Mercurial > repos > iuc > ncbi_eutils_efetch

annotate efetch.xml @ 0:1b4ac594d02a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
author iuc
date Sat, 31 Oct 2015 12:44:54 -0400
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children a42fa980bbd5
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1b4ac594d02a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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1 <?xml version="1.0"?>
1b4ac594d02a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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2 <tool id="ncbi_eutils_efetch" name="NCBI EFetch" version="@WRAPPER_VERSION@">
1b4ac594d02a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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3 <description>fetch records from NCBI</description>
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4 <macros>
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5 <import>macros.xml</import>
1b4ac594d02a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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6 </macros>
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7 <expand macro="requirements"/>
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8 <expand macro="stdio"/>
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9 <version_command>python efetch.py --version</version_command>
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10 <command interpreter="python"><![CDATA[efetch.py
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11 $db.db_select
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12
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13 @LIST_OR_HIST@
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15 #set retmode, rettype = str($db.output_format).split('-')
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16 ## Otherwise, defaults to a None/empty which implies 'default' to NCBI
1b4ac594d02a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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17 #if retmode != "null":
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18 --retmode $retmode
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19 #end if
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20 --rettype $rettype
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21
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22 @EMAIL_ARGUMENTS@
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23 $whole
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24 > $default]]></command>
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25 <inputs>
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26 <expand macro="db"/>
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27 <expand macro="list_or_hist"/>
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28 <param checked="false" label="Download all records associated with query" name="whole" type="boolean" truevalue="--whole" falsevalue=""/>
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29 </inputs>
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30 <outputs>
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31 <data format="txt" name="default" label="NCBI EFetch Results">
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32 <discover_datasets pattern="__designation__.out" ext="txt"/>
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33 <change_format>
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34 <when input="output_format" value="abstract-text" format="txt"/>
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35 <when input="output_format" value="acc-text" format="txt"/>
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36 <when input="output_format" value="alignmentscores-text" format="txt"/>
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37 <when input="output_format" value="chr-text" format="txt"/>
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38 <when input="output_format" value="docset-text" format="txt"/>
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39 <when input="output_format" value="docsum-xml" format="xml"/>
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40 <when input="output_format" value="est-text" format="txt"/>
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41 <when input="output_format" value="fasta_cds_aa-text" format="fasta"/>
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42 <when input="output_format" value="fasta-text" format="fasta"/>
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43 <when input="output_format" value="fasta-xml" format="xml"/>
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44 <when input="output_format" value="flt-text" format="txt"/>
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45 <when input="output_format" value="ft-text" format="txt"/>
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46 <when input="output_format" value="full-text" format="txt"/>
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47 <when input="output_format" value="full-xml" format="xml"/>
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48 <when input="output_format" value="gbc-xml" format="xml"/>
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49 <when input="output_format" value="gbwithparts-text" format="genbank"/>
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50 <when input="output_format" value="gb-text" format="genbank"/>
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51 <when input="output_format" value="gb-xml" format="xml"/>
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52 <when input="output_format" value="gene_table-text" format="txt"/>
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53 <when input="output_format" value="gpc-xml" format="xml"/>
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54 <when input="output_format" value="gp-text" format="txt"/>
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55 <when input="output_format" value="gp-xml" format="xml"/>
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56 <when input="output_format" value="gss-text" format="txt"/>
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57 <when input="output_format" value="homologene-text" format="txt"/>
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58 <when input="output_format" value="ipg-xml" format="xml"/>
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59 <when input="output_format" value="medline-text" format="txt"/>
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60 <when input="output_format" value="native-xml" format="xml"/>
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61 <when input="output_format" value="null-asn.1" format="asn1"/>
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62 <when input="output_format" value="null-text" format="txt"/>
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63 <when input="output_format" value="null-xml" format="xml"/>
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64 <when input="output_format" value="rsr-text" format="txt"/>
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65 <when input="output_format" value="seqid-text" format="txt"/>
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66 <when input="output_format" value="ssexemplar-text" format="txt"/>
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67 <when input="output_format" value="summary-text" format="txt"/>
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68 <when input="output_format" value="uilist-xml" format="xml"/>
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69 <when input="output_format" value="xml-xml" format="xml"/>
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70 </change_format>
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71 </data>
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72 </outputs>
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73 <tests>
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74 <test>
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75 <param name="db_select" value="taxonomy"/>
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76 <param name="output_format" value="docsum-xml"/>
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77 <param name="qss" value="id_list"/>
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78 <param name="id_list" value="10239"/>
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79 <output name="default" file="viruses.tax.xml">
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80 <!--<discovered_datasets designation="0" ftytpe="xml" file="viruses.tax.xml" />-->
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81 </output>
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82 </test>
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83 </tests>
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84 <help><![CDATA[
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85 NCBI Entrez EFetch
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86 ==================
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87
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88 Responds to a list of UIDs in a given database with the corresponding data
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89 records in a specified format.
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90
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91 Example Queries
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92 ---------------
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93
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94 Fetch PMIDs 17284678 and 9997 as text abstracts:
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95
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96 +----------------------+--------------------------------------+
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97 | Parameter | Value |
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98 +======================+======================================+
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99 | NCBI Database to Use | PubMed |
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100 +----------------------+--------------------------------------+
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101 | ID List | 17284678 9997 |
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102 +----------------------+--------------------------------------+
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103 | Output Format | Abstract |
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104 +----------------------+--------------------------------------+
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105
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106 Fetch FASTA for a transcript and its protein product (GIs 312836839 and 34577063)
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107
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108 +----------------------+--------------------------------------+
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109 | Parameter | Value |
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110 +======================+======================================+
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111 | NCBI Database to Use | Protein |
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112 +----------------------+--------------------------------------+
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113 | ID List | 312836839 34577063 |
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114 +----------------------+--------------------------------------+
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115 | Output Format | Fasta |
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116 +----------------------+--------------------------------------+
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117
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118 @REFERENCES@
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119
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120 @DISCLAIMER@
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121 ]]></help>
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122 <expand macro="citations"/>
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123 </tool>