Mercurial > repos > iuc > ncbi_eutils_efetch

annotate efetch.xml @ 1:a42fa980bbd5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
author iuc
date Mon, 02 Nov 2015 12:59:23 -0500
parents 1b4ac594d02a
children aa88712a7536
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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"?>
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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 <version_command>python efetch.py --version</version_command>
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9 <command detect_errors="aggressive" interpreter="python"><![CDATA[efetch.py
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10 $db.db_select
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12 @LIST_OR_HIST@
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1b4ac594d02a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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14 #set retmode, rettype = str($db.output_format).split('-')
1b4ac594d02a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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15 ## 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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16 #if retmode != "null":
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17 --retmode $retmode
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18 #end if
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19 --rettype $rettype
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21 @EMAIL_ARGUMENTS@
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22 $whole
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23 > $default]]></command>
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24 <inputs>
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25 <expand macro="db"/>
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26 <expand macro="list_or_hist"/>
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27 <param checked="false" label="Download all records associated with query" name="whole" type="boolean" truevalue="--whole" falsevalue=""/>
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28 </inputs>
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29 <outputs>
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30 <data format="txt" name="default" label="NCBI EFetch Results">
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31 <discover_datasets pattern="__designation__.out" ext="txt"/>
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32 <change_format>
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33 <when input="output_format" value="abstract-text" format="txt"/>
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34 <when input="output_format" value="acc-text" format="txt"/>
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35 <when input="output_format" value="alignmentscores-text" format="txt"/>
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36 <when input="output_format" value="chr-text" format="txt"/>
1b4ac594d02a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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37 <when input="output_format" value="docset-text" format="txt"/>
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38 <when input="output_format" value="docsum-xml" format="xml"/>
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39 <when input="output_format" value="est-text" format="txt"/>
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40 <when input="output_format" value="fasta_cds_aa-text" format="fasta"/>
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41 <when input="output_format" value="fasta-text" format="fasta"/>
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42 <when input="output_format" value="fasta-xml" format="xml"/>
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43 <when input="output_format" value="flt-text" format="txt"/>
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44 <when input="output_format" value="ft-text" format="txt"/>
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45 <when input="output_format" value="full-text" format="txt"/>
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46 <when input="output_format" value="full-xml" format="xml"/>
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47 <when input="output_format" value="gbc-xml" format="xml"/>
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48 <when input="output_format" value="gbwithparts-text" format="genbank"/>
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49 <when input="output_format" value="gb-text" format="genbank"/>
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50 <when input="output_format" value="gb-xml" format="xml"/>
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51 <when input="output_format" value="gene_table-text" format="txt"/>
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52 <when input="output_format" value="gpc-xml" format="xml"/>
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53 <when input="output_format" value="gp-text" format="txt"/>
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54 <when input="output_format" value="gp-xml" format="xml"/>
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55 <when input="output_format" value="gss-text" format="txt"/>
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56 <when input="output_format" value="homologene-text" format="txt"/>
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57 <when input="output_format" value="ipg-xml" format="xml"/>
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58 <when input="output_format" value="medline-text" format="txt"/>
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59 <when input="output_format" value="native-xml" format="xml"/>
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60 <when input="output_format" value="null-asn.1" format="asn1"/>
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61 <when input="output_format" value="null-text" format="txt"/>
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62 <when input="output_format" value="null-xml" format="xml"/>
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63 <when input="output_format" value="rsr-text" format="txt"/>
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64 <when input="output_format" value="seqid-text" format="txt"/>
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65 <when input="output_format" value="ssexemplar-text" format="txt"/>
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66 <when input="output_format" value="summary-text" format="txt"/>
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67 <when input="output_format" value="uilist-xml" format="xml"/>
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68 <when input="output_format" value="xml-xml" format="xml"/>
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69 </change_format>
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70 </data>
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71 </outputs>
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72 <tests>
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73 <test>
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74 <param name="db_select" value="taxonomy"/>
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75 <param name="output_format" value="docsum-xml"/>
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76 <param name="qss" value="id_list"/>
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77 <param name="id_list" value="10239"/>
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78 <output name="default" file="viruses.tax.xml">
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79 </output>
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80 </test>
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81 </tests>
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82 <help><![CDATA[
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83 NCBI Entrez EFetch
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84 ==================
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85
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86 Responds to a list of UIDs in a given database with the corresponding data
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87 records in a specified format.
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88
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89 Example Queries
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90 ---------------
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91
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92 Fetch PMIDs 17284678 and 9997 as text abstracts:
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93
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94 +----------------------+--------------------------------------+
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95 | Parameter | Value |
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96 +======================+======================================+
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97 | NCBI Database to Use | PubMed |
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98 +----------------------+--------------------------------------+
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99 | ID List | 17284678 9997 |
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100 +----------------------+--------------------------------------+
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101 | Output Format | Abstract |
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102 +----------------------+--------------------------------------+
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103
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104 Fetch FASTA for a transcript and its protein product (GIs 312836839 and 34577063)
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105
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106 +----------------------+--------------------------------------+
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107 | Parameter | Value |
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108 +======================+======================================+
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109 | NCBI Database to Use | Protein |
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110 +----------------------+--------------------------------------+
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111 | ID List | 312836839 34577063 |
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112 +----------------------+--------------------------------------+
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113 | Output Format | Fasta |
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114 +----------------------+--------------------------------------+
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115
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116 @REFERENCES@
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117
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118 @DISCLAIMER@
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119 ]]></help>
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120 <expand macro="citations"/>
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121 </tool>