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comparison macros.xml @ 0:ec65a2a93d57 draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87
author iuc
date Tue, 29 Aug 2017 04:10:18 -0400
parents
children ac35ab2b3915
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-1:000000000000 0:ec65a2a93d57
1 <?xml version="1.0" ?>
2 <macros>
3 <token name="@WRAPPER_VERSION@">0.1.1</token>
4 <xml name="version">
5 <version_command>@WRAPPER_VERSION@</version_command>
6 </xml>
7 <xml name="requirements">
8 <requirements>
9 <requirement type="package" version="@WRAPPER_VERSION@">enasearch</requirement>
10 <yield/>
11 </requirements>
12 </xml>
13 <xml name="citations"/>
14 <token name="@IDS@">
15 <![CDATA[
16 #for $id in str($ids).split(',')
17 --ids '$id'
18 #end for
19 ]]>
20 </token>
21 <xml name="display_opt">
22 <conditional name="display_opt">
23 <param argument="--display" type="select" label="Display option to specify the display format">
24 <expand macro="display_options"/>
25 </param>
26 <expand macro="when_display_options"/>
27 </conditional>
28 </xml>
29 <token name="@DISPLAY@">
30 <![CDATA[
31 --display '$display_opt.display'
32 #if $display_opt.display == 'fasta' or $display_opt.display == 'fastq'
33 #if str($display_opt.range_start) != '' and str($display_opt.range_stop) != ''
34 --subseq_range '$display_opt.range_start'-'$display_opt.range_stop'
35 #end if
36 #else
37 #if str($display_opt.offset) != ''
38 --offset '$display_opt.offset'
39 #end if
40 #if str($display_opt.length) != ''
41 --length '$display_opt.length'
42 #end if
43 #end if
44 ]]>
45 </token>
46 <xml name="expanded">
47 <param argument="--expanded" type="boolean" truevalue="--expanded" falsevalue="" label="Expand a CON record?"/>
48 </xml>
49 <xml name="header">
50 <param argument="--header" type="boolean" truevalue="--header" falsevalue="" label="Obtain only the header of a record?"/>
51 </xml>
52 <xml name="accession">
53 <param argument="--accession" type="text" label="Accession id" help="Study accessions (ERP, SRP, DRP, PRJ prefixes), experiment accessions (ERX, SRX, DRX prefixes), sample accessions (ERS, SRS, DRS, SAM prefixes) and run accessions"/>
54 </xml>
55 <token name="@FIELDS@">
56 <![CDATA[
57 #if $fields
58 #for $f in str($fields).split(',')
59 --fields '$f'
60 #end for
61 #end if
62 ]]>
63 </token>
64 <xml name="change_format">
65 <change_format>
66 <when input="display_opt.display" value="fasta" format="fasta" />
67 <when input="display_opt.display" value="fastq" format="fastq" />
68 <when input="display_opt.display" value="html" format="html" />
69 <when input="display_opt.display" value="text" format="text" />
70 <when input="display_opt.display" value="xml" format="xml" />
71 </change_format>
72 </xml>
73 <token name="@SEARCH_DATA_DISPLAY@">
74 <![CDATA[
75 --display '$query_type.res.display_opt.display'
76 #if $query_type.res.display_opt.display != 'fasta' and $query_type.res.display_opt.display != 'fastq'
77 #if str($query_type.res.display_opt.offset) != ''
78 --offset '$query_type.res.display_opt.offset'
79 #end if
80 #if str($query_type.res.display_opt.length) != ''
81 --length '$query_type.res.display_opt.length'
82 #end if
83 #if $query_type.res.display_opt.display == 'report'
84 #for $f in str($query_type.res.display_opt.fields).split(',')
85 --fields '$f'
86 #end for
87 #if $query_type.res.display_opt.sortfields
88 #for $f in str($query_type.res.display_opt.sortfields).split(',')
89 --sortfields '$f'
90 #end for
91 #end if
92 #end if
93 #end if
94 ]]>
95 </token>
96 </macros>