF00001753756"/>
<param name="reference_name" value="1"/>
<param name="file_id" value="EGAF00001770106"/>
<param name="reference_name" value="chrM"/>
<param name="start" value="100"/>
<param name="end" value="10000"/>
<param name="end" value="1000"/>
<output name="downloaded_file" ftype="bam" md5="e576a38748feec45aa45191f6e902ce2"/>
</test>
</tests>
Expand Down