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Merged
bgruening merged 2 commits into from
May 12, 2026
Merged

fixes for ncbi_entrez_eutils #7728

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25899ae
fixes for ncbi_entrez_eutils
bernt-matthias Feb 26, 2026
a8581c2
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bernt-matthias Feb 26, 2026
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9 changes: 5 additions & 4 deletions tools/ncbi_entrez_eutils/ecitmatch.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@
<import>macros.xml</import>
</macros>
<expand macro="requirements"/>
<version_command>python ecitmatch.py --version</version_command>
<version_command>python '$__tool_directory__/ecitmatch.py' --version</version_command>
<command detect_errors="aggressive"><![CDATA[
python '$__tool_directory__/ecitmatch.py'

Expand Down Expand Up @@ -51,15 +51,16 @@ python '$__tool_directory__/ecitmatch.py'
</repeat>
</when>
</conditional>

</inputs>
<outputs>
<data format="tabular" name="default" label="ECitMatch Results"/>
</outputs>
<tests>
<test>
<param name="method" value="file"/>
<param name="citation_file" value="ecitmatch.tsv"/>
<conditional name="input">
<param name="method" value="file"/>
<param name="citation_file" value="ecitmatch.tsv"/>
</conditional>
<output name="default" file="ecitmatch.results.tsv" ftype="tabular"/>
</test>
</tests>
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26 changes: 17 additions & 9 deletions tools/ncbi_entrez_eutils/efetch.xml
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Expand Up @@ -4,7 +4,7 @@
<import>macros.xml</import>
</macros>
<expand macro="requirements"/>
<version_command>python efetch.py --version</version_command>
<version_command>python '$__tool_directory__/efetch.py' --version</version_command>
<command detect_errors="aggressive"><![CDATA[

python '$__tool_directory__/efetch.py'
Expand All @@ -29,19 +29,27 @@
</outputs>
<tests>
<test>
<param name="db_select" value="taxonomy"/>
<param name="output_format" value="none-xml-xml"/>
<param name="qss" value="id_list"/>
<param name="id_list" value="10239"/>
<conditional name="db">
<param name="db_select" value="taxonomy"/>
<param name="output_format" value="none-xml-xml"/>
</conditional>
<conditional name="query_source">
<param name="qss" value="id_list"/>
<param name="id_list" value="10239"/>
</conditional>
<output_collection name="output1" type="list" count="1">
<element name="EFetch-None-xml-chunk1" ftype="xml" file="viruses.tax.xml" lines_diff="2" />
</output_collection>
</test>
<test>
<param name="db_select" value="nuccore"/>
<param name="output_format" value="fasta-text-fasta"/>
<param name="qss" value="id_file"/>
<param name="id_file" value="efetchin.tabular"/>
<conditional name="db">
<param name="db_select" value="nuccore"/>
<param name="output_format" value="fasta-text-fasta"/>
</conditional>
<conditional name="query_source">
<param name="qss" value="id_file"/>
<param name="id_file" value="efetchin.tabular"/>
</conditional>
<output_collection name="output1" type="list" count="1">
<element name="EFetch-fasta-text-chunk1" ftype="fasta">
<assert_contents>
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14 changes: 9 additions & 5 deletions tools/ncbi_entrez_eutils/einfo.xml
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Expand Up @@ -4,7 +4,7 @@
<import>macros.xml</import>
</macros>
<expand macro="requirements"/>
<version_command>python einfo.py --version</version_command>
<version_command>python '$__tool_directory__/einfo.py' --version</version_command>
<command detect_errors="aggressive"><![CDATA[

python '$__tool_directory__/einfo.py'
Expand Down Expand Up @@ -37,17 +37,21 @@
</outputs>
<tests>
<test>
<param name="query_type" value="Description"/>
<param name="db_select" value="pubmed"/>
<conditional name="query_type">
<param name="query_type" value="Description"/>
<param name="db_select" value="pubmed"/>
</conditional>
<output name="default" file="pubmed.metadata.xml" compare="re_match_multiline" ftype="xml">
<assert_contents>
<is_valid_xml/>
</assert_contents>
</output>
</test>
<test>
<param name="query_type" value="list"/>
<param name="db_select" value="Database list"/>
<conditional name="query_type">
<param name="query_type" value="list"/>
<param name="db_select" value="Database list"/>
</conditional>
<output name="default" ftype="xml">
<assert_contents>
<has_text text="&lt;DbName&gt;pubmed&lt;/DbName&gt;"/>
Expand Down
156 changes: 106 additions & 50 deletions tools/ncbi_entrez_eutils/elink.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@
<import>macros.xml</import>
</macros>
<expand macro="requirements"/>
<version_command>python elink.py --version</version_command>
<version_command>python '$__tool_directory__/elink.py' --version</version_command>
<command detect_errors="aggressive"><![CDATA[
python '$__tool_directory__/elink.py'

Expand Down Expand Up @@ -35,23 +35,39 @@ python '$__tool_directory__/elink.py'
</outputs>
<tests>
<test expect_num_outputs="1">
<param name="cmd_select" value="neighbor"/>
<param name="db_select_to" value="pubmed"/>
<param name="db_select_from_link" value="taxonomy"/>
<param name="qss" value="id_list"/>
<param name="id_list" value="510899"/>
<param name="output_format" value="xml"/>
<param name="linkname" value="None"/>
<conditional name="cmd">
<param name="cmd_select" value="neighbor"/>
<conditional name="db_from_link">
<param name="db_select_from_link" value="taxonomy"/>
<conditional name="db_to">
<param name="db_select_to" value="pubmed"/>
<param name="linkname" value="None"/>
</conditional>
</conditional>
<param name="output_format" value="xml"/>
</conditional>
<conditional name="query_source">
<param name="qss" value="id_list"/>
<param name="id_list" value="510899"/>
</conditional>
<output name="default" file="pm-tax-neighbor.xml" ftype="xml"/>
</test>
<test expect_num_outputs="1">
<param name="cmd_select" value="neighbor"/>
<param name="db_select_to" value="nuccore"/>
<param name="db_select_from_link" value="gene"/>
<param name="qss" value="id_xml"/>
<param name="id_xml" value="elink.esearch_in_xmlid.xml"/>
<param name="output_format" value="text"/>
<param name="linkname" value="gene_nuccore"/>
<conditional name="cmd">
<param name="cmd_select" value="neighbor"/>
<conditional name="db_from_link">
<param name="db_select_from_link" value="gene"/>
<conditional name="db_to">
<param name="db_select_to" value="nuccore"/>
<param name="linkname" value="gene_nuccore"/>
</conditional>
</conditional>
<param name="output_format" value="text"/>
</conditional>
<conditional name="query_source">
<param name="qss" value="id_xml"/>
<param name="id_xml" value="elink.esearch_in_xmlid.xml"/>
</conditional>
<output name="default" ftype="tabular">
<assert_contents>
<has_line line="1899688395"/>
Expand All @@ -60,13 +76,21 @@ python '$__tool_directory__/elink.py'
</output>
</test>
<test expect_num_outputs="1">
<param name="cmd_select" value="neighbor"/>
<param name="db_select_to" value="nuccore"/>
<param name="db_select_from_link" value="gene"/>
<param name="qss" value="id_json"/>
<param name="id_json" value="elink.esearchin_id.json"/>
<param name="output_format" value="json"/>
<param name="linkname" value="None"/>
<conditional name="cmd">
<param name="cmd_select" value="neighbor"/>
<conditional name="db_from_link">
<param name="db_select_from_link" value="gene"/>
<conditional name="db_to">
<param name="db_select_to" value="nuccore"/>
<param name="linkname" value="None"/>
</conditional>
</conditional>
<param name="output_format" value="json"/>
</conditional>
<conditional name="query_source">
<param name="qss" value="id_json"/>
<param name="id_json" value="elink.esearchin_id.json"/>
</conditional>
<output name="default" ftype="json">
<assert_contents>
<has_text text="gene_nuccore_refseqrna"/>
Expand All @@ -76,43 +100,75 @@ python '$__tool_directory__/elink.py'
</output>
</test>
<test expect_num_outputs="1">
<param name="cmd_select" value="neighbor"/>
<param name="db_select_to" value="nuccore"/>
<param name="db_select_from_link" value="gene"/>
<param name="qss" value="id_file"/>
<param name="id_file" value="elink.esearchin_id.tabular"/>
<param name="output_format" value="xml"/>
<param name="linkname" value="gene_nuccore_refseqrna"/>
<conditional name="cmd">
<param name="cmd_select" value="neighbor"/>
<conditional name="db_from_link">
<param name="db_select_from_link" value="gene"/>
<conditional name="db_to">
<param name="db_select_to" value="nuccore"/>
<param name="linkname" value="gene_nuccore_refseqrna"/>
</conditional>
</conditional>
<param name="output_format" value="xml"/>
</conditional>
<conditional name="query_source">
<param name="qss" value="id_file"/>
<param name="id_file" value="elink.esearchin_id.tabular"/>
</conditional>
<output name="default" file="elink.esearchin_id_1link.xml" ftype="xml"/>
</test>
<test expect_num_outputs="1">
<param name="cmd_select" value="neighbor_history"/>
<param name="db_select_to" value="gene"/>
<param name="db_select_from_link" value="nuccore"/>
<param name="qss" value="id_json"/>
<param name="id_json" value="elink.elinkin_1link.json"/>
<param name="output_format" value="json"/>
<param name="linkname" value="nuccore_gene"/>
<conditional name="cmd">
<param name="cmd_select" value="neighbor_history"/>
<conditional name="db_from_link">
<param name="db_select_from_link" value="nuccore"/>
<conditional name="db_to">
<param name="db_select_to" value="gene"/>
<param name="linkname" value="nuccore_gene"/>
</conditional>
</conditional>
<param name="output_format" value="json"/>
</conditional>
<conditional name="query_source">
<param name="qss" value="id_json"/>
<param name="id_json" value="elink.elinkin_1link.json"/>
</conditional>
<output name="default" file="elink.elinkin_1link_hist.json" ftype="json" lines_diff="2"/>
</test>
<test expect_num_outputs="1">
<param name="cmd_select" value="neighbor_history"/>
<param name="db_select_to" value="gene"/>
<param name="db_select_from_link" value="nuccore"/>
<param name="qss" value="id_xml"/>
<param name="id_xml" value="elink.elinkin_alllinks_id.xml"/>
<param name="output_format" value="xml"/>
<param name="linkname" value="nuccore_gene"/>
<conditional name="cmd">
<param name="cmd_select" value="neighbor_history"/>
<conditional name="db_from_link">
<param name="db_select_from_link" value="nuccore"/>
<conditional name="db_to">
<param name="db_select_to" value="gene"/>
<param name="linkname" value="nuccore_gene"/>
</conditional>
</conditional>
<param name="output_format" value="xml"/>
</conditional>
<conditional name="query_source">
<param name="qss" value="id_xml"/>
<param name="id_xml" value="elink.elinkin_alllinks_id.xml"/>
</conditional>
<output name="default" file="elink.elinkin_allalllinks_id.xml" ftype="xml" lines_diff="2"/>
</test>
<test expect_num_outputs="1">
<param name="cmd_select" value="neighbor_score"/>
<param name="db_select_to" value="gene"/>
<param name="db_select_from_link" value="nuccore"/>
<param name="qss" value="id_list"/>
<param name="id_list" value="1899688395"/>
<param name="output_format" value="text"/>
<param name="linkname" value="nuccore_gene"/>
<conditional name="cmd">
<param name="cmd_select" value="neighbor_score"/>
<conditional name="db_from_link">
<param name="db_select_from_link" value="nuccore"/>
<conditional name="db_to">
<param name="db_select_to" value="gene"/>
<param name="linkname" value="nuccore_gene"/>
</conditional>
</conditional>
<param name="output_format" value="text"/>
</conditional>
<conditional name="query_source">
<param name="qss" value="id_list"/>
<param name="id_list" value="1899688395"/>
</conditional>
<output name="default" file="elink.elinkin_1link_id.tabular" ftype="tabular"/>
</test>
</tests>
Expand Down
14 changes: 9 additions & 5 deletions tools/ncbi_entrez_eutils/epost.xml
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Expand Up @@ -4,7 +4,7 @@
<import>macros.xml</import>
</macros>
<expand macro="requirements"/>
<version_command>python epost.py --version</version_command>
<version_command>python '$__tool_directory__/epost.py' --version</version_command>
<command detect_errors="aggressive">
<![CDATA[

Expand Down Expand Up @@ -45,7 +45,7 @@
<option value="id_list">Paste IDs</option>
</param>
<when value="id_file">
<param label="ID File (Text)" name="id_file" type="data" format="text,tabular" help="A Text file containing one ID per line"/>
<param label="ID File (Text)" name="id_file" type="data" format="txt,tabular" help="A Text file containing one ID per line"/>
</when>
<when value="id_xml">
<param label="ID File (XML)" name="id_xml" type="data" format="xml" help="ESearch or ELink Result XML file"/>
Expand Down Expand Up @@ -92,9 +92,13 @@
<tests>
<test>
<param name="db_select" value="nuccore"/>
<param name="qss" value="id_list"/>
<param name="id_list" value="126697566"/>
<param name="history_type" value="create"/>
<conditional name="query_source">
<param name="qss" value="id_list"/>
<param name="id_list" value="126697566"/>
</conditional>
<conditional name="update_history">
<param name="history_type" value="create"/>
</conditional>
<output name="history" file="example.history.json" compare="sim_size" delta="70" ftype="json"/>
</test>
</tests>
Expand Down
14 changes: 8 additions & 6 deletions tools/ncbi_entrez_eutils/esearch.xml
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Expand Up @@ -4,7 +4,7 @@
<import>macros.xml</import>
</macros>
<expand macro="requirements"/>
<version_command>python esearch.py --version</version_command>
<version_command>python '$__tool_directory__/esearch.py' --version</version_command>
<command detect_errors="aggressive">
<![CDATA[

Expand Down Expand Up @@ -61,7 +61,7 @@

@EMAIL_ARGUMENTS@

> $default
> '$default'

]]>
</command>
Expand Down Expand Up @@ -131,10 +131,12 @@
<param name="retstart" value="0"/>
<param name="retmax" value="20"/>
<param name="output_format" value="id_xml"/>
<param name="enabled" value="True"/>
<param name="datetype" value="PDAT"/>
<param name="mindate" value="2014/01/01"/>
<param name="maxdate" value="2014/02/01"/>
<conditional name="date">
<param name="enabled" value="True"/>
<param name="datetype" value="PDAT"/>
<param name="mindate" value="2014/01/01"/>
<param name="maxdate" value="2014/02/01"/>
</conditional>
<output name="default" file="esearch.pubmed.2014-01-pnas.xml" ftype="xml" lines_diff="2"/>
</test>
<test>
Expand Down
8 changes: 5 additions & 3 deletions tools/ncbi_entrez_eutils/esummary.xml
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Expand Up @@ -4,7 +4,7 @@
<import>macros.xml</import>
</macros>
<expand macro="requirements"/>
<version_command>python esummary.py --version</version_command>
<version_command>python '$__tool_directory__/esummary.py' --version</version_command>
<command detect_errors="aggressive">
<![CDATA[

Expand Down Expand Up @@ -59,8 +59,10 @@
</outputs>
<tests>
<test expect_num_outputs="1">
<param name="qss" value="id_list"/>
<param name="id_list" value="10239"/>
<conditional name="query_source">
<param name="qss" value="id_list"/>
<param name="id_list" value="10239"/>
</conditional>
<param name="db_select" value="taxonomy"/>
<param name="retstart" value="0"/>
<param name="retmax" value="100000"/>
Expand Down
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