Mercurial > repos > proteore > proteore_data_manager

comparison data_manager_conf.xml @ 2:9ec42cb35abd draft

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planemo upload commit 339ab77a83db03409c8001324f10b36ff5b13a39-dirty
author proteore
date Wed, 19 Jun 2019 04:42:03 -0400
parents 9e31ea9fc7ea
children e967a99d66b3
comparison
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1:f3507260b30f 2:9ec42cb35abd
17 </output> 17 </output>
18 </data_table> 18 </data_table>
19 <data_table name="proteore_protein_atlas_normal_tissue"> 19 <data_table name="proteore_protein_atlas_normal_tissue">
20 <output> 20 <output>
21 <column name="id"/> 21 <column name="id"/>
22 <column name="release"/>
22 <column name="name" /> 23 <column name="name" />
23 <column name="tissue" /> 24 <column name="tissue" />
24 <column name="value" output_ref="output" > 25 <column name="value" output_ref="output" >
25 <move type="file"> 26 <move type="file">
26 <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">protein_atlas/</target> 27 <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">protein_atlas/</target>
27 </move> 28 </move>
28 <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/protein_atlas/${id}.tsv</value_translation> 29 <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/protein_atlas/${release}.tsv</value_translation>
29 <value_translation type="function">abspath</value_translation> 30 <value_translation type="function">abspath</value_translation>
30 </column> 31 </column>
31 </output> 32 </output>
32 </data_table> 33 </data_table>
33 <data_table name="proteore_protein_atlas_tumor_tissue"> 34 <data_table name="proteore_protein_atlas_tumor_tissue">
34 <output> 35 <output>
35 <column name="id"/> 36 <column name="id"/>
37 <column name="release"/>
36 <column name="name" /> 38 <column name="name" />
37 <column name="tissue" /> 39 <column name="tissue" />
38 <column name="value" output_ref="output" > 40 <column name="value" output_ref="output" >
39 <move type="file"> 41 <move type="file">
40 <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">protein_atlas/</target> 42 <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">protein_atlas/</target>
41 </move> 43 </move>
42 <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/protein_atlas/${id}.tsv</value_translation> 44 <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/protein_atlas/${release}.tsv</value_translation>
43 <value_translation type="function">abspath</value_translation> 45 <value_translation type="function">abspath</value_translation>
44 </column> 46 </column>
45 </output> 47 </output>
46 </data_table> 48 </data_table>
47 <data_table name="proteore_id_mapping_Human"> 49 <data_table name="proteore_id_mapping_Human">
48 <output> 50 <output>
49 <column name="id" /> 51 <column name="id" />
52 <column name="release"/>
50 <column name="name" /> 53 <column name="name" />
51 <column name="species" /> 54 <column name="species" />
52 <column name="value" output_ref="output" > 55 <column name="value" output_ref="output" >
53 <move type="file"> 56 <move type="file">
54 <!--source>${path}</source--> 57 <!--source>${path}</source-->
55 <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">id_mapping/</target> 58 <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">id_mapping/</target>
56 </move> 59 </move>
57 <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/id_mapping/${id}.tsv</value_translation> 60 <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/id_mapping/${release}.tsv</value_translation>
58 <value_translation type="function">abspath</value_translation> 61 <value_translation type="function">abspath</value_translation>
59 </column> 62 </column>
60 </output> 63 </output>
61 </data_table> 64 </data_table>
62 <data_table name="proteore_id_mapping_Mouse"> 65 <data_table name="proteore_id_mapping_Mouse">
63 <output> 66 <output>
64 <column name="id" /> 67 <column name="id" />
68 <column name="release"/>
65 <column name="name" /> 69 <column name="name" />
66 <column name="species" /> 70 <column name="species" />
67 <column name="value" output_ref="output" > 71 <column name="value" output_ref="output" >
68 <move type="file"> 72 <move type="file">
69 <!--source>${path}</source--> 73 <!--source>${path}</source-->
70 <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">id_mapping/</target> 74 <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">id_mapping/</target>
71 </move> 75 </move>
72 <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/id_mapping/${id}.tsv</value_translation> 76 <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/id_mapping/${release}.tsv</value_translation>
73 <value_translation type="function">abspath</value_translation> 77 <value_translation type="function">abspath</value_translation>
74 </column> 78 </column>
75 </output> 79 </output>
76 </data_table> 80 </data_table>
77 <data_table name="proteore_id_mapping_Rat"> 81 <data_table name="proteore_id_mapping_Rat">
78 <output> 82 <output>
79 <column name="id" /> 83 <column name="id" />
84 <column name="release"/>
80 <column name="name" /> 85 <column name="name" />
81 <column name="species" /> 86 <column name="species" />
82 <column name="value" output_ref="output" > 87 <column name="value" output_ref="output" >
83 <move type="file"> 88 <move type="file">
84 <!--source>${path}</source--> 89 <!--source>${path}</source-->
85 <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">id_mapping/</target> 90 <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">id_mapping/</target>
86 </move> 91 </move>
87 <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/id_mapping/${id}.tsv</value_translation> 92 <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/id_mapping/${release}.tsv</value_translation>
88 <value_translation type="function">abspath</value_translation> 93 <value_translation type="function">abspath</value_translation>
89 </column> 94 </column>
90 </output> 95 </output>
91 </data_table> 96 </data_table>
92 <data_table name="proteore_biogrid_dictionaries"> 97 <data_table name="proteore_biogrid_dictionaries">
93 <output> 98 <output>
94 <column name="id" /> 99 <column name="id" />
100 <column name="release"/>
95 <column name="name" /> 101 <column name="name" />
96 <column name="species" /> 102 <column name="species" />
97 <column name="value" output_ref="output" > 103 <column name="value" output_ref="output" >
98 <move type="file"> 104 <move type="file">
99 <!--source>${path}</source--> 105 <!--source>${path}</source-->
100 <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">PPI_dictionaries/</target> 106 <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">PPI_dictionaries/</target>
101 </move> 107 </move>
102 <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/PPI_dictionaries/${id}.json</value_translation> 108 <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/PPI_dictionaries/${release}.json</value_translation>
103 <value_translation type="function">abspath</value_translation> 109 <value_translation type="function">abspath</value_translation>
104 </column> 110 </column>
105 </output> 111 </output>
106 </data_table> 112 </data_table>
107 <data_table name="proteore_bioplex_dictionaries"> 113 <data_table name="proteore_bioplex_dictionaries">
108 <output> 114 <output>
109 <column name="id" /> 115 <column name="id" />
116 <column name="release"/>
110 <column name="name" /> 117 <column name="name" />
111 <column name="species" /> 118 <column name="species" />
112 <column name="value" output_ref="output" > 119 <column name="value" output_ref="output" >
113 <move type="file"> 120 <move type="file">
114 <!--source>${path}</source--> 121 <!--source>${path}</source-->
115 <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">PPI_dictionaries/</target> 122 <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">PPI_dictionaries/</target>
116 </move> 123 </move>
117 <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/PPI_dictionaries/${id}.json</value_translation> 124 <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/PPI_dictionaries/${release}.json</value_translation>
118 <value_translation type="function">abspath</value_translation> 125 <value_translation type="function">abspath</value_translation>
119 </column> 126 </column>
120 </output> 127 </output>
121 </data_table> 128 </data_table>
122 <data_table name="proteore_humap_dictionaries"> 129 <data_table name="proteore_humap_dictionaries">
123 <output> 130 <output>
124 <column name="id" /> 131 <column name="id" />
132 <column name="release"/>
125 <column name="name" /> 133 <column name="name" />
126 <column name="species" /> 134 <column name="species" />
127 <column name="value" output_ref="output" > 135 <column name="value" output_ref="output" >
128 <move type="file"> 136 <move type="file">
129 <!--source>${path}</source--> 137 <!--source>${path}</source-->
130 <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">PPI_dictionaries/</target> 138 <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">PPI_dictionaries/</target>
131 </move> 139 </move>
132 <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/PPI_dictionaries/${id}.json</value_translation> 140 <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/PPI_dictionaries/${release}.json</value_translation>
133 <value_translation type="function">abspath</value_translation> 141 <value_translation type="function">abspath</value_translation>
134 </column> 142 </column>
135 </output> 143 </output>
136 </data_table> 144 </data_table>
137 <data_table name="proteore_nextprot_ref"> 145 <data_table name="proteore_nextprot_ref">
138 <output> 146 <output>
139 <column name="id" /> 147 <column name="id" />
148 <column name="release"/>
140 <column name="name" /> 149 <column name="name" />
141 <column name="value" output_ref="output" > 150 <column name="value" output_ref="output" >
142 <move type="file"> 151 <move type="file">
143 <!--source>${path}</source--> 152 <!--source>${path}</source-->
144 <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">proteore_nextprot_ref/</target> 153 <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">proteore_nextprot_ref/</target>
145 </move> 154 </move>
146 <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/proteore_nextprot_ref/${id}.tsv</value_translation> 155 <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/proteore_nextprot_ref/${release}.tsv</value_translation>
147 <value_translation type="function">abspath</value_translation> 156 <value_translation type="function">abspath</value_translation>
148 </column> 157 </column>
149 </output> 158 </output>
150 </data_table> 159 </data_table>
151 </data_manager> 160 </data_manager>