Mercurial > repos > dchristiany > data_manager_proteore

annotate data_manager/resource_building.xml @ 52:a34897a85cda draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 12b0b3e18cd7af9a8588906fa2ec199b9d2a770f-dirty
author dchristiany
date Fri, 01 Mar 2019 09:59:08 -0500
parents 8f6ddad93e9f
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
52
a34897a85cda planemo upload commit 12b0b3e18cd7af9a8588906fa2ec199b9d2a770f-dirty
dchristiany
parents: 51
diff changeset
1 <tool id="data_manager_proteore" name="Get source files for proteore tools" version="2019.03.01.1" tool_type="manage_data">
0
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
2 <description>
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
3 to create or update reference files for proteore tools
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
4 </description>
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
5 <requirements>
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
6 </requirements>
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
7 <stdio>
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
8 <exit_code range="1:" />
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
9 </stdio>
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
10 <command><![CDATA[
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
11
19
85532a48e4e4 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 18
diff changeset
12 python $__tool_directory__/resource_building.py
0
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
13 #if $database.database == "human_protein_atlas"
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
14 --hpa "$database.tissues"
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
15 #else if $database.database == "peptide_atlas"
15
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
16 --peptideatlas="$database.tissues"
43
3febf3d1139a planemo upload commit 9b701c1faf8be4835b4e7236780ee9ee26f9a373-dirty
dchristiany
parents: 42
diff changeset
17 --date="$database.date"
0
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
18 #else if $database.database == "id_mapping"
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
19 --id_mapping="$database.species"
15
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
20 #else if $database.database == "PPI"
46
80fc0b28e227 planemo upload commit cb633de1f04ef7b7133728909716b6c6594533d1-dirty
dchristiany
parents: 45
diff changeset
21 --interactome="$database.base.interactome"
47
7b486b0fba4e planemo upload commit cb633de1f04ef7b7133728909716b6c6594533d1-dirty
dchristiany
parents: 46
diff changeset
22 #if $database.base.interactome == "biogrid"
46
80fc0b28e227 planemo upload commit cb633de1f04ef7b7133728909716b6c6594533d1-dirty
dchristiany
parents: 45
diff changeset
23 --species="$database.base.species"
80fc0b28e227 planemo upload commit cb633de1f04ef7b7133728909716b6c6594533d1-dirty
dchristiany
parents: 45
diff changeset
24 #end if
0
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
25 #end if
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
26 --output "$output"
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
27
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
28 ]]></command>
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
29
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
30 <inputs>
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
31 <conditional name="database">
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
32 <param name="database" type="select">
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
33 <option value="human_protein_atlas">Human Protein Atlas</option>
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
34 <option value="peptide_atlas">Peptide Atlas</option>
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
35 <option value="id_mapping">ID mapping</option>
15
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
36 <option value="PPI">Build protein interaction maps</option>
0
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
37 </param>
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
38 <when value="human_protein_atlas">
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
39 <param name="tissues" type="select" multiple="false" label="Please select tissue">
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
40 <option value="HPA_normal_tissue">Normal tissue</option>
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
41 <option value="HPA_pathology">Pathology</option>
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
42 <option value="HPA_full_atlas">Full Atlas</option>
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
43 </param>
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
44 </when>
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
45 <when value="peptide_atlas">
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
46 <param name="tissues" type="select" multiple="false" label="Please select the tissue">
34
0c0586ac3e29 planemo upload commit c89c5deac442c0c2aa52b24f2c5af4b290773fc0-dirty
dchristiany
parents: 33
diff changeset
47 <option value="432.Human_Adrenal_gland">Human Adrenal gland proteome</option>
0c0586ac3e29 planemo upload commit c89c5deac442c0c2aa52b24f2c5af4b290773fc0-dirty
dchristiany
parents: 33
diff changeset
48 <option value="441.Human_Brain">Human Brain proteome</option>
0c0586ac3e29 planemo upload commit c89c5deac442c0c2aa52b24f2c5af4b290773fc0-dirty
dchristiany
parents: 33
diff changeset
49 <option value="427.Human_Breast">Human Breast proteome</option>
0c0586ac3e29 planemo upload commit c89c5deac442c0c2aa52b24f2c5af4b290773fc0-dirty
dchristiany
parents: 33
diff changeset
50 <option value="434.Human_CSF">Human CSF (Cerebro Spinal Fluid) proteome</option>
0c0586ac3e29 planemo upload commit c89c5deac442c0c2aa52b24f2c5af4b290773fc0-dirty
dchristiany
parents: 33
diff changeset
51 <option value="374.Human_Colon_cancer">Human Colon cancer proteome</option>
0c0586ac3e29 planemo upload commit c89c5deac442c0c2aa52b24f2c5af4b290773fc0-dirty
dchristiany
parents: 33
diff changeset
52 <option value="429.Human_Digestive_system">Human Digestive system proteome</option>
0c0586ac3e29 planemo upload commit c89c5deac442c0c2aa52b24f2c5af4b290773fc0-dirty
dchristiany
parents: 33
diff changeset
53 <option value="430.Human_Female_reproductive_system">Human Female reproductive system proteome</option>
0c0586ac3e29 planemo upload commit c89c5deac442c0c2aa52b24f2c5af4b290773fc0-dirty
dchristiany
parents: 33
diff changeset
54 <option value="418.Human_Heart">Human Heart proteome</option>
0c0586ac3e29 planemo upload commit c89c5deac442c0c2aa52b24f2c5af4b290773fc0-dirty
dchristiany
parents: 33
diff changeset
55 <option value="424.Human_Kidney">Human Kidney proteome</option>
0c0586ac3e29 planemo upload commit c89c5deac442c0c2aa52b24f2c5af4b290773fc0-dirty
dchristiany
parents: 33
diff changeset
56 <option value="425.Human_Liver">Human Liver proteome</option>
0c0586ac3e29 planemo upload commit c89c5deac442c0c2aa52b24f2c5af4b290773fc0-dirty
dchristiany
parents: 33
diff changeset
57 <option value="419.Human_Lung">Human Lung proteome</option>
0c0586ac3e29 planemo upload commit c89c5deac442c0c2aa52b24f2c5af4b290773fc0-dirty
dchristiany
parents: 33
diff changeset
58 <option value="431.Human_Male_reproductive_system">Human Male reproductive system proteome</option>
0c0586ac3e29 planemo upload commit c89c5deac442c0c2aa52b24f2c5af4b290773fc0-dirty
dchristiany
parents: 33
diff changeset
59 <option value="420.Human_Pancreas">Human Pancreas proteome</option>
0c0586ac3e29 planemo upload commit c89c5deac442c0c2aa52b24f2c5af4b290773fc0-dirty
dchristiany
parents: 33
diff changeset
60 <option value="465.Human_Plasma_non_glyco">Human Plasma non glyco proteome</option>
0c0586ac3e29 planemo upload commit c89c5deac442c0c2aa52b24f2c5af4b290773fc0-dirty
dchristiany
parents: 33
diff changeset
61 <option value="421.Human_Spleen">Human Spleen proteome</option>
0c0586ac3e29 planemo upload commit c89c5deac442c0c2aa52b24f2c5af4b290773fc0-dirty
dchristiany
parents: 33
diff changeset
62 <option value="463.Human_Testis">Human Testis proteome</option>
0c0586ac3e29 planemo upload commit c89c5deac442c0c2aa52b24f2c5af4b290773fc0-dirty
dchristiany
parents: 33
diff changeset
63 <option value="422.Human_Urinary_bladder">Human Bladder proteome</option>
0c0586ac3e29 planemo upload commit c89c5deac442c0c2aa52b24f2c5af4b290773fc0-dirty
dchristiany
parents: 33
diff changeset
64 <option value="423.Human_Urine">Human Urine proteome</option>
0
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
65 </param>
45
ec7a4d773c45 planemo upload commit 9b701c1faf8be4835b4e7236780ee9ee26f9a373-dirty
dchristiany
parents: 44
diff changeset
66 <param name="date" type="text" value="" label="enter the build date" help="for example: '2018-04'"/>
0
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
67 </when>
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
68 <when value="id_mapping">
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
69 <param name="species" type="select" multiple="false" label="Please select the species">
28
d235909789ca planemo upload commit e694c4b0df30a4286ba09721696e8ec3af25fd97-dirty
dchristiany
parents: 27
diff changeset
70 <option value="Human">Human (Homo sapiens)</option>
d235909789ca planemo upload commit e694c4b0df30a4286ba09721696e8ec3af25fd97-dirty
dchristiany
parents: 27
diff changeset
71 <option value="Mouse">Mouse (Mus musculus)</option>
d235909789ca planemo upload commit e694c4b0df30a4286ba09721696e8ec3af25fd97-dirty
dchristiany
parents: 27
diff changeset
72 <option value="Rat">Rat (Rattus norvegicus)</option>
0
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
73 </param>
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
74 </when>
15
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
75 <when value="PPI">
46
80fc0b28e227 planemo upload commit cb633de1f04ef7b7133728909716b6c6594533d1-dirty
dchristiany
parents: 45
diff changeset
76 <conditional name="base">
80fc0b28e227 planemo upload commit cb633de1f04ef7b7133728909716b6c6594533d1-dirty
dchristiany
parents: 45
diff changeset
77 <param name="interactome" type="select" multiple="false" label="Please select interactome">
80fc0b28e227 planemo upload commit cb633de1f04ef7b7133728909716b6c6594533d1-dirty
dchristiany
parents: 45
diff changeset
78 <option value="biogrid">BioGRID</option>
80fc0b28e227 planemo upload commit cb633de1f04ef7b7133728909716b6c6594533d1-dirty
dchristiany
parents: 45
diff changeset
79 <option value="bioplex">Human Bioplex 2.0</option>
80fc0b28e227 planemo upload commit cb633de1f04ef7b7133728909716b6c6594533d1-dirty
dchristiany
parents: 45
diff changeset
80 <option value="humap">Human protein complex Map (Hu.map)</option>
80fc0b28e227 planemo upload commit cb633de1f04ef7b7133728909716b6c6594533d1-dirty
dchristiany
parents: 45
diff changeset
81 </param>
80fc0b28e227 planemo upload commit cb633de1f04ef7b7133728909716b6c6594533d1-dirty
dchristiany
parents: 45
diff changeset
82 <when value="biogrid">
80fc0b28e227 planemo upload commit cb633de1f04ef7b7133728909716b6c6594533d1-dirty
dchristiany
parents: 45
diff changeset
83 <param name="species" type="select" multiple="false" label="Please select the species">
80fc0b28e227 planemo upload commit cb633de1f04ef7b7133728909716b6c6594533d1-dirty
dchristiany
parents: 45
diff changeset
84 <option value="Human">Human (Homo sapiens)</option>
80fc0b28e227 planemo upload commit cb633de1f04ef7b7133728909716b6c6594533d1-dirty
dchristiany
parents: 45
diff changeset
85 <option value="Mouse">Mouse (Mus musculus)</option>
80fc0b28e227 planemo upload commit cb633de1f04ef7b7133728909716b6c6594533d1-dirty
dchristiany
parents: 45
diff changeset
86 <option value="Rat">Rat (Rattus norvegicus)</option>
80fc0b28e227 planemo upload commit cb633de1f04ef7b7133728909716b6c6594533d1-dirty
dchristiany
parents: 45
diff changeset
87 </param>
80fc0b28e227 planemo upload commit cb633de1f04ef7b7133728909716b6c6594533d1-dirty
dchristiany
parents: 45
diff changeset
88 </when>
80fc0b28e227 planemo upload commit cb633de1f04ef7b7133728909716b6c6594533d1-dirty
dchristiany
parents: 45
diff changeset
89 <when value="bioplex"/>
80fc0b28e227 planemo upload commit cb633de1f04ef7b7133728909716b6c6594533d1-dirty
dchristiany
parents: 45
diff changeset
90 <when value="humap"/>
80fc0b28e227 planemo upload commit cb633de1f04ef7b7133728909716b6c6594533d1-dirty
dchristiany
parents: 45
diff changeset
91 </conditional>
15
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
92 </when>
0
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
93 </conditional>
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
94 </inputs>
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
95
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
96 <outputs>
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
97 <!--data format="tabular" name="output">
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
98 <discover_datasets pattern="(?P&lt;designation&gt;.+).tsv" ext="tabular" visible="true" assign_primary_output="true" />
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
99 </data-->
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
100 <data name="output" format="data_manager_json"/>
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
101 </outputs>
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
102
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
103 <tests>
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
104 </tests>
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
105
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
106 <help><![CDATA[
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
107
15
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
108 **Description**
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
109
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
110 This tool is a data manager designed to update resources files of ProteoRe tools. For now, only resources files for tools listed below are handled:
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
111
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
112 * "Get MS/MS observations in tissue/fluid [Peptide Atlas]"
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
113 * "Get expression profiles by (normal or tumor) tissue/cell type [Human Protein Atlas]"
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
114 * "ID converter"
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
115
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
116 -----
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
117
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
118 **Input**
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
119
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
120 There's no input needed, once you selected the tool and file you want to update, it will be generated automatically.
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
121
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
122 -----
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
123
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
124 **Parameters**
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
125
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
126 * database: the database to update (for now one per tool)
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
127
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
128 Once a database is selected, there's a second dropdown menu to select the specific file you want to update.
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
129
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
130 * for 'Human Protein Atlas': 'Normal tissue', 'Pathology' and 'Full Atlas'
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
131
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
132 * for 'Peptide Atlas': 'Human liver', 'Human brain', 'Human heart', 'Human kidney', 'Human blood plasma', 'Human urine' and 'Human cerebrospinal fluid'
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
133
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
134 * for 'ID mapping': 'Human (Homo sapiens)', 'Mouse (Mus musculus)' and 'Rat (Rattus norvegicus)'
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
135
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
136 * for 'Build protein interaction maps': "BioGRID", "Bioplex" and "Human (Homo sapiens)", "Mouse (Mus musculus)", "Rat (Rattus norvegicus)"
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
137
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
138 -----
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
139
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
140 **Output**
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
141
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
142 The output is the reference file selected for update in input.
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
143
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
144 For example, if you select database="Human Protein Atlas" and Please select tissue="Normal tissue":
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
145
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
146 the output is a new reference file for "Get expression profiles by (normal or tumor) tissue/cell type [Human Protein Atlas]"
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
147 dated from the day and listed in the dropdown menu "Normal tissue HPA version".
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
148
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
149 .. class:: warningmark
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
150
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
151 A reference file created with this data manager will appears in the concerned ProteoRE tool. It can not be removed with the data manager.
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
152
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
153 -----
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
154
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
155 **Data sources**
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
156
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
157 For 'Human Protein Atlas':
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
158
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
159 * `Normal Tissue <https://www.proteinatlas.org/download/normal_tissue.tsv.zip>`_.
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
160 * `Pathology <https://www.proteinatlas.org/download/pathology.tsv.zip>`_.
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
161 * `Full Atlas <https://www.proteinatlas.org/download/proteinatlas.tsv.zip>`_.
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
162
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
163 For 'Peptide Atlas':
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
164
37
93338a36da6e planemo upload commit c89c5deac442c0c2aa52b24f2c5af4b290773fc0-dirty
dchristiany
parents: 36
diff changeset
165
38
49467e5f78a6 planemo upload commit c89c5deac442c0c2aa52b24f2c5af4b290773fc0-dirty
dchristiany
parents: 37
diff changeset
166 * `Human Adrenal gland proteome <https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id=432&display_options=ShowAbundances&organism_id=2&redundancy_constraint=4&presence_level_constraint=1%2C2&gene_annotation_level_constraint=leaf&QUERY_NAME=AT_GetProteins&action=QUERY&output_mode=tsv&apply_action=QUERY>`_.
49467e5f78a6 planemo upload commit c89c5deac442c0c2aa52b24f2c5af4b290773fc0-dirty
dchristiany
parents: 37
diff changeset
167 * `Human Brain proteome <https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id=441&display_options=ShowAbundances&organism_id=2&redundancy_constraint=4&presence_level_constraint=1%2C2&gene_annotation_level_constraint=leaf&QUERY_NAME=AT_GetProteins&action=QUERY&output_mode=tsv&apply_action=QUERY>`_.
49467e5f78a6 planemo upload commit c89c5deac442c0c2aa52b24f2c5af4b290773fc0-dirty
dchristiany
parents: 37
diff changeset
168 * `Human Breast Proteome <https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id=427&display_options=ShowAbundances&organism_id=2&redundancy_constraint=4&presence_level_constraint=1%2C2&gene_annotation_level_constraint=leaf&QUERY_NAME=AT_GetProteins&action=QUERY&output_mode=tsv&apply_action=QUERY>`_.
49467e5f78a6 planemo upload commit c89c5deac442c0c2aa52b24f2c5af4b290773fc0-dirty
dchristiany
parents: 37
diff changeset
169 * `Human CSF proteome <https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id=434&display_options=ShowAbundances&organism_id=2&redundancy_constraint=4&presence_level_constraint=1%2C2&gene_annotation_level_constraint=leaf&QUERY_NAME=AT_GetProteins&action=QUERY&output_mode=tsv&apply_action=QUERY>`_.
49467e5f78a6 planemo upload commit c89c5deac442c0c2aa52b24f2c5af4b290773fc0-dirty
dchristiany
parents: 37
diff changeset
170 * `Human Digestive System proteome <https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id=429&display_options=ShowAbundances&organism_id=2&redundancy_constraint=4&presence_level_constraint=1%2C2&gene_annotation_level_constraint=leaf&QUERY_NAME=AT_GetProteins&action=QUERY&output_mode=tsv&apply_action=QUERY>`_.
49467e5f78a6 planemo upload commit c89c5deac442c0c2aa52b24f2c5af4b290773fc0-dirty
dchristiany
parents: 37
diff changeset
171 * `Human female reproductive system proteome <https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id=430&display_options=ShowAbundances&organism_id=2&redundancy_constraint=4&presence_level_constraint=1%2C2&gene_annotation_level_constraint=leaf&QUERY_NAME=AT_GetProteins&action=QUERY&output_mode=tsv&apply_action=QUERY>`_.
49467e5f78a6 planemo upload commit c89c5deac442c0c2aa52b24f2c5af4b290773fc0-dirty
dchristiany
parents: 37
diff changeset
172 * `Human Heart proteome <https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id=418&display_options=ShowAbundances&organism_id=2&redundancy_constraint=4&presence_level_constraint=1%2C2&gene_annotation_level_constraint=leaf&QUERY_NAME=AT_GetProteins&action=QUERY&output_mode=tsv&apply_action=QUERY>`_.
49467e5f78a6 planemo upload commit c89c5deac442c0c2aa52b24f2c5af4b290773fc0-dirty
dchristiany
parents: 37
diff changeset
173 * `Human Kidney man Kidney Proteome <https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id=424&display_options=ShowAbundances&organism_id=2&redundancy_constraint=4&presence_level_constraint=1%2C2&gene_annotation_level_constraint=leaf&QUERY_NAME=AT_GetProteins&action=QUERY&output_mode=tsv&apply_action=QUERY>`_.
49467e5f78a6 planemo upload commit c89c5deac442c0c2aa52b24f2c5af4b290773fc0-dirty
dchristiany
parents: 37
diff changeset
174 * `Human Liver proteome <https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id=425&display_options=ShowAbundances&organism_id=2&redundancy_constraint=4&presence_level_constraint=1%2C2&gene_annotation_level_constraint=leaf&QUERY_NAME=AT_GetProteins&action=QUERY&output_mode=tsv&apply_action=QUERY>`_.
49467e5f78a6 planemo upload commit c89c5deac442c0c2aa52b24f2c5af4b290773fc0-dirty
dchristiany
parents: 37
diff changeset
175 * `Human Lung proteome <https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id=419&display_options=ShowAbundances&organism_id=2&redundancy_constraint=4&presence_level_constraint=1%2C2&gene_annotation_level_constraint=leaf&QUERY_NAME=AT_GetProteins&action=QUERY&output_mode=tsv&apply_action=QUERY>`_.
49467e5f78a6 planemo upload commit c89c5deac442c0c2aa52b24f2c5af4b290773fc0-dirty
dchristiany
parents: 37
diff changeset
176 * `Human Male Reproductive System proteome <https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id=431&display_options=ShowAbundances&organism_id=2&redundancy_constraint=4&presence_level_constraint=1%2C2&gene_annotation_level_constraint=leaf&QUERY_NAME=AT_GetProteins&action=QUERY&output_mode=tsv&apply_action=QUERY>`_.
49467e5f78a6 planemo upload commit c89c5deac442c0c2aa52b24f2c5af4b290773fc0-dirty
dchristiany
parents: 37
diff changeset
177 * `Human Pancreas proteome <https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id=420&display_options=ShowAbundances&organism_id=2&redundancy_constraint=4&presence_level_constraint=1%2C2&gene_annotation_level_constraint=leaf&QUERY_NAME=AT_GetProteins&action=QUERY&output_mode=tsv&apply_action=QUERY>`_.
49467e5f78a6 planemo upload commit c89c5deac442c0c2aa52b24f2c5af4b290773fc0-dirty
dchristiany
parents: 37
diff changeset
178 * `Human Plasma Non-Glyco proteome <https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id=465&display_options=ShowAbundances&organism_id=2&redundancy_constraint=4&presence_level_constraint=1%2C2&gene_annotation_level_constraint=leaf&QUERY_NAME=AT_GetProteins&action=QUERY&output_mode=tsv&apply_action=QUERY>`_.
49467e5f78a6 planemo upload commit c89c5deac442c0c2aa52b24f2c5af4b290773fc0-dirty
dchristiany
parents: 37
diff changeset
179 * `Human Spleen proteome <https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id=421&display_options=ShowAbundances&organism_id=2&redundancy_constraint=4&presence_level_constraint=1%2C2&gene_annotation_level_constraint=leaf&QUERY_NAME=AT_GetProteins&action=QUERY&output_mode=tsv&apply_action=QUERY>`_.
49467e5f78a6 planemo upload commit c89c5deac442c0c2aa52b24f2c5af4b290773fc0-dirty
dchristiany
parents: 37
diff changeset
180 * `Human Testis proteome <https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id=463&display_options=ShowAbundances&organism_id=2&redundancy_constraint=4&presence_level_constraint=1%2C2&gene_annotation_level_constraint=leaf&QUERY_NAME=AT_GetProteins&action=QUERY&output_mode=tsv&apply_action=QUERY>`_.
49467e5f78a6 planemo upload commit c89c5deac442c0c2aa52b24f2c5af4b290773fc0-dirty
dchristiany
parents: 37
diff changeset
181 * `Human Urinary Bladder proteome <https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id=422&display_options=ShowAbundances&organism_id=2&redundancy_constraint=4&presence_level_constraint=1%2C2&gene_annotation_level_constraint=leaf&QUERY_NAME=AT_GetProteins&action=QUERY&output_mode=tsv&apply_action=QUERY>`_.
49467e5f78a6 planemo upload commit c89c5deac442c0c2aa52b24f2c5af4b290773fc0-dirty
dchristiany
parents: 37
diff changeset
182 * `Human Urine proteome <https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id=423&display_options=ShowAbundances&organism_id=2&redundancy_constraint=4&presence_level_constraint=1%2C2&gene_annotation_level_constraint=leaf&QUERY_NAME=AT_GetProteins&action=QUERY&output_mode=tsv&apply_action=QUERY>`_.
15
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
183
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
184 For ID mapping:
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
185
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
186 * `HUMAN_9606_idmapping_selected.tab <ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/HUMAN_9606_idmapping_selected.tab.gz>`_.
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
187 * `HUMAN_9606_idmapping.dat <ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/HUMAN_9606_idmapping.dat.gz>`_.
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
188 * `nextprot_ac_list_all.txt <ftp://ftp.nextprot.org/pub/current_release/ac_lists/nextprot_ac_list_all.txt>`_.
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
189 * `MOUSE_10090_idmapping_selected.tab <ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/MOUSE_10090_idmapping_selected.tab.gz>`_.
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
190 * `MOUSE_10090_idmapping.dat <ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/MOUSE_10090_idmapping.dat.gz>`_.
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
191 * `RAT_10116_idmapping_selected.tab <ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/RAT_10116_idmapping_selected.tab.gz>`_.
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
192 * `RAT_10116_idmapping.dat <ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/RAT_10116_idmapping.dat.gz>`_.
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
193
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
194 For Build protein interaction maps:
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
195
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
196 * `BIOGRID_oragism <https://downloads.thebiogrid.org/Download/BioGRID/Release-Archive/BIOGRID-3.5.167/BIOGRID-ORGANISM-3.5.167.tab2.zip>`_.
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
197 * `NCBI2Reactome.txt <https://www.reactome.org/download/current/NCBI2Reactome.txt>`_.
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
198 * `Bioplex_interactionList_v4a.tsv <http://bioplex.hms.harvard.edu/data/BioPlex_interactionList_v4a.tsv>`_.
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
199 * `UniProt2Reactome.txt <https://reactome.org/download/current/UniProt2Reactome.txt>`_.
0
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
200
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
201 -----
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
202
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
203 .. class:: infomark
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
204
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
205 **Authors**
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
206
15
83f57ba70416 planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty
dchristiany
parents: 13
diff changeset
207 David Christiany, Lisa Peru, T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
0
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
208
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
209 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
210
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
211 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
212
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
213 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
214
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
215 ]]></help>
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
216 <citations>
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
217 </citations>
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
218
2de84fea8367 planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
dchristiany
parents:
diff changeset
219 </tool>