Mercurial > repos > gga > apollo_create_or_update

comparison macros.xml @ 10:d72192ec8e39 draft

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"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
author gga
date Mon, 02 Dec 2019 05:46:45 -0500
parents 29ce13734a5c
children 63ad8934b189
comparison
equal deleted inserted replaced
9:29ce13734a5c 10:d72192ec8e39
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <macros> 2 <macros>
3 <token name="@WRAPPER_VERSION@">4.0.0</token> 3 <token name="@WRAPPER_VERSION@">4.1</token>
4 4
5 <xml name="requirements"> 5 <xml name="requirements">
6 <requirements> 6 <requirements>
7 <requirement type="package" version="2.7">python</requirement> 7 <requirement type="package" version="4.1">apollo</requirement>
8 <requirement type="package" version="1.65">biopython</requirement>
9 <requirement type="package" version="0.6.2">bcbiogff</requirement>
10 <requirement type="package" version="2.12.4">requests</requirement>
11 <requirement type="package" version="1.11.0">six</requirement>
12 <yield/> 8 <yield/>
13 </requirements> 9 </requirements>
14 </xml> 10 </xml>
15 <token name="@DATA_DIR@">\$GALAXY_SHARED_DIR</token> 11 <token name="@DATA_DIR@">\$GALAXY_SHARED_DIR</token>
16 <token name="@EXT_URL@"> 12 <token name="@EXT_URL@">
17 "\$GALAXY_WEBAPOLLO_EXT_URL" 13 "\$GALAXY_WEBAPOLLO_EXT_URL"
18 </token> 14 </token>
19 <token name="@URL@"> 15 <token name="@URL@">
20 "\$GALAXY_WEBAPOLLO_URL" 16 "\$GALAXY_WEBAPOLLO_URL"
21 </token> 17 </token>
22 <token name="@ADMIN_AUTH@"> 18
23 "\$GALAXY_WEBAPOLLO_URL" 19 <token name="@AUTH@"><![CDATA[
24 "\$GALAXY_WEBAPOLLO_USER" 20 if [ -z "\$ARROW_GLOBAL_CONFIG_PATH" ]; then
25 "\$GALAXY_WEBAPOLLO_PASSWORD" 21 echo "__default: local" > '.auth.yml' &&
26 </token> 22 echo "local:" >> '.auth.yml' &&
23 echo " url: \"\$GALAXY_WEBAPOLLO_URL\"" >> '.auth.yml' &&
24 echo " username: \"\$GALAXY_WEBAPOLLO_USER\"" >> '.auth.yml' &&
25 echo " password: \"\$GALAXY_WEBAPOLLO_PASSWORD\"" >> '.auth.yml' &&
26
27 export ARROW_GLOBAL_CONFIG_PATH='.auth.yml'
28 ; fi &&
29 ]]></token>
27 30
28 <token name="@ORG_OR_GUESS@"> 31 <token name="@ORG_OR_GUESS@">
29 <![CDATA[ 32 <![CDATA[
30 #if $org_source.source_select == "auto_json": 33 #if $org_source.source_select == "auto_json":
31 --org_json "${org_source.org_file}" 34 --org_json '${org_source.org_file}'
32 #elif $org_source.source_select == "select": 35 #elif $org_source.source_select == "select":
33 --org_id "${org_source.org_select}" 36 --org_id '${org_source.org_select}'
34 #else: 37 #else:
35 --org_raw "${org_source.org_raw}" 38 --org_raw '${org_source.org_raw}'
36 #end if 39 #end if
37 ]]> 40 ]]>
38 </token> 41 </token>
39 <token name="@ORG_CN_OR_GUESS@"> 42 <token name="@ORG_CN_OR_GUESS@">
40 <![CDATA[ 43 <![CDATA[
41 @ORG_OR_GUESS@ 44 @ORG_OR_GUESS@
42 45
43 #if $cn_source.source_select == "auto": 46 #if $cn_source.source_select == "auto":
44 #if str($cn_source.cn_file) != "None": 47 #if str($cn_source.cn_file) != "None":
45 --seq_fasta $cn_source.cn_file 48 --seq_fasta '$cn_source.cn_file'
46 #end if 49 #end if
47 #else 50 #else
48 #if $cn_source.source_select != "all" and len($cn_source.refseqs) > 0: 51 #if $cn_source.source_select != "all" and len($cn_source.refseqs) > 0:
49 --seq_raw 52 --seq_raw
50 #for $item in $cn_source.refseqs: 53 #for $item in $cn_source.refseqs:
51 "${item.refseq}" 54 '${item.refseq}'
52 #end for 55 #end for
53 #end if 56 #end if
54 #end if 57 #end if
55 ]]> 58 ]]>
56 </token> 59 </token>
91 </repeat> 94 </repeat>
92 </when> 95 </when>
93 </conditional> 96 </conditional>
94 </xml> 97 </xml>
95 98
96 <xml name="test_result">
97 <assert_stderr>
98 <has_text text="MissingSchema" />
99 </assert_stderr>
100 </xml>
101
102 <xml name="citations"> 99 <xml name="citations">
103 <citations> 100 <citations>
104 <citation type="doi">10.1371/journal.pcbi.1006790</citation> 101 <citation type="doi">10.1371/journal.pcbi.1006790</citation>
105 </citations> 102 </citations>
106 </xml> 103 </xml>
107 <xml name="gff3_input"> 104 <xml name="gff3_input">
108 <param label="GFF3 Annotations" name="gff3_data" type="data" format="gff3"/> 105 <param label="GFF3 Annotations" name="gff3_data" type="data" format="gff3"/>
109 </xml> 106 </xml>
110 <token name="@GENOME_SELECTOR_PRE@"> 107 <token name="@GENOME_SELECTOR_PRE@">
111 #if $reference_genome.reference_genome_source == 'history': 108 #if $reference_genome.reference_genome_source == 'history':
112 ln -s $reference_genome.genome_fasta genomeref.fa; 109 ln -s '$reference_genome.genome_fasta' genomeref.fa;
113 #end if 110 #end if
114 </token> 111 </token>
115 <token name="@GENOME_SELECTOR@"> 112 <token name="@GENOME_SELECTOR@">
116 #if $reference_genome.reference_genome_source == 'cached': 113 #if $reference_genome.reference_genome_source == 'cached':
117 "${reference_genome.fasta_indexes.fields.path}" 114 '${reference_genome.fasta_indexes.fields.path}'
118 #elif $reference_genome.reference_genome_source == 'history': 115 #elif $reference_genome.reference_genome_source == 'history':
119 genomeref.fa 116 genomeref.fa
120 #end if 117 #end if
121 </token> 118 </token>
122 <token name="@REFERENCES@"> 119 <token name="@REFERENCES@">