Mercurial > repos > iuc > ncbi_eutils_ecitmatch

annotate ecitmatch.xml @ 0:68cd8d564e0a draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
author iuc
date Thu, 07 Jul 2016 02:39:21 -0400
parents
children 1dff3adb0a97
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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68cd8d564e0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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1 <?xml version="1.0"?>
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2 <tool id="ncbi_eutils_ecitmatch" name="NCBI ECitMatch" version="@WRAPPER_VERSION@">
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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"/>
68cd8d564e0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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8 <version_command>python ecitmatch.py --version</version_command>
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9 <command detect_errors="aggressive" interpreter="python"><![CDATA[ecitmatch.py
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10
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11 #if str($input.method) == "file":
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12 --file $input.citation_file
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13 #else
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14 #set keys = '" "'.join( [ str( $citation.key ) for $citation in $input.citations ] )
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15 #set journal_title = '" "'.join( [ str( $citation.key ) for $citation in $input.citations ] )
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16 #set year = '" "'.join( [ str( $citation.key ) for $citation in $input.citations ] )
68cd8d564e0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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17 #set volume = '" "'.join( [ str( $citation.key ) for $citation in $input.citations ] )
68cd8d564e0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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18 #set first_page = '" "'.join( [ str( $citation.key ) for $citation in $input.citations ] )
68cd8d564e0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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19 #set author = '" "'.join( [ str( $citation.key ) for $citation in $input.citations ] )
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20
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21 --key "$keys"
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22 --journal_title "$journal_title"
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23 --key "$year"
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24 --key "$volume"
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25 --key "$first_page"
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26 --key "$author"
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27 #end if
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28
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29 @EMAIL_ARGUMENTS@
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30 > $default]]></command>
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31 <inputs>
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32 <conditional name="input">
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33 <param name="method" type="select" label="Input method">
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34 <option value="file">Load citations from a formatted table</option>
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35 <option value="direct">Direct Input</option>
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36 </param>
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37 <when value="file">
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38 <param label="Citation table" name="citation_file" type="data"
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39 format="tabular" help="Columns must be in a specific order, see help documentation"/>
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40 </when>
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41 <when value="direct">
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42 <repeat name="citations" title="Citations">
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43 <param name="journal_title" type="text" label="Journal Title"
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44 help="E.g. proc natl acad sci u s a" />
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45 <param name="year" type="integer" label="Year" value="2000"/>
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46 <param name="volume" type="integer" label="Volume" value="88"/>
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47 <param name="first_page" type="integer" label="First Page" value="1"/>
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48 <param name="author" type="text" label="Author's Name" />
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49 <param name="key" type="text" label="Citation key"
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50 help="Used to match input results to NCBI's output" />
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51 </repeat>
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52 </when>
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53 </conditional>
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54
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55 </inputs>
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56 <outputs>
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57 <data format="tabular" name="default" label="ECitMatch Results"/>
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58 </outputs>
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59 <tests>
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60 <test>
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61 <param name="method" value="file"/>
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62 <param name="citation_file" value="ecitmatch.tsv"/>
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63 <output name="default" file="ecitmatch.results.tsv" ftype="tabular"/>
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64 </test>
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65 </tests>
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66 <help><![CDATA[
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67 NCBI ECitMatch
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68 ==============
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69
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70 Search for citation PubMed IDs. These can be provided via a tabular file, or
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71 via direct input. If provided via file, the columns should be ordered:
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72
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73 1. Journal Name
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74 2. Year
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75 3. Volume
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76 4. First Page
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77 5. Author Name
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78 6. Citation Key
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79
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80
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81 An example query:
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82
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83 +---------------+--------------------------+
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84 | Parameter | Value |
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85 +===============+==========================+
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86 | Journal Title | proc natl acad sci u s a |
68cd8d564e0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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87 +---------------+--------------------------+
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88 | Year | 1991 |
68cd8d564e0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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89 +---------------+--------------------------+
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90 | Volume | 88 |
68cd8d564e0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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91 +---------------+--------------------------+
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92 | 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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93 +---------------+--------------------------+
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94 | 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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95 +---------------+--------------------------+
68cd8d564e0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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96 | 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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97 +---------------+--------------------------+
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98
68cd8d564e0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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99
68cd8d564e0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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100 @REFERENCES@
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101
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102 @DISCLAIMER@
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103 ]]></help>
68cd8d564e0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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104 <expand macro="citations"/>
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105 </tool>