| Previous changeset 1:4d0b8d9aee09 (2022-12-17) Next changeset 3:cc652cd06b0c (2024-06-14) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 1bd7defa5ac7ea1e619c519d719f5bd10452339b |
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modified:
efetch.xml macros.xml |
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| diff -r 4d0b8d9aee09 -r 59dfa639e78e efetch.xml --- a/efetch.xml Sat Dec 17 20:44:47 2022 +0000 +++ b/efetch.xml Sat May 18 20:23:07 2024 +0000 |
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| b'@@ -1,11 +1,11 @@\n <tool id="ncbi_entrez_direct_efetch" name="NCBI EFetch" version="@TOOL_VERSION@">\n- <description>fetch records from NCBI</description>\n- <macros>\n- <import>macros.xml</import>\n- </macros>\n- <expand macro="requirements"/>\n- <version_command>efetch -version</version_command>\n- <command detect_errors="exit_code"><![CDATA[\n+ <description>fetch records from NCBI</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="requirements"/>\n+ <version_command>efetch -version</version_command>\n+ <command detect_errors="exit_code"><![CDATA[\n @ECONTACT@\n efetch\n #if str( $db.db ) == "":\n@@ -55,2493 +55,2488 @@\n > \'${output_result}\'\n ]]>\n </command>\n- <inputs>\n- <conditional name="query">\n- <param name="source" type="select" label="Select query source">\n- <option value="history">NCBI WebEnv History</option>\n- <option value="id">Direct Entry</option>\n- </param>\n- <when value="history">\n- <param label="Input File" name="input_file" type="data" format="xml"/>\n- </when>\n- <when value="id">\n- <param label="Query ID" name="id" type="text" argument="-id"/>\n- </when>\n- </conditional>\n-\n-<conditional name="db">\n- <param name="db" type="select" label="Database" argument="-db">\n- <option value="annotinfo">annotinfo</option>\n- <option value="assembly">assembly</option>\n- <option value="bioproject">bioproject</option>\n- <option value="biosample">biosample</option>\n- <option value="biosystems">biosystems</option>\n- <option value="blastdbinfo">blastdbinfo</option>\n- <option value="books">books</option>\n- <option value="cdd">cdd</option>\n- <option value="clinvar">clinvar</option>\n- <option value="clone">clone</option>\n- <option value="dbvar">dbvar</option>\n- <option value="gap">gap</option>\n- <option value="gapplus">gapplus</option>\n- <option value="gds">gds</option>\n- <option value="gencoll">gencoll</option>\n- <option value="gene">gene</option>\n- <option value="genome">genome</option>\n- <option value="geoprofiles">geoprofiles</option>\n- <option value="grasp">grasp</option>\n- <option value="gtr">gtr</option>\n- <option value="homologene">homologene</option>\n- <option value="medgen">medgen</option>\n- <option value="mesh">mesh</option>\n- <option value="ncbisearch">ncbisearch</option>\n- <option value="nlmcatalog">nlmcatalog</option>\n- <option value="nuccore">nuccore</option>\n- <option value="nucest">nucest</option>\n- <option value="nucgss">nucgss</option>\n- <option value="nucleotide">nucleotide</option>\n- <option value="omim">omim</option>\n- <option value="orgtrack">orgtrack</option>\n- <option value="pcassay">pcassay</option>\n- <option value="pccompound">pccompound</option>\n- <option value="pcsubstance">pcsubstance</option>\n- <option value="pmc">pmc</option>\n- <option value="popset">popset</option>\n- <option value="probe">probe</option>\n- <option value="protein">protein</option>\n- <option value="proteinclusters">proteinclusters</option>\n- <option value="pubmed">pubmed</option>\n- <option value="pubmedhealth">pubmedhealth</option>\n- <option value="seqannot">seqannot</option>\n- <option value="sequences">sequences</option>\n- <option value="snp">snp</option>\n- <option value="sra">sra</option>\n- <option value="structure">structure</option>\n- <option value="taxonomy">taxonomy</option>\n- <option value="unigene">unigene</option>\n- <option value="">Manual Entry</option>\n- </param>\n- <when value="annotinfo">\n- <conditional name="format">\n- <param name="format" type="select" label="Format" argument="-format">\n- <option value='..b' name="ranges" title="Set Ranges" expanded="False">\n- <param label="Seq Start" name="seq_start" type="integer" optional="True" min="0" argument="-seq_start"/>\n- <param label="Seq End" name="seq_stop" type="integer" optional="True" min="0" argument="-seq_stop"/>\n- <param label="strand" name="strand" type="text" argument="-strand"/>\n- <param label="Complexity" name="complexity" type="integer" optional="True" min="0" argument="-complexity"/>\n- <param label="Chr Start" name="chr_start" type="integer" optional="True" min="0" argument="-chr_start"/>\n- <param label="Chr End" name="chr_stop" type="integer" optional="True" min="0" argument="-chr_stop"/>\n- </section>\n- </inputs>\n- <outputs>\n- <data format="txt" name="output_result">\n- <change_format>\n- <when input="db.format" value="xml" format="xml"/>\n- <when input="db.format.mode" value="xml" format="xml"/>\n- <when input="db.format.mode" value="json" format="json"/>\n- <when input="db.format" value="tabular" format="tabular"/>\n- <when input="db.format" value="fasta" format="fasta"/>\n- <when input="db.format" value="fasta_cds_aa" format="fasta"/>\n- <when input="db.format" value="fasta_cds_na" format="fasta"/>\n- <when input="db.format" value="gene_fasta" format="fasta"/>\n- </change_format>\n- </data>\n- </outputs>\n- <tests>\n- <test>\n- <param name="db|db" value=""/>\n- <param name="db|db_manual" value="sra"/>\n- <param name="db|format" value="runinfo"/>\n- <param name="query|source" value="id"/>\n- <param name="query|id" value="SRX8542266"/>\n- <output name="output_result">\n- <assert_contents>\n- <has_text_matching expression="Run" />\n- </assert_contents>\n- </output>\n- </test>\n- </tests>\n- <help><![CDATA[\n+ <section name="ranges" title="Set Ranges" expanded="False">\n+ <param argument="-seq_start" type="integer" min="0" optional="True" label="Seq Start"/>\n+ <param argument="-seq_stop" type="integer" min="0" optional="True" label="Seq End"/>\n+ <param argument="-strand" type="text" label="strand"/>\n+ <param argument="-complexity" type="integer" min="0" optional="True" label="Complexity"/>\n+ <param argument="-chr_start" type="integer" min="0" optional="True" label="Chr Start"/>\n+ <param argument="-chr_stop" type="integer" min="0" optional="True" label="Chr End"/>\n+ </section>\n+ </inputs>\n+ <outputs>\n+ <data format="txt" name="output_result">\n+ <change_format>\n+ <when input="db.format" value="xml" format="xml"/>\n+ <when input="db.format.mode" value="xml" format="xml"/>\n+ <when input="db.format.mode" value="json" format="json"/>\n+ <when input="db.format" value="tabular" format="tabular"/>\n+ <when input="db.format" value="fasta" format="fasta"/>\n+ <when input="db.format" value="fasta_cds_aa" format="fasta"/>\n+ <when input="db.format" value="fasta_cds_na" format="fasta"/>\n+ <when input="db.format" value="gene_fasta" format="fasta"/>\n+ </change_format>\n+ </data>\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="db|db" value=""/>\n+ <param name="db|db_manual" value="sra"/>\n+ <param name="db|format" value="runinfo"/>\n+ <param name="query|source" value="id"/>\n+ <param name="query|id" value="SRX8542266"/>\n+ <output name="output_result">\n+ <assert_contents>\n+ <has_text_matching expression="Run"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n NCBI Entrez EFetch\n ==================\n \n@@ -2577,5 +2572,5 @@\n \n @DISCLAIMER@\n ]]></help>\n- <expand macro="citations"/>\n+ <expand macro="citations"/>\n </tool>\n' |
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| diff -r 4d0b8d9aee09 -r 59dfa639e78e macros.xml --- a/macros.xml Sat Dec 17 20:44:47 2022 +0000 +++ b/macros.xml Sat May 18 20:23:07 2024 +0000 |
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| @@ -1,5 +1,5 @@ <macros> - <token name="@TOOL_VERSION@">16.2</token> + <token name="@TOOL_VERSION@">21.6</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">entrez-direct</requirement> |