Mercurial > repos > iuc > intermine_galaxy_exchange
annotate intermine_galaxy_exchange.xml @ 3:faef2b1622a3 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit dc9ef5c4acb92d7d4950c3b67dcbf2691bee44e4
author | iuc |
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date | Sat, 05 Oct 2024 11:29:49 +0000 |
parents | c24014d80001 |
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rev | line source |
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3d09554c8a47
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
iuc
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1 <tool id="galaxy_intermine_exchange" name="Create InterMine Interchange" version="0.0.1"> |
3d09554c8a47
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
iuc
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2 <description>Dataset</description> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
iuc
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3 <requirements> |
3d09554c8a47
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
iuc
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4 <requirement type="package" version="8.25">coreutils</requirement> |
3d09554c8a47
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
iuc
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5 </requirements> |
3d09554c8a47
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
iuc
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6 <command detect_errors="exit_code"><![CDATA[ |
3d09554c8a47
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
iuc
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7 awk -F \$'\t' ' { |
3d09554c8a47
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
iuc
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8 #if str($feature_text): |
3d09554c8a47
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
iuc
parents:
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9 f = "${feature_text}"; |
3d09554c8a47
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
iuc
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10 #else: |
3d09554c8a47
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
iuc
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11 f = \$${feature_column}; |
3d09554c8a47
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
iuc
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12 #end if |
3d09554c8a47
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
iuc
parents:
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13 |
3d09554c8a47
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
iuc
parents:
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14 #if str($feature_id_text): |
3d09554c8a47
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
iuc
parents:
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15 i = "${feature_id_text}"; |
3d09554c8a47
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
iuc
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16 #else: |
3d09554c8a47
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
iuc
parents:
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17 i = \$${feature_id_column}; |
3d09554c8a47
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
iuc
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18 #end if |
3d09554c8a47
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
iuc
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19 |
3d09554c8a47
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
iuc
parents:
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20 #if str($organism_text): |
3d09554c8a47
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
iuc
parents:
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21 o = "${organism_text}"; |
3d09554c8a47
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
iuc
parents:
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22 #elif $organism_column: |
3d09554c8a47
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
iuc
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23 o = \$${organism_column}; |
3d09554c8a47
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
iuc
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24 #else: |
3d09554c8a47
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
iuc
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25 o= ""; |
3d09554c8a47
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
iuc
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26 #end if |
3d09554c8a47
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
iuc
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27 |
3d09554c8a47
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
iuc
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28 print f, i, o; } ' OFS=\$'\t' '${input_tabular}' > '${intermine_output}' |
3d09554c8a47
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
iuc
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29 ]]> |
3d09554c8a47
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
iuc
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30 </command> |
3d09554c8a47
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
iuc
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31 <inputs> |
3d09554c8a47
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
iuc
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32 <param name="input_tabular" type="data" format="txt" multiple="False" optional="False" label="Tabular file"/> |
3d09554c8a47
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
iuc
parents:
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33 <param name="feature_column" type="data_column" data_ref="input_tabular" optional="False" label="Feature Type column" value="1"/> |
3d09554c8a47
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
iuc
parents:
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34 <param name="feature_text" type="text" value="" optional="True" label="Feature Type" help="Optional, will override column selection with static text value"/> |
2
c24014d80001
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 5e5aad34017f77d01169d4ade23ef553d94741c4
iuc
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35 <param name="feature_id_column" type="data_column" data_ref="input_tabular" optional="False" label="Feature Identifier column" value="2"/> |
c24014d80001
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 5e5aad34017f77d01169d4ade23ef553d94741c4
iuc
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36 <param name="feature_id_text" type="text" value="" optional="True" label="Feature Identifier" help="Optional, will override column selection with static text value"/> |
c24014d80001
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 5e5aad34017f77d01169d4ade23ef553d94741c4
iuc
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37 <param name="organism_column" type="data_column" data_ref="input_tabular" optional="True" label="Organism Name column" value="3"/> |
c24014d80001
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 5e5aad34017f77d01169d4ade23ef553d94741c4
iuc
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38 <param name="organism_text" type="text" value="" optional="True" label="Organism Name" help="Optional, will override column selection with static text value"/> |
0
3d09554c8a47
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
iuc
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39 </inputs> |
3d09554c8a47
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
iuc
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40 <outputs> |
3d09554c8a47
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
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41 <data format="intermine_tabular" name="intermine_output"/> |
3d09554c8a47
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
iuc
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42 </outputs> |
3d09554c8a47
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
iuc
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43 <tests> |
3d09554c8a47
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
iuc
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44 <test> |
3d09554c8a47
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
iuc
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45 <param name="input_tabular" value="intermine-format-example.tsv" ftype="tabular"/> |
3d09554c8a47
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
iuc
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46 <param name="feature_column" value="1"/> |
3d09554c8a47
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
iuc
parents:
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47 <param name="feature_id_text" value=""/> |
3d09554c8a47
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
iuc
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48 <param name="feature_id_column" value="2"/> |
3d09554c8a47
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
iuc
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49 <param name="feature_text" value=""/> |
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faef2b1622a3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit dc9ef5c4acb92d7d4950c3b67dcbf2691bee44e4
iuc
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50 <param name="organism_column" value="3"/> |
0
3d09554c8a47
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
iuc
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51 <param name="organism_text" value=""/> |
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5673140f2d5a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit bb1afe7092cd4f9440d3434379a93270907bf175
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52 <output name="intermine_output" file="intermine-format-example.tsv" ftype="intermine_tabular"/> |
0
3d09554c8a47
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
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53 </test> |
3d09554c8a47
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
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54 </tests> |
3d09554c8a47
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
iuc
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55 <help> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
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56 <![CDATA[ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
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57 InterMine-Galaxy exchange format |
3d09554c8a47
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
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58 ================================ |
3d09554c8a47
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
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59 This file format exists as an intermediate step to import from Galaxy to InterMines and is not in itself a data format intended to be used for data storage or any purpose apart from Galaxy->InterMine interoperability. |
3d09554c8a47
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
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60 |
3d09554c8a47
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
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61 This file has two mandatory columns and one optional column |
3d09554c8a47
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
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62 |
3d09554c8a47
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
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63 Column 1 (mandatory) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
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64 -------------------- |
3d09554c8a47
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
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65 **Type of identifier**, e.g. `Gene` or `Protein`. Must be a class in the `InterMine data model`_. Gene or Protein is always a safe option. |
3d09554c8a47
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
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66 |
3d09554c8a47
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
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67 Column 2 (mandatory) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
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68 -------------------- |
3d09554c8a47
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
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69 **Identifier** this could be, as an example, a gene symbol like `GATA1` or another other identifier, e.g. `FBGN0000099` or perhaps a protein accession, or some other identifier. |
3d09554c8a47
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
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70 |
3d09554c8a47
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
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71 Column 3 (optional) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
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72 ------------------- |
3d09554c8a47
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
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73 **Organism name** - e.g. `H. sapiens` or `Drosophila melanogaster`. This is optional and does not have to be precise, but is good to provide if it is known. |
3d09554c8a47
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
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74 |
3d09554c8a47
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
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75 ---- |
3d09554c8a47
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
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76 |
3d09554c8a47
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
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77 For additional information, please see: |
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78 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
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79 - https://github.com/intermine/galaxy-integration/blob/master/intermine-file-format/intermine-format-definition.md |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
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80 - https://raw.githubusercontent.com/intermine/galaxy-integration/master/intermine-file-format/intermine-format-example.tsv |
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81 |
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82 .. _InterMine data model: http://intermine.readthedocs.io/en/latest/data-model/model/#a-short-example |
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83 ]]> |
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84 </help> |
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85 <citations> |
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86 <citation type="doi">10.1093/nar/gku301</citation> |
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87 </citations> |
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88 </tool> |