Mercurial > repos > iuc > ncbi_eutils_efetch

comparison efetch.xml @ 3:c09fcbe4b16a draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
author iuc
date Wed, 23 Sep 2020 09:48:53 +0000
parents 0977ec0f3ba8
children 4194e47b45d4
comparison
equal deleted inserted replaced
2:0977ec0f3ba8 3:c09fcbe4b16a
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
8 <version_command>python efetch.py --version</version_command> 8 <version_command>python efetch.py --version</version_command>
9 <command detect_errors="aggressive"><![CDATA[ 9 <command detect_errors="aggressive"><![CDATA[
10 python '$__tool_directory__/efetch.py'
11 $db.db_select
12 10
13 @LIST_OR_HIST@ 11 python '$__tool_directory__/efetch.py'
14 12
15 #set rettype, retmode = str($db.output_format).split('-') 13 $db.db_select
16 ## Otherwise, defaults to a None/empty which implies 'default' to NCBI
17 #if retmode != "null":
18 --retmode $retmode
19 #end if
20 --rettype $rettype
21 14
22 @EMAIL_ARGUMENTS@ 15 @LIST_OR_HIST@
16
17 @EMAIL_ARGUMENTS@
18
19 @EFETCH_FORMAT_TOKEN@
20
23 ]]></command> 21 ]]></command>
24 <inputs> 22 <inputs>
25 <expand macro="db"/>
26 <expand macro="list_or_hist"/> 23 <expand macro="list_or_hist"/>
24 <expand macro="efetchdb"/>
27 </inputs> 25 </inputs>
28 <outputs> 26 <outputs>
29 <collection name="output1" type="list" label="NCBI EFetch results"> 27 <collection name="output1" type="list" label="NCBI EFetch results">
30 <discover_datasets pattern="__designation_and_ext__" directory="downloads"/> 28 <discover_datasets pattern="__designation_and_ext__" directory="downloads"/>
31 </collection> 29 </collection>
32 </outputs> 30 </outputs>
33 <tests> 31 <tests>
34 <test> 32 <test>
35 <param name="db_select" value="taxonomy"/> 33 <param name="db_select" value="taxonomy"/>
36 <param name="output_format" value="full-xml"/> 34 <param name="output_format" value="none-xml-xml"/>
37 <param name="qss" value="id_list"/> 35 <param name="qss" value="id_list"/>
38 <param name="id_list" value="10239"/> 36 <param name="id_list" value="10239"/>
39 <output_collection name="output1" type="list" count="1"> 37 <output_collection name="output1" type="list" count="1">
40 <element name="EFetch Results Chunk 0" ftype="xml" file="viruses.tax.xml" lines_diff="2" /> 38 <element name="EFetch-None-xml-chunk1" ftype="xml" file="viruses.tax.xml" lines_diff="2" />
39 </output_collection>
40 </test>
41 <test>
42 <param name="db_select" value="nuccore"/>
43 <param name="output_format" value="fasta-text-fasta"/>
44 <param name="qss" value="id_file"/>
45 <param name="id_file" value="efetchin.tabular"/>
46 <output_collection name="output1" type="list" count="1">
47 <element name="EFetch-fasta-text-chunk1" ftype="xml" file="efetch.tabin.fasta" />
41 </output_collection> 48 </output_collection>
42 </test> 49 </test>
43 </tests> 50 </tests>
44 <help><![CDATA[ 51 <help><![CDATA[
45 NCBI Entrez EFetch 52 NCBI Entrez EFetch