Mercurial > repos > iuc > data_manager_interproscan

annotate data_manager/interproscan.xml @ 3:0df47f8552f6 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 01e8e726d711c0685f46d3146e4fe0f2a1306036
author iuc
date Wed, 07 Dec 2022 13:41:38 +0000
parents 7776cb18fdf8
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
0df47f8552f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 01e8e726d711c0685f46d3146e4fe0f2a1306036
iuc
parents: 2
diff changeset
1 <tool id="data_manager_interproscan" name="InterProScan data manager" version="0.0.3" tool_type="manage_data" profile="20.01">
0
e93e32359b67 "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>
3
0df47f8552f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 01e8e726d711c0685f46d3146e4fe0f2a1306036
iuc
parents: 2
diff changeset
3 <requirement type="package" version="5.59-91.0">interproscan</requirement>
0
e93e32359b67 "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
7776cb18fdf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 9282e18219e7e3ed6a5ee46839d17663c3134993"
iuc
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5 <!-- Forcing an old hmmer version for indexing due to https://github.com/ebi-pf-team/interproscan/issues/232 -->
7776cb18fdf8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 9282e18219e7e3ed6a5ee46839d17663c3134993"
iuc
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6 <requirement type="package" version="3.1b2">hmmer</requirement>
0
e93e32359b67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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7 </requirements>
e93e32359b67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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8 <command detect_errors="exit_code"><![CDATA[
1
0db4f153d86d "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
e93e32359b67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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10 $partial_data
e93e32359b67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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11 --version '$version'
e93e32359b67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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12 'interproscan'
e93e32359b67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
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13 '${output_file}'
e93e32359b67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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14 ]]></command>
e93e32359b67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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15 <inputs>
e93e32359b67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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16 <param name="partial_data" type="hidden" value="" help="Used for testing"/>
e93e32359b67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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17 <param name="version" type="text" value="" label="Version to download" help="Leave empty to download the latest version">
3
0df47f8552f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 01e8e726d711c0685f46d3146e4fe0f2a1306036
iuc
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diff changeset
18 <validator type="regex" message="Version must be a valid InterProScan version (e.g. 5.59-91.0)">^([0-9]+\.[0-9]+-[0-9]+\.[0-9]+)?$</validator>
0
e93e32359b67 "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>
e93e32359b67 "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>
e93e32359b67 "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>
e93e32359b67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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22 <data name="output_file" format="data_manager_json"/>
e93e32359b67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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23 </outputs>
e93e32359b67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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24 <tests>
e93e32359b67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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25 <test>
e93e32359b67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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26 <param name="partial_data" value="--partial"/>
e93e32359b67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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27 <output name="output_file">
e93e32359b67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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28 <assert_contents>
e93e32359b67 "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."/>
e93e32359b67 "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.'/>
e93e32359b67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
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31 </assert_contents>
e93e32359b67 "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>
e93e32359b67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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33 <assert_stdout>
3
0df47f8552f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 01e8e726d711c0685f46d3146e4fe0f2a1306036
iuc
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34 <has_text text="Finished." />
0
e93e32359b67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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35 </assert_stdout>
e93e32359b67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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36 </test>
e93e32359b67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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37 <test>
e93e32359b67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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38 <param name="partial_data" value="--partial"/>
3
0df47f8552f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 01e8e726d711c0685f46d3146e4fe0f2a1306036
iuc
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39 <param name="version" value="5.58-91.0"/>
0
e93e32359b67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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40 <output name="output_file">
e93e32359b67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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41 <assert_contents>
3
0df47f8552f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 01e8e726d711c0685f46d3146e4fe0f2a1306036
iuc
parents: 2
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42 <has_text text="InterProScan 5.58-91.0"/>
0df47f8552f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 01e8e726d711c0685f46d3146e4fe0f2a1306036
iuc
parents: 2
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43 <has_text text='"interproscan_version": "5.58-91.0'/>
0
e93e32359b67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
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44 </assert_contents>
e93e32359b67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
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45 </output>
e93e32359b67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
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46 <assert_stdout>
3
0df47f8552f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 01e8e726d711c0685f46d3146e4fe0f2a1306036
iuc
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47 <has_text text="Finished." />
0
e93e32359b67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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48 </assert_stdout>
e93e32359b67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
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49 </test>
e93e32359b67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
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50 <test expect_failure="true">
e93e32359b67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
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51 <param name="partial_data" value="--partial"/>
3
0df47f8552f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 01e8e726d711c0685f46d3146e4fe0f2a1306036
iuc
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52 <param name="version" value="5.51-85.0"/>
0df47f8552f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 01e8e726d711c0685f46d3146e4fe0f2a1306036
iuc
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53 <assert_stderr>
0df47f8552f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 01e8e726d711c0685f46d3146e4fe0f2a1306036
iuc
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54 <has_text text="Sorry, this data manager can only download data for InterProScan >= 5.58-91.0. Use the 0.0.2 version for older versions of InterProScan." />
0df47f8552f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 01e8e726d711c0685f46d3146e4fe0f2a1306036
iuc
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55 </assert_stderr>
0df47f8552f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 01e8e726d711c0685f46d3146e4fe0f2a1306036
iuc
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56 </test>
0df47f8552f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 01e8e726d711c0685f46d3146e4fe0f2a1306036
iuc
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57 <test expect_failure="true">
0df47f8552f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 01e8e726d711c0685f46d3146e4fe0f2a1306036
iuc
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58 <param name="partial_data" value="--partial"/>
0
e93e32359b67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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59 <param name="version" value="xxxx"/>
e93e32359b67 "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 <assert_stderr>
e93e32359b67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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61 <has_text text="Version must be a valid InterProScan version" />
e93e32359b67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
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62 </assert_stderr>
e93e32359b67 "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 </test>
e93e32359b67 "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 </tests>
e93e32359b67 "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 <help><![CDATA[
e93e32359b67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
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66 This data managers fetches data from EBI FTP server for the InterProScan
e93e32359b67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
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67 annotation tool and updates the InterProScan data table.
e93e32359b67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
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68 ]]></help>
e93e32359b67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
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69 <citations>
e93e32359b67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
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70 <citation type="doi">10.1093/bioinformatics/btu031</citation>
e93e32359b67 "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 <citation type="doi">10.7717/peerj.167</citation>
e93e32359b67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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72 <citation type="doi">10.1093/bioinformatics/17.9.847</citation>
e93e32359b67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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73 <citation type="doi">10.1093/nar/gki442</citation>
e93e32359b67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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74 <citation type="doi">10.1093/nar/gkn785</citation>
e93e32359b67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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75 </citations>
e93e32359b67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
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76 </tool>