Mercurial > repos > iuc > ncbi_eutils_esearch
diff esearch.xml @ 3:e267701c187b draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
| author | iuc |
|---|---|
| date | Wed, 23 Sep 2020 09:48:26 +0000 |
| parents | c6096cd97120 |
| children | f3a84eecaf8b |
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--- a/esearch.xml Wed Mar 11 04:03:14 2020 -0400 +++ b/esearch.xml Wed Sep 23 09:48:26 2020 +0000 @@ -6,14 +6,21 @@ </macros> <expand macro="requirements"/> <version_command>python esearch.py --version</version_command> - <command detect_errors="aggressive"><![CDATA[ -python '$__tool_directory__/esearch.py' -$db_select -"$term" + <command detect_errors="aggressive"> + <![CDATA[ + + ##Doing replacement here so that dataset label doesn't have slashes + #set saniterm = $term.replace('"','\\"') + + python '$__tool_directory__/esearch.py' -#if $history_file and $history_file is not None: - --history_file '$history_file' -#end if + $db_select + + "$saniterm" + + #if $history_file and $history_file is not None: + --history_file '$history_file' + #end if #if $date.enabled == 'True' --datetype $date.datetype @@ -31,12 +38,34 @@ #end if #end if -#if $use_history: - --history_out $history -#end if + #if $retstart is not None: + --retstart '$retstart' + #end if + + #if $retmax is not None: + --retmax '$retmax' + #end if -@EMAIL_ARGUMENTS@ -> $default]]></command> + #if $output_format == 'history_xml': + --history_out + --retmode xml + #elif $output_format == 'history_json': + --history_out + --retmode json + #elif $output_format == 'id_xml': + --retmode xml + #elif $output_format == 'id_json': + --retmode json + #elif $output_format == 'id_text': + --retmode text + #end if + + @EMAIL_ARGUMENTS@ + + > $default + + ]]> + </command> <inputs> <expand macro="dbselect"/> <param name="term" type="text" label="Search term"> @@ -45,11 +74,18 @@ <add value="'"/> <add value="["/> <add value="]"/> + <add value='"'/> </valid> </sanitizer> </param> <param name="history_file" type="data" format="json" optional="true" label="Filter existing history" /> - <param name="use_history" type="boolean" truevalue="--use_history" falsevalue="" checked="false" label="Store results to history server" /> + <param name="output_format" type="select" label="Output Format"> + <option value="history_json">History File (json)</option> + <option value="history_xml">History File (xml)</option> + <option value="id_xml">ID File (xml)</option> + <option value="id_json">ID File (json)</option> + <option value="id_text" selected="true">ID File (tabular)</option> + </param> <conditional name="date"> <param name="enabled" type="select" label="Filter by date"> <option value="False">No</option> @@ -67,32 +103,73 @@ </when> <when value="False"/> </conditional> + <param name="retstart" type="integer" value="0" min="0" max="99999" label="Starting record to return (--retstart)" /> + <param name="retmax" type="integer" value="100000" min="1" max="100000" label="Maximum number of records to return (--retmax)" /> </inputs> <outputs> - <data name="default" format="json" label="ESearch results for $term"> + <data name="default" format="xml" label="ESearch results for $db_select database query: $term"> <change_format> - <when input="use_history" value="" format="xml"/> + <when input="output_format" value="history_json" format="json" /> + <when input="output_format" value="history_xml" format="xml" /> + <when input="output_format" value="id_xml" format="xml" /> + <when input="output_format" value="id_json" format="json" /> + <when input="output_format" value="id_text" format="tabular" /> </change_format> </data> - <expand macro="history_out"> - <filter>use_history</filter> - </expand> </outputs> <tests> <test> <param name="db_select" value="pubmed"/> <param name="term" value="(PNAS[ta] AND 97[vi])"/> + <param name="retstart" value="0"/> + <param name="retmax" value="20"/> + <param name="output_format" value="id_xml"/> <output name="default" file="esearch.pubmed.xml" ftype="xml" lines_diff="2"/> </test> <test> <param name="db_select" value="pubmed"/> <param name="term" value="PNAS[ta]"/> + <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"/> <output name="default" file="esearch.pubmed.2014-01-pnas.xml" ftype="xml" lines_diff="2"/> </test> + <test> + <param name="db_select" value="gene"/> + <param name="term" value=""genetype rrna"[Properties] AND "Homo sapiens"[Organism] AND ("srcdb refseq"[Properties] AND alive[prop])"/> + <param name="retstart" value="2"/> + <param name="retmax" value="22"/> + <param name="output_format" value="id_text"/> + <output name="default" file="esearch.gene.tabular" ftype="tabular" lines_diff="2"/> + </test> + <test> + <param name="db_select" value="gene"/> + <param name="term" value="118502329"/> + <param name="retstart" value="0"/> + <param name="retmax" value="1"/> + <param name="output_format" value="id_json"/> + <output name="default" file="esearch.gene.json" ftype="json" lines_diff="2"/> + </test> + <test> + <param name="db_select" value="gene"/> + <param name="term" value="118502329"/> + <param name="retstart" value="0"/> + <param name="retmax" value="1"/> + <param name="output_format" value="history_json"/> + <output name="default" file="esearch.gene.hist.json" ftype="json" lines_diff="2"/> + </test> + <test> + <param name="db_select" value="gene"/> + <param name="term" value="118502329"/> + <param name="retstart" value="0"/> + <param name="retmax" value="1"/> + <param name="output_format" value="history_xml"/> + <output name="default" file="esearch.gene.hist.xml" ftype="xml" lines_diff="2"/> + </test> </tests> <help><![CDATA[ NCBI Entrez ESearch