Mercurial > repos > gga > apollo_delete_features
annotate macros.xml @ 5:f7e9c792047b draft
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 85194fa009ead2c34720faab61a4143fc29d17c2
author | gga |
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date | Fri, 31 Aug 2018 09:34:42 -0400 |
parents | 40b26f8269a3 |
children | 2adc3aa47d15 |
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0
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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1 <?xml version="1.0"?> |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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2 <macros> |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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3 <xml name="requirements"> |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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4 <requirements> |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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5 <requirement type="package" version="2.7">python</requirement> |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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6 <requirement type="package" version="1.65">biopython</requirement> |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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7 <requirement type="package" version="0.6.2">bcbiogff</requirement> |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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8 <requirement type="package" version="2.12.4">requests</requirement> |
4
40b26f8269a3
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 70fbb41d4c6b0a08a7bed4849a5ae7c865e1ab1e
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9 <requirement type="package" version="1.11.0">six</requirement> |
0
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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10 <yield/> |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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11 </requirements> |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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12 </xml> |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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13 <token name="@DATA_DIR@">\$GALAXY_SHARED_DIR</token> |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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14 <token name="@EXT_URL@"> |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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15 "\$GALAXY_WEBAPOLLO_EXT_URL" |
4dd45d2fd904
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 </token> |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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17 <token name="@URL@"> |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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18 "\$GALAXY_WEBAPOLLO_URL" |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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19 </token> |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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20 <token name="@ADMIN_AUTH@"> |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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21 "\$GALAXY_WEBAPOLLO_URL" |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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22 "\$GALAXY_WEBAPOLLO_USER" |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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23 "\$GALAXY_WEBAPOLLO_PASSWORD" |
4dd45d2fd904
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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24 </token> |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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25 |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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26 <token name="@ORG_OR_GUESS@"> |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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27 <![CDATA[ |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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28 #if $org_source.source_select == "auto_json": |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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29 --org_json "${org_source.org_file}" |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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30 #elif $org_source.source_select == "select": |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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31 --org_id "${org_source.org_select}" |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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32 #else: |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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33 --org_raw "${org_source.org_raw}" |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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34 #end if |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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35 ]]> |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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36 </token> |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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37 <token name="@ORG_CN_OR_GUESS@"> |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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38 <![CDATA[ |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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39 @ORG_OR_GUESS@ |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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40 |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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41 #if $cn_source.source_select == "auto": |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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42 #if str($cn_source.cn_file) != "None": |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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43 --seq_fasta $cn_source.cn_file |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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44 #end if |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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45 #else |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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46 #if $cn_source.source_select != "all" and len($cn_source.refseqs) > 0: |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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47 --seq_raw |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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48 #for $item in $cn_source.refseqs: |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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49 "${item.refseq}" |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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50 #end for |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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51 #end if |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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52 #end if |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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53 ]]> |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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54 </token> |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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55 <xml name="org_or_guess"> |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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56 <conditional name="org_source"> |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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57 <param name="source_select" type="select" label="Organism Common Name Source"> |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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58 <option value="select">Select</option> |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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59 <option value="direct">Direct Entry</option> |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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60 <option value="auto_json">Autodetect from Apollo JSON</option> |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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61 </param> |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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62 <when value="select"> |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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63 <param name="org_select" type="select" dynamic_options="galaxy_list_orgs(__trans__)" label="Organism" /> |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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64 </when> |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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65 <when value="direct"> |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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66 <param name="org_raw" type="text" label="Organism Common Name" optional="False" /> |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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67 </when> |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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68 <when value="auto_json"> |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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69 <param name="org_file" type="data" format="json" label="Apollo Organism File" help="Will only fetch first organism" /> |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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70 </when> |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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71 </conditional> |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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72 </xml> |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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73 <xml name="cn_or_guess"> |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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74 <expand macro="org_or_guess" /> |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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75 <conditional name="cn_source"> |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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76 <param name="source_select" type="select" label="Organism Sequence(s) Source"> |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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77 <option value="all">All Refseqs</option> |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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78 <option value="direct">Direct Entry</option> |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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79 <option value="auto">Autodetect from Fasta</option> |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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80 </param> |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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81 <when value="all"> |
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82 </when> |
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83 <when value="auto"> |
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84 <param name="cn_file" type="data" format="fasta" label="Reference sequence(s)" optional="true"/> |
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85 </when> |
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86 <when value="direct"> |
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87 <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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88 <param name="refseq" type="text" label="Reference sequence(s)" /> |
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89 </repeat> |
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90 </when> |
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91 </conditional> |
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92 </xml> |
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93 |
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94 <xml name="test_result"> |
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95 <assert_stderr> |
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96 <has_text text="MissingSchema" /> |
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97 </assert_stderr> |
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98 </xml> |
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99 |
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100 <xml name="citations"> |
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101 <citations> |
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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 Eric Rasche (2016), `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> |