Mercurial > repos > iuc > ncbi_entrez_direct_einfo

annotate einfo.xml @ 0:c66f2400ecf8 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
author iuc
date Tue, 22 Mar 2022 22:30:36 +0000
parents
children df0df73c8bda
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0
c66f2400ecf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
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1 <tool id="ncbi_entrez_direct_einfo" name="NCBI EInfo" version="@TOOL_VERSION@">
c66f2400ecf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
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2 <description>fetch NCBI database metadata</description>
c66f2400ecf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
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3 <macros>
c66f2400ecf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
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4 <import>macros.xml</import>
c66f2400ecf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
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5 </macros>
c66f2400ecf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
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6 <expand macro="requirements"/>
c66f2400ecf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
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7 <version_command>einfo -version</version_command>
c66f2400ecf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
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8 <command detect_errors="exit_code"><![CDATA[
c66f2400ecf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
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9 @ECONTACT@
c66f2400ecf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
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10 einfo
c66f2400ecf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
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11 #if str( $db.target ) == "dbs":
c66f2400ecf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
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12 -dbs
c66f2400ecf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
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13 #else:
c66f2400ecf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
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14 -db "${db.db}"
c66f2400ecf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
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15 #end if
c66f2400ecf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
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16 > '${output_xml}'
c66f2400ecf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
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17 ]]>
c66f2400ecf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
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18 </command>
c66f2400ecf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
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19 <inputs>
c66f2400ecf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
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20 <conditional name="db">
c66f2400ecf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
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21 <param name="target" type="select" label="List DBs or Info on a DB">
c66f2400ecf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
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22 <option value="db" selected="True">DB info</option>
c66f2400ecf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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23 <option value="dbs">List of DBs</option>
c66f2400ecf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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24 </param>
c66f2400ecf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
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25 <when value="dbs"/>
c66f2400ecf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
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26 <when value="db">
c66f2400ecf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
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27 <param name="db" type="select" label="Choose your DB" argument="-db">
c66f2400ecf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
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28 <option value="annotinfo">annotinfo</option>
c66f2400ecf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
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29 <option value="assembly">assembly</option>
c66f2400ecf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
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30 <option value="bioproject">bioproject</option>
c66f2400ecf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
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31 <option value="biosample">biosample</option>
c66f2400ecf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
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32 <option value="biosystems">biosystems</option>
c66f2400ecf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
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33 <option value="blastdbinfo">blastdbinfo</option>
c66f2400ecf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
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34 <option value="books">books</option>
c66f2400ecf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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35 <option value="cdd">cdd</option>
c66f2400ecf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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36 <option value="clinvar">clinvar</option>
c66f2400ecf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
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37 <option value="clone">clone</option>
c66f2400ecf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
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38 <option value="dbvar">dbvar</option>
c66f2400ecf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
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39 <option value="gap">gap</option>
c66f2400ecf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
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40 <option value="gapplus">gapplus</option>
c66f2400ecf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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41 <option value="gds">gds</option>
c66f2400ecf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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42 <option value="gencoll">gencoll</option>
c66f2400ecf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
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43 <option value="gene">gene</option>
c66f2400ecf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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44 <option value="genome">genome</option>
c66f2400ecf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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45 <option value="geoprofiles">geoprofiles</option>
c66f2400ecf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
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46 <option value="grasp">grasp</option>
c66f2400ecf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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47 <option value="gtr">gtr</option>
c66f2400ecf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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48 <option value="homologene">homologene</option>
c66f2400ecf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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49 <option value="medgen">medgen</option>
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50 <option value="mesh">mesh</option>
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51 <option value="ncbisearch">ncbisearch</option>
c66f2400ecf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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52 <option value="nlmcatalog">nlmcatalog</option>
c66f2400ecf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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53 <option value="nuccore">nuccore</option>
c66f2400ecf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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54 <option value="nucest">nucest</option>
c66f2400ecf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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55 <option value="nucgss">nucgss</option>
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56 <option value="nucleotide">nucleotide</option>
c66f2400ecf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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57 <option value="omim">omim</option>
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58 <option value="orgtrack">orgtrack</option>
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59 <option value="pcassay">pcassay</option>
c66f2400ecf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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60 <option value="pccompound">pccompound</option>
c66f2400ecf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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61 <option value="pcsubstance">pcsubstance</option>
c66f2400ecf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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62 <option value="pmc">pmc</option>
c66f2400ecf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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63 <option value="popset">popset</option>
c66f2400ecf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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64 <option value="probe">probe</option>
c66f2400ecf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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65 <option value="protein">protein</option>
c66f2400ecf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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66 <option value="proteinclusters">proteinclusters</option>
c66f2400ecf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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67 <option value="pubmed">pubmed</option>
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68 <option value="pubmedhealth">pubmedhealth</option>
c66f2400ecf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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69 <option value="seqannot">seqannot</option>
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70 <option value="snp">snp</option>
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71 <option value="sra">sra</option>
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72 <option value="structure">structure</option>
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73 <option value="taxonomy">taxonomy</option>
c66f2400ecf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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74 <option value="unigene">unigene</option>
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75 </param>
c66f2400ecf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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76 </when>
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77 </conditional>
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78 </inputs>
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79 <outputs>
c66f2400ecf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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80 <data format="xml" name="output_xml"/>
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81 </outputs>
c66f2400ecf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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82 <tests>
c66f2400ecf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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83 <test>
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84 <param name="db|target" value="db"/>
c66f2400ecf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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85 <param name="db|db" value="sra"/>
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86 <output name="output_xml">
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87 <assert_contents>
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88 <has_text_matching expression="SRA" />
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89 </assert_contents>
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90 </output>
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91 </test>
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92 </tests>
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93 <help><![CDATA[
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94 NCBI Entrez EInfo
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95 =================
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96
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97 Provides the number of records indexed in each field of a given database, the
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98 date of the last update of the database, and the available links from the
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99 database to other Entrez databases.
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100
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101 @DISCLAIMER@
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102 ]]></help>
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103 <expand macro="citations"/>
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104 </tool>