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comparison macros.xml @ 0:f889e757ca93 draft

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
author gga
date Mon, 11 Sep 2017 05:45:08 -0400
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children 08f8e19005a8
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-1:000000000000 0:f889e757ca93
1 <?xml version="1.0"?>
2 <macros>
3 <xml name="requirements">
4 <requirements>
5 <requirement type="package" version="2.7">python</requirement>
6 <requirement type="package" version="1.65">biopython</requirement>
7 <requirement type="package" version="0.6.2">bcbiogff</requirement>
8 <requirement type="package" version="2.12.4">requests</requirement>
9 <requirement type="package" version="0.16.0">future</requirement>
10 <yield/>
11 </requirements>
12 </xml>
13 <token name="@DATA_DIR@">\$GALAXY_SHARED_DIR</token>
14 <token name="@EXT_URL@">
15 "\$GALAXY_WEBAPOLLO_EXT_URL"
16 </token>
17 <token name="@URL@">
18 "\$GALAXY_WEBAPOLLO_URL"
19 </token>
20 <token name="@ADMIN_AUTH@">
21 "\$GALAXY_WEBAPOLLO_URL"
22 "\$GALAXY_WEBAPOLLO_USER"
23 "\$GALAXY_WEBAPOLLO_PASSWORD"
24 </token>
25
26 <token name="@ORG_OR_GUESS@">
27 <![CDATA[
28 #if $org_source.source_select == "auto_json":
29 --org_json "${org_source.org_file}"
30 #elif $org_source.source_select == "select":
31 --org_id "${org_source.org_select}"
32 #else:
33 --org_raw "${org_source.org_raw}"
34 #end if
35 ]]>
36 </token>
37 <token name="@ORG_CN_OR_GUESS@">
38 <![CDATA[
39 @ORG_OR_GUESS@
40
41 #if $cn_source.source_select == "auto":
42 #if str($cn_source.cn_file) != "None":
43 --seq_fasta $cn_source.cn_file
44 #end if
45 #else
46 #if $cn_source.source_select != "all" and len($cn_source.refseqs) > 0:
47 --seq_raw
48 #for $item in $cn_source.refseqs:
49 "${item.refseq}"
50 #end for
51 #end if
52 #end if
53 ]]>
54 </token>
55 <xml name="org_or_guess">
56 <conditional name="org_source">
57 <param name="source_select" type="select" label="Organism Common Name Source">
58 <option value="select">Select</option>
59 <option value="direct">Direct Entry</option>
60 <option value="auto_json">Autodetect from Apollo JSON</option>
61 </param>
62 <when value="select">
63 <param name="org_select" type="select" dynamic_options="galaxy_list_orgs(__trans__)" label="Organism" />
64 </when>
65 <when value="direct">
66 <param name="org_raw" type="text" label="Organism Common Name" optional="False" />
67 </when>
68 <when value="auto_json">
69 <param name="org_file" type="data" format="json" label="Apollo Organism File" help="Will only fetch first organism" />
70 </when>
71 </conditional>
72 </xml>
73 <xml name="cn_or_guess">
74 <expand macro="org_or_guess" />
75 <conditional name="cn_source">
76 <param name="source_select" type="select" label="Organism Sequence(s) Source">
77 <option value="all">All Refseqs</option>
78 <option value="direct">Direct Entry</option>
79 <option value="auto">Autodetect from Fasta</option>
80 </param>
81 <when value="all">
82 </when>
83 <when value="auto">
84 <param name="cn_file" type="data" format="fasta" label="Reference sequence(s)" optional="true"/>
85 </when>
86 <when value="direct">
87 <repeat name="refseqs" title="Reference Sequences" help="These are used to identify sequences within an organism that you wish to extract">
88 <param name="refseq" type="text" label="Reference sequence(s)" />
89 </repeat>
90 </when>
91 </conditional>
92 </xml>
93
94 <xml name="test_result">
95 <assert_stderr>
96 <has_text text="MissingSchema" />
97 </assert_stderr>
98 </xml>
99
100 <xml name="citations">
101 <citations>
102 </citations>
103 </xml>
104 <xml name="gff3_input">
105 <param label="GFF3 Annotations" name="gff3_data" type="data" format="gff3"/>
106 </xml>
107 <token name="@GENOME_SELECTOR_PRE@">
108 #if $reference_genome.reference_genome_source == 'history':
109 ln -s $reference_genome.genome_fasta genomeref.fa;
110 #end if
111 </token>
112 <token name="@GENOME_SELECTOR@">
113 #if $reference_genome.reference_genome_source == 'cached':
114 "${reference_genome.fasta_indexes.fields.path}"
115 #elif $reference_genome.reference_genome_source == 'history':
116 genomeref.fa
117 #end if
118 </token>
119 <token name="@REFERENCES@">
120 <![CDATA[
121 ------
122
123 **Citation**
124
125 If you use this tool in Galaxy, please cite:
126 Eric Rasche (2016), `Galaxy Apollo Tools <https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo>`_
127 ]]>
128 </token>
129 </macros>