Mercurial > repos > iuc > ncbi_entrez_direct_einfo
comparison einfo.xml @ 2:df0df73c8bda draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 1bd7defa5ac7ea1e619c519d719f5bd10452339b
| author | iuc |
|---|---|
| date | Sat, 18 May 2024 20:23:10 +0000 |
| parents | c66f2400ecf8 |
| children |
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| 1:c06dcadf986c | 2:df0df73c8bda |
|---|---|
| 1 <tool id="ncbi_entrez_direct_einfo" name="NCBI EInfo" version="@TOOL_VERSION@"> | 1 <tool id="ncbi_entrez_direct_einfo" name="NCBI EInfo" version="@TOOL_VERSION@"> |
| 2 <description>fetch NCBI database metadata</description> | 2 <description>fetch NCBI database metadata</description> |
| 3 <macros> | 3 <macros> |
| 4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
| 5 </macros> | 5 </macros> |
| 6 <expand macro="requirements"/> | 6 <expand macro="requirements"/> |
| 7 <version_command>einfo -version</version_command> | 7 <version_command>einfo -version</version_command> |
| 8 <command detect_errors="exit_code"><![CDATA[ | 8 <command detect_errors="exit_code"><![CDATA[ |
| 9 @ECONTACT@ | 9 @ECONTACT@ |
| 10 einfo | 10 einfo |
| 11 #if str( $db.target ) == "dbs": | 11 #if str( $db.target ) == "dbs": |
| 12 -dbs | 12 -dbs |
| 13 #else: | 13 #else: |
| 14 -db "${db.db}" | 14 -db "${db.db}" |
| 15 #end if | 15 #end if |
| 16 > '${output_xml}' | 16 > '${output_xml}' |
| 17 ]]> | 17 ]]> |
| 18 </command> | 18 </command> |
| 19 <inputs> | 19 <inputs> |
| 20 <conditional name="db"> | 20 <conditional name="db"> |
| 21 <param name="target" type="select" label="List DBs or Info on a DB"> | 21 <param name="target" type="select" label="List DBs or Info on a DB"> |
| 22 <option value="db" selected="True">DB info</option> | 22 <option value="db" selected="True">DB info</option> |
| 23 <option value="dbs">List of DBs</option> | 23 <option value="dbs">List of DBs</option> |
| 24 </param> | 24 </param> |
| 25 <when value="dbs"/> | 25 <when value="dbs"/> |
| 26 <when value="db"> | 26 <when value="db"> |
| 27 <param name="db" type="select" label="Choose your DB" argument="-db"> | 27 <param argument="-db" type="select" label="Choose your DB"> |
| 28 <option value="annotinfo">annotinfo</option> | 28 <option value="annotinfo">annotinfo</option> |
| 29 <option value="assembly">assembly</option> | 29 <option value="assembly">assembly</option> |
| 30 <option value="bioproject">bioproject</option> | 30 <option value="bioproject">bioproject</option> |
| 31 <option value="biosample">biosample</option> | 31 <option value="biosample">biosample</option> |
| 32 <option value="biosystems">biosystems</option> | 32 <option value="biosystems">biosystems</option> |
| 33 <option value="blastdbinfo">blastdbinfo</option> | 33 <option value="blastdbinfo">blastdbinfo</option> |
| 34 <option value="books">books</option> | 34 <option value="books">books</option> |
| 35 <option value="cdd">cdd</option> | 35 <option value="cdd">cdd</option> |
| 36 <option value="clinvar">clinvar</option> | 36 <option value="clinvar">clinvar</option> |
| 37 <option value="clone">clone</option> | 37 <option value="clone">clone</option> |
| 38 <option value="dbvar">dbvar</option> | 38 <option value="dbvar">dbvar</option> |
| 39 <option value="gap">gap</option> | 39 <option value="gap">gap</option> |
| 40 <option value="gapplus">gapplus</option> | 40 <option value="gapplus">gapplus</option> |
| 41 <option value="gds">gds</option> | 41 <option value="gds">gds</option> |
| 42 <option value="gencoll">gencoll</option> | 42 <option value="gencoll">gencoll</option> |
| 43 <option value="gene">gene</option> | 43 <option value="gene">gene</option> |
| 44 <option value="genome">genome</option> | 44 <option value="genome">genome</option> |
| 45 <option value="geoprofiles">geoprofiles</option> | 45 <option value="geoprofiles">geoprofiles</option> |
| 46 <option value="grasp">grasp</option> | 46 <option value="grasp">grasp</option> |
| 47 <option value="gtr">gtr</option> | 47 <option value="gtr">gtr</option> |
| 48 <option value="homologene">homologene</option> | 48 <option value="homologene">homologene</option> |
| 49 <option value="medgen">medgen</option> | 49 <option value="medgen">medgen</option> |
| 50 <option value="mesh">mesh</option> | 50 <option value="mesh">mesh</option> |
| 51 <option value="ncbisearch">ncbisearch</option> | 51 <option value="ncbisearch">ncbisearch</option> |
| 52 <option value="nlmcatalog">nlmcatalog</option> | 52 <option value="nlmcatalog">nlmcatalog</option> |
| 53 <option value="nuccore">nuccore</option> | 53 <option value="nuccore">nuccore</option> |
| 54 <option value="nucest">nucest</option> | 54 <option value="nucest">nucest</option> |
| 55 <option value="nucgss">nucgss</option> | 55 <option value="nucgss">nucgss</option> |
| 56 <option value="nucleotide">nucleotide</option> | 56 <option value="nucleotide">nucleotide</option> |
| 57 <option value="omim">omim</option> | 57 <option value="omim">omim</option> |
| 58 <option value="orgtrack">orgtrack</option> | 58 <option value="orgtrack">orgtrack</option> |
| 59 <option value="pcassay">pcassay</option> | 59 <option value="pcassay">pcassay</option> |
| 60 <option value="pccompound">pccompound</option> | 60 <option value="pccompound">pccompound</option> |
| 61 <option value="pcsubstance">pcsubstance</option> | 61 <option value="pcsubstance">pcsubstance</option> |
| 62 <option value="pmc">pmc</option> | 62 <option value="pmc">pmc</option> |
| 63 <option value="popset">popset</option> | 63 <option value="popset">popset</option> |
| 64 <option value="probe">probe</option> | 64 <option value="probe">probe</option> |
| 65 <option value="protein">protein</option> | 65 <option value="protein">protein</option> |
| 66 <option value="proteinclusters">proteinclusters</option> | 66 <option value="proteinclusters">proteinclusters</option> |
| 67 <option value="pubmed">pubmed</option> | 67 <option value="pubmed">pubmed</option> |
| 68 <option value="pubmedhealth">pubmedhealth</option> | 68 <option value="pubmedhealth">pubmedhealth</option> |
| 69 <option value="seqannot">seqannot</option> | 69 <option value="seqannot">seqannot</option> |
| 70 <option value="snp">snp</option> | 70 <option value="snp">snp</option> |
| 71 <option value="sra">sra</option> | 71 <option value="sra">sra</option> |
| 72 <option value="structure">structure</option> | 72 <option value="structure">structure</option> |
| 73 <option value="taxonomy">taxonomy</option> | 73 <option value="taxonomy">taxonomy</option> |
| 74 <option value="unigene">unigene</option> | 74 <option value="unigene">unigene</option> |
| 75 </param> | 75 </param> |
| 76 </when> | 76 </when> |
| 77 </conditional> | 77 </conditional> |
| 78 </inputs> | 78 </inputs> |
| 79 <outputs> | 79 <outputs> |
| 80 <data format="xml" name="output_xml"/> | 80 <data format="xml" name="output_xml"/> |
| 81 </outputs> | 81 </outputs> |
| 82 <tests> | 82 <tests> |
| 83 <test> | 83 <test> |
| 84 <param name="db|target" value="db"/> | 84 <param name="db|target" value="db"/> |
| 85 <param name="db|db" value="sra"/> | 85 <param name="db|db" value="sra"/> |
| 86 <output name="output_xml"> | 86 <output name="output_xml"> |
| 87 <assert_contents> | 87 <assert_contents> |
| 88 <has_text_matching expression="SRA" /> | 88 <has_text_matching expression="SRA"/> |
| 89 </assert_contents> | 89 </assert_contents> |
| 90 </output> | 90 </output> |
| 91 </test> | 91 </test> |
| 92 </tests> | 92 </tests> |
| 93 <help><![CDATA[ | 93 <help><![CDATA[ |
| 94 NCBI Entrez EInfo | 94 NCBI Entrez EInfo |
| 95 ================= | 95 ================= |
| 96 | 96 |
| 97 Provides the number of records indexed in each field of a given database, the | 97 Provides the number of records indexed in each field of a given database, the |
| 98 date of the last update of the database, and the available links from the | 98 date of the last update of the database, and the available links from the |
| 99 database to other Entrez databases. | 99 database to other Entrez databases. |
| 100 | 100 |
| 101 @DISCLAIMER@ | 101 @DISCLAIMER@ |
| 102 ]]></help> | 102 ]]></help> |
| 103 <expand macro="citations"/> | 103 <expand macro="citations"/> |
| 104 </tool> | 104 </tool> |