Mercurial > repos > iuc > ncbi_eutils_ecitmatch

annotate ecitmatch.xml @ 2:1dff3adb0a97 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit db33413a06c275efd4cc8e771c37facf543a2cfa"
author iuc
date Wed, 11 Mar 2020 04:03:55 -0400
parents 68cd8d564e0a
children 62614b5a7834
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1 <?xml version="1.0"?>
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1dff3adb0a97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit db33413a06c275efd4cc8e771c37facf543a2cfa"
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2 <tool id="ncbi_eutils_ecitmatch" name="NCBI ECitMatch" version="@WRAPPER_VERSION@" profile="@PROFILE@">
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3 <description>search NCBI for citations in PubMed</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <version_command>python ecitmatch.py --version</version_command>
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9 <command detect_errors="aggressive"><![CDATA[
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10 python '$__tool_directory__/ecitmatch.py'
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12 #if str($input.method) == "file":
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13 --file $input.citation_file
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14 #else
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15 #set keys = '" "'.join( [ str( $citation.key ) for $citation in $input.citations ] )
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16 #set journal_title = '" "'.join( [ str( $citation.key ) for $citation in $input.citations ] )
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17 #set year = '" "'.join( [ str( $citation.key ) for $citation in $input.citations ] )
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18 #set volume = '" "'.join( [ str( $citation.key ) for $citation in $input.citations ] )
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19 #set first_page = '" "'.join( [ str( $citation.key ) for $citation in $input.citations ] )
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20 #set author = '" "'.join( [ str( $citation.key ) for $citation in $input.citations ] )
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21
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22 --key "$keys"
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23 --journal_title "$journal_title"
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24 --key "$year"
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25 --key "$volume"
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26 --key "$first_page"
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27 --key "$author"
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28 #end if
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30 @EMAIL_ARGUMENTS@
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31 > $default]]></command>
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32 <inputs>
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33 <conditional name="input">
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34 <param name="method" type="select" label="Input method">
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35 <option value="file">Load citations from a formatted table</option>
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36 <option value="direct">Direct Input</option>
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37 </param>
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38 <when value="file">
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39 <param label="Citation table" name="citation_file" type="data"
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40 format="tabular" help="Columns must be in a specific order, see help documentation"/>
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41 </when>
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42 <when value="direct">
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43 <repeat name="citations" title="Citations">
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44 <param name="journal_title" type="text" label="Journal Title"
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45 help="E.g. proc natl acad sci u s a" />
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46 <param name="year" type="integer" label="Year" value="2000"/>
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47 <param name="volume" type="integer" label="Volume" value="88"/>
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48 <param name="first_page" type="integer" label="First Page" value="1"/>
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49 <param name="author" type="text" label="Author's Name" />
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50 <param name="key" type="text" label="Citation key"
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51 help="Used to match input results to NCBI's output" />
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52 </repeat>
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53 </when>
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54 </conditional>
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55
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56 </inputs>
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57 <outputs>
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58 <data format="tabular" name="default" label="ECitMatch Results"/>
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59 </outputs>
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60 <tests>
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61 <test>
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62 <param name="method" value="file"/>
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63 <param name="citation_file" value="ecitmatch.tsv"/>
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64 <output name="default" file="ecitmatch.results.tsv" ftype="tabular"/>
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65 </test>
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66 </tests>
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67 <help><![CDATA[
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68 NCBI ECitMatch
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69 ==============
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70
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71 Search for citation PubMed IDs. These can be provided via a tabular file, or
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72 via direct input. If provided via file, the columns should be ordered:
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73
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74 1. Journal Name
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75 2. Year
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76 3. Volume
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77 4. First Page
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78 5. Author Name
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79 6. Citation Key
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80
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81
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82 An example query:
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83
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84 +---------------+--------------------------+
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85 | Parameter | Value |
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86 +===============+==========================+
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87 | Journal Title | proc natl acad sci u s a |
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88 +---------------+--------------------------+
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89 | Year | 1991 |
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90 +---------------+--------------------------+
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91 | Volume | 88 |
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92 +---------------+--------------------------+
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93 | First Page | 3248 |
68cd8d564e0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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94 +---------------+--------------------------+
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95 | Author Name | mann bj |
68cd8d564e0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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96 +---------------+--------------------------+
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97 | Citation Key | citation_1 |
68cd8d564e0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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98 +---------------+--------------------------+
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99
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100
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101 @REFERENCES@
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102
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103 @DISCLAIMER@
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104 ]]></help>
68cd8d564e0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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105 <expand macro="citations"/>
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106 </tool>