Mercurial > repos > iuc > data_manager_interproscan

annotate data_manager/interproscan.xml @ 2:b7e169861045 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 9282e18219e7e3ed6a5ee46839d17663c3134993"
author iuc
date Tue, 01 Feb 2022 17:55:30 +0000
parents d9a238ff2bc3
children f1287724d7f9
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2
b7e169861045 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 9282e18219e7e3ed6a5ee46839d17663c3134993"
iuc
parents: 1
diff changeset
1 <tool id="data_manager_interproscan" name="InterProScan data manager" version="0.0.2" tool_type="manage_data" profile="20.01">
0
3e344aedb267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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diff changeset
2 <requirements>
2
b7e169861045 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 9282e18219e7e3ed6a5ee46839d17663c3134993"
iuc
parents: 1
diff changeset
3 <requirement type="package" version="5.54-87.0">interproscan</requirement>
0
3e344aedb267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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diff changeset
4 <requirement type="package" version="2.26.0">requests</requirement>
2
b7e169861045 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 9282e18219e7e3ed6a5ee46839d17663c3134993"
iuc
parents: 1
diff changeset
5 <!-- Forcing an old hmmer version for indexing due to https://github.com/ebi-pf-team/interproscan/issues/232 -->
b7e169861045 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 9282e18219e7e3ed6a5ee46839d17663c3134993"
iuc
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diff changeset
6 <requirement type="package" version="3.1b2">hmmer</requirement>
0
3e344aedb267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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diff changeset
7 </requirements>
3e344aedb267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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diff changeset
8 <command detect_errors="exit_code"><![CDATA[
1
d9a238ff2bc3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 7fbeae66de8617e525cd968a2ef89b0be448a618"
iuc
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diff changeset
9 python -u '$__tool_directory__/interproscan.py'
0
3e344aedb267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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diff changeset
10 $partial_data
3e344aedb267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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11 --version '$version'
3e344aedb267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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diff changeset
12 'interproscan'
3e344aedb267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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13 '${output_file}'
3e344aedb267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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diff changeset
14 ]]></command>
3e344aedb267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents:
diff changeset
15 <inputs>
3e344aedb267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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16 <param name="partial_data" type="hidden" value="" help="Used for testing"/>
3e344aedb267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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diff changeset
17 <param name="version" type="text" value="" label="Version to download" help="Leave empty to download the latest version">
3e344aedb267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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diff changeset
18 <validator type="regex" message="Version must be a valid InterProScan version (e.g. 5.52-86.0)">^([0-9]+\.[0-9]+-[0-9]+\.[0-9]+)?$</validator>
3e344aedb267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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19 </param>
3e344aedb267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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20 </inputs>
3e344aedb267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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21 <outputs>
3e344aedb267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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diff changeset
22 <data name="output_file" format="data_manager_json"/>
3e344aedb267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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diff changeset
23 </outputs>
3e344aedb267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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diff changeset
24 <tests>
3e344aedb267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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diff changeset
25 <test>
3e344aedb267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents:
diff changeset
26 <param name="partial_data" value="--partial"/>
3e344aedb267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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diff changeset
27 <output name="output_file">
3e344aedb267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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diff changeset
28 <assert_contents>
3e344aedb267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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29 <has_text text="InterProScan 5."/>
3e344aedb267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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30 <has_text text='"interproscan_version": "5.'/>
3e344aedb267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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diff changeset
31 </assert_contents>
3e344aedb267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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32 </output>
3e344aedb267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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diff changeset
33 <assert_stdout>
3e344aedb267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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diff changeset
34 <has_text text="Pressed and indexed" />
3e344aedb267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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diff changeset
35 <has_text text="Completed indexing the hmm models" />
3e344aedb267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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diff changeset
36 </assert_stdout>
3e344aedb267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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diff changeset
37 </test>
3e344aedb267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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diff changeset
38 <test>
3e344aedb267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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diff changeset
39 <param name="partial_data" value="--partial"/>
3e344aedb267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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diff changeset
40 <param name="version" value="5.51-85.0"/>
3e344aedb267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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diff changeset
41 <output name="output_file">
3e344aedb267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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diff changeset
42 <assert_contents>
3e344aedb267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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diff changeset
43 <has_text text="InterProScan 5.51-85.0"/>
3e344aedb267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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diff changeset
44 <has_text text='"interproscan_version": "5.51-85.0'/>
3e344aedb267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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diff changeset
45 </assert_contents>
3e344aedb267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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diff changeset
46 </output>
3e344aedb267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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47 <assert_stdout>
3e344aedb267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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diff changeset
48 <has_text text="Pressed and indexed" />
3e344aedb267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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49 <has_text text="Completed indexing the hmm models" />
3e344aedb267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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diff changeset
50 </assert_stdout>
3e344aedb267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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51 </test>
3e344aedb267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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52 <test expect_failure="true">
3e344aedb267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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53 <param name="partial_data" value="--partial"/>
3e344aedb267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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54 <param name="version" value="xxxx"/>
3e344aedb267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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55 <assert_stderr>
3e344aedb267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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diff changeset
56 <has_text text="Version must be a valid InterProScan version" />
3e344aedb267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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57 </assert_stderr>
3e344aedb267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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58 </test>
3e344aedb267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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diff changeset
59 </tests>
3e344aedb267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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60 <help><![CDATA[
3e344aedb267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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diff changeset
61 This data managers fetches data from EBI FTP server for the InterProScan
3e344aedb267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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62 annotation tool and updates the InterProScan data table.
3e344aedb267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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63 ]]></help>
3e344aedb267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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64 <citations>
3e344aedb267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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65 <citation type="doi">10.1093/bioinformatics/btu031</citation>
3e344aedb267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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66 <citation type="doi">10.7717/peerj.167</citation>
3e344aedb267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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67 <citation type="doi">10.1093/bioinformatics/17.9.847</citation>
3e344aedb267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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68 <citation type="doi">10.1093/nar/gki442</citation>
3e344aedb267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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69 <citation type="doi">10.1093/nar/gkn785</citation>
3e344aedb267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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70 </citations>
3e344aedb267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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71 </tool>