Mercurial > repos > gga > apollo_fetch_jbrowse
annotate macros.xml @ 11:fa5ae4bf7f65 draft
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 81492a9c8b9e5649a3867bc30afe617a30fb47a1"
author | gga |
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date | Tue, 14 Apr 2020 10:40:21 -0400 |
parents | dca2fb399ee6 |
children | 30ea2be4a236 |
rev | line source |
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0
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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1 <?xml version="1.0"?> |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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2 <macros> |
10
dca2fb399ee6
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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3 <token name="@WRAPPER_VERSION@">4.1</token> |
9
d8bb1f9b85b2
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 49fe23e3fb330234900946352fbc3a86deeeb639
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4 |
0
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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5 <xml name="requirements"> |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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parents:
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6 <requirements> |
10
dca2fb399ee6
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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7 <requirement type="package" version="4.1">apollo</requirement> |
0
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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8 <yield/> |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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9 </requirements> |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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10 </xml> |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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11 <token name="@DATA_DIR@">\$GALAXY_SHARED_DIR</token> |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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12 <token name="@EXT_URL@"> |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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13 "\$GALAXY_WEBAPOLLO_EXT_URL" |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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14 </token> |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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15 <token name="@URL@"> |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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16 "\$GALAXY_WEBAPOLLO_URL" |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
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17 </token> |
10
dca2fb399ee6
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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18 |
dca2fb399ee6
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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19 <token name="@AUTH@"><![CDATA[ |
dca2fb399ee6
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
gga
parents:
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20 if [ -z "\$ARROW_GLOBAL_CONFIG_PATH" ]; then |
dca2fb399ee6
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
gga
parents:
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21 echo "__default: local" > '.auth.yml' && |
dca2fb399ee6
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
gga
parents:
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22 echo "local:" >> '.auth.yml' && |
dca2fb399ee6
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
gga
parents:
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23 echo " url: \"\$GALAXY_WEBAPOLLO_URL\"" >> '.auth.yml' && |
dca2fb399ee6
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
gga
parents:
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24 echo " username: \"\$GALAXY_WEBAPOLLO_USER\"" >> '.auth.yml' && |
dca2fb399ee6
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
gga
parents:
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25 echo " password: \"\$GALAXY_WEBAPOLLO_PASSWORD\"" >> '.auth.yml' && |
dca2fb399ee6
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
gga
parents:
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26 |
dca2fb399ee6
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
gga
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27 export ARROW_GLOBAL_CONFIG_PATH='.auth.yml' |
dca2fb399ee6
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
gga
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28 ; fi && |
dca2fb399ee6
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
gga
parents:
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29 ]]></token> |
0
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
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30 |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
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31 <token name="@ORG_OR_GUESS@"> |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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32 <![CDATA[ |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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33 #if $org_source.source_select == "auto_json": |
10
dca2fb399ee6
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
gga
parents:
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34 --org_json '${org_source.org_file}' |
0
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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35 #elif $org_source.source_select == "select": |
10
dca2fb399ee6
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
gga
parents:
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36 --org_id '${org_source.org_select}' |
0
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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37 #else: |
10
dca2fb399ee6
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
gga
parents:
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38 --org_raw '${org_source.org_raw}' |
0
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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39 #end if |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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40 ]]> |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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41 </token> |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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42 <token name="@ORG_CN_OR_GUESS@"> |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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43 <![CDATA[ |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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44 @ORG_OR_GUESS@ |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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45 |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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46 #if $cn_source.source_select == "auto": |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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47 #if str($cn_source.cn_file) != "None": |
10
dca2fb399ee6
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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48 --seq_fasta '$cn_source.cn_file' |
0
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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49 #end if |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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50 #else |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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51 #if $cn_source.source_select != "all" and len($cn_source.refseqs) > 0: |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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52 --seq_raw |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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53 #for $item in $cn_source.refseqs: |
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dca2fb399ee6
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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54 '${item.refseq}' |
0
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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55 #end for |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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56 #end if |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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57 #end if |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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58 ]]> |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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59 </token> |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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60 <xml name="org_or_guess"> |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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61 <conditional name="org_source"> |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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62 <param name="source_select" type="select" label="Organism Common Name Source"> |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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63 <option value="select">Select</option> |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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64 <option value="direct">Direct Entry</option> |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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65 <option value="auto_json">Autodetect from Apollo JSON</option> |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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66 </param> |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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67 <when value="select"> |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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68 <param name="org_select" type="select" dynamic_options="galaxy_list_orgs(__trans__)" label="Organism" /> |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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69 </when> |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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70 <when value="direct"> |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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71 <param name="org_raw" type="text" label="Organism Common Name" optional="False" /> |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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72 </when> |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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73 <when value="auto_json"> |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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74 <param name="org_file" type="data" format="json" label="Apollo Organism File" help="Will only fetch first organism" /> |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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75 </when> |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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76 </conditional> |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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77 </xml> |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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78 <xml name="cn_or_guess"> |
c6d7f19953a6
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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79 <expand macro="org_or_guess" /> |
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80 <conditional name="cn_source"> |
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81 <param name="source_select" type="select" label="Organism Sequence(s) Source"> |
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82 <option value="all">All Refseqs</option> |
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83 <option value="direct">Direct Entry</option> |
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84 <option value="auto">Autodetect from Fasta</option> |
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85 </param> |
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86 <when value="all"> |
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87 </when> |
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88 <when value="auto"> |
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89 <param name="cn_file" type="data" format="fasta" label="Reference sequence(s)" optional="true"/> |
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90 </when> |
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91 <when value="direct"> |
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92 <repeat name="refseqs" title="Reference Sequences" help="These are used to identify sequences within an organism that you wish to extract"> |
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93 <param name="refseq" type="text" label="Reference sequence(s)" /> |
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94 </repeat> |
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95 </when> |
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96 </conditional> |
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97 </xml> |
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98 |
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99 <xml name="citations"> |
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100 <citations> |
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101 <citation type="doi">10.1371/journal.pcbi.1006790</citation> |
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102 </citations> |
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103 </xml> |
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104 <xml name="gff3_input"> |
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105 <param label="GFF3 Annotations" name="gff3_data" type="data" format="gff3"/> |
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106 </xml> |
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107 <token name="@GENOME_SELECTOR_PRE@"> |
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108 #if $reference_genome.reference_genome_source == 'history': |
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109 ln -s '$reference_genome.genome_fasta' genomeref.fa; |
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110 #end if |
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111 </token> |
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112 <token name="@GENOME_SELECTOR@"> |
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113 #if $reference_genome.reference_genome_source == 'cached': |
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114 '${reference_genome.fasta_indexes.fields.path}' |
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115 #elif $reference_genome.reference_genome_source == 'history': |
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116 genomeref.fa |
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117 #end if |
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118 </token> |
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119 <token name="@REFERENCES@"> |
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120 <![CDATA[ |
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121 ------ |
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122 |
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123 **Citation** |
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124 |
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125 If you use this tool in Galaxy, please cite: |
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126 Helena Rasche, Anthony Bretaudeau, and Mateo Boudet (2019), `Galaxy Apollo Tools <https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo>`_ |
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127 ]]> |
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128 </token> |
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129 </macros> |