Mercurial > repos > gga > apollo_export
comparison macros.xml @ 0:b4a85d0c85b8 draft
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
author | gga |
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date | Mon, 11 Sep 2017 05:47:07 -0400 |
parents | |
children | 5559e41721c3 |
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-1:000000000000 | 0:b4a85d0c85b8 |
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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> |