Mercurial > repos > eric-rasche > apollo
annotate macros.xml @ 5:7610987e0c48 draft
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
author | eric-rasche |
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date | Wed, 01 Mar 2017 22:39:58 -0500 |
parents | d4ae83dedb14 |
children | f9a6e151b3b4 |
rev | line source |
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0
6002cc0df04e
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
diff
changeset
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1 <?xml version="1.0"?> |
6002cc0df04e
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
diff
changeset
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2 <macros> |
6002cc0df04e
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
diff
changeset
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3 <xml name="requirements"> |
6002cc0df04e
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
diff
changeset
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4 <requirements> |
6002cc0df04e
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
diff
changeset
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5 <requirement type="package" version="2.7">python</requirement> |
3
d4ae83dedb14
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
eric-rasche
parents:
2
diff
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6 <requirement type="package" version="1.65">biopython</requirement> |
d4ae83dedb14
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
eric-rasche
parents:
2
diff
changeset
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7 <requirement type="package" version="0.6.2">bcbiogff</requirement> |
5
7610987e0c48
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
parents:
3
diff
changeset
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8 <requirement type="package" version="2.12.4">requests</requirement> |
0
6002cc0df04e
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
diff
changeset
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9 <yield/> |
6002cc0df04e
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
diff
changeset
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10 </requirements> |
6002cc0df04e
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
diff
changeset
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11 </xml> |
3
d4ae83dedb14
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
eric-rasche
parents:
2
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12 <token name="@DATA_DIR@">\$GALAXY_SHARED_DIR</token> |
d4ae83dedb14
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
eric-rasche
parents:
2
diff
changeset
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13 <token name="@EXT_URL@"> |
d4ae83dedb14
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
eric-rasche
parents:
2
diff
changeset
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14 \$GALAXY_WEBAPOLLO_EXT_URL |
d4ae83dedb14
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
eric-rasche
parents:
2
diff
changeset
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15 </token> |
0
6002cc0df04e
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
diff
changeset
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16 <token name="@URL@"> |
2
c8e16c8eff98
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 6944305517dcccad3e6b37f8aba0b43ccb004540
eric-rasche
parents:
0
diff
changeset
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17 \$GALAXY_WEBAPOLLO_URL |
0
6002cc0df04e
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
diff
changeset
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18 </token> |
3
d4ae83dedb14
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
eric-rasche
parents:
2
diff
changeset
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19 <token name="@ADMIN_AUTH@"> |
d4ae83dedb14
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
eric-rasche
parents:
2
diff
changeset
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20 \$GALAXY_WEBAPOLLO_URL |
d4ae83dedb14
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
eric-rasche
parents:
2
diff
changeset
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21 \$GALAXY_WEBAPOLLO_USER |
0
6002cc0df04e
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
diff
changeset
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22 \$GALAXY_WEBAPOLLO_PASSWORD |
6002cc0df04e
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
diff
changeset
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23 </token> |
6002cc0df04e
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
diff
changeset
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24 |
3
d4ae83dedb14
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
eric-rasche
parents:
2
diff
changeset
|
25 <token name="@ORG_OR_GUESS@"> |
0
6002cc0df04e
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
diff
changeset
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26 <![CDATA[ |
3
d4ae83dedb14
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
eric-rasche
parents:
2
diff
changeset
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27 #if $org_source.source_select == "auto_json": |
d4ae83dedb14
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
eric-rasche
parents:
2
diff
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28 --org_json "${org_source.org_file}" |
d4ae83dedb14
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
eric-rasche
parents:
2
diff
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29 #elif $org_source.source_select == "select": |
d4ae83dedb14
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
eric-rasche
parents:
2
diff
changeset
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30 --org_id "${org_source.org_select}" |
d4ae83dedb14
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
eric-rasche
parents:
2
diff
changeset
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31 #else: |
d4ae83dedb14
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
eric-rasche
parents:
2
diff
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32 --org_raw "${org_source.org_raw}" |
0
6002cc0df04e
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
diff
changeset
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33 #end if |
6002cc0df04e
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
diff
changeset
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34 ]]> |
6002cc0df04e
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
diff
changeset
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35 </token> |
3
d4ae83dedb14
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
eric-rasche
parents:
2
diff
changeset
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36 <token name="@ORG_CN_OR_GUESS@"> |
d4ae83dedb14
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
eric-rasche
parents:
2
diff
changeset
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37 <![CDATA[ |
d4ae83dedb14
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
eric-rasche
parents:
2
diff
changeset
|
38 @ORG_OR_GUESS@ |
d4ae83dedb14
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
eric-rasche
parents:
2
diff
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39 |
d4ae83dedb14
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
eric-rasche
parents:
2
diff
changeset
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40 #if $cn_source.source_select == "auto": |
d4ae83dedb14
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
eric-rasche
parents:
2
diff
changeset
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41 #if str($cn_source.cn_file) != "None": |
d4ae83dedb14
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
eric-rasche
parents:
2
diff
changeset
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42 --seq_fasta $cn_source.cn_file |
d4ae83dedb14
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
eric-rasche
parents:
2
diff
changeset
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43 #end if |
d4ae83dedb14
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
eric-rasche
parents:
2
diff
changeset
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44 #else |
d4ae83dedb14
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
eric-rasche
parents:
2
diff
changeset
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45 #if $cn_source.source_select != "all" and len($cn_source.refseqs) > 0: |
d4ae83dedb14
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
eric-rasche
parents:
2
diff
changeset
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46 --seq_raw |
d4ae83dedb14
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
eric-rasche
parents:
2
diff
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47 #for $item in $cn_source.refseqs: |
d4ae83dedb14
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
eric-rasche
parents:
2
diff
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48 "${item.refseq}" |
d4ae83dedb14
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
eric-rasche
parents:
2
diff
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49 #end for |
d4ae83dedb14
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
eric-rasche
parents:
2
diff
changeset
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50 #end if |
d4ae83dedb14
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
eric-rasche
parents:
2
diff
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51 #end if |
d4ae83dedb14
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
eric-rasche
parents:
2
diff
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52 ]]> |
d4ae83dedb14
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
eric-rasche
parents:
2
diff
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53 </token> |
d4ae83dedb14
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
eric-rasche
parents:
2
diff
changeset
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54 <xml name="org_or_guess"> |
d4ae83dedb14
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
eric-rasche
parents:
2
diff
changeset
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55 <conditional name="org_source"> |
0
6002cc0df04e
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
diff
changeset
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56 <param name="source_select" type="select" label="Organism Common Name Source"> |
3
d4ae83dedb14
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
eric-rasche
parents:
2
diff
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57 <option value="select">Select</option> |
d4ae83dedb14
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
eric-rasche
parents:
2
diff
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58 <option value="direct">Direct Entry</option> |
0
6002cc0df04e
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
diff
changeset
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59 <option value="auto_json">Autodetect from Apollo JSON</option> |
6002cc0df04e
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
diff
changeset
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60 </param> |
3
d4ae83dedb14
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
eric-rasche
parents:
2
diff
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61 <when value="select"> |
d4ae83dedb14
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
eric-rasche
parents:
2
diff
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62 <param name="org_select" type="select" dynamic_options="galaxy_list_orgs(__trans__)" label="Organism" /> |
d4ae83dedb14
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
eric-rasche
parents:
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diff
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63 </when> |
d4ae83dedb14
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
eric-rasche
parents:
2
diff
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64 <when value="direct"> |
5
7610987e0c48
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
parents:
3
diff
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65 <param name="org_raw" type="text" label="Organism Common Name" optional="False" /> |
0
6002cc0df04e
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
diff
changeset
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66 </when> |
6002cc0df04e
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
diff
changeset
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67 <when value="auto_json"> |
3
d4ae83dedb14
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
eric-rasche
parents:
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68 <param name="org_file" type="data" format="json" label="Apollo Organism File" help="Will only fetch first organism" /> |
d4ae83dedb14
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
eric-rasche
parents:
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diff
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69 </when> |
d4ae83dedb14
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
eric-rasche
parents:
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70 </conditional> |
d4ae83dedb14
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
eric-rasche
parents:
2
diff
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71 </xml> |
d4ae83dedb14
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
eric-rasche
parents:
2
diff
changeset
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72 <xml name="cn_or_guess"> |
d4ae83dedb14
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
eric-rasche
parents:
2
diff
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73 <expand macro="org_or_guess" /> |
d4ae83dedb14
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
eric-rasche
parents:
2
diff
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74 <conditional name="cn_source"> |
d4ae83dedb14
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
eric-rasche
parents:
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diff
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75 <param name="source_select" type="select" label="Organism Sequence(s) Source"> |
d4ae83dedb14
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
eric-rasche
parents:
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76 <option value="all">All Refseqs</option> |
d4ae83dedb14
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
eric-rasche
parents:
2
diff
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77 <option value="direct">Direct Entry</option> |
d4ae83dedb14
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
eric-rasche
parents:
2
diff
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78 <option value="auto">Autodetect from Fasta</option> |
d4ae83dedb14
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
eric-rasche
parents:
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diff
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79 </param> |
d4ae83dedb14
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
eric-rasche
parents:
2
diff
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80 <when value="all"> |
d4ae83dedb14
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
eric-rasche
parents:
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81 </when> |
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82 <when value="auto"> |
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83 <param name="cn_file" type="data" format="fasta" label="Reference sequence(s)" optional="true"/> |
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84 </when> |
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85 <when value="direct"> |
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86 <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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87 <param name="refseq" type="text" label="Reference sequence(s)" /> |
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88 </repeat> |
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89 </when> |
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90 </conditional> |
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91 </xml> |
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92 |
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93 <xml name="citations"> |
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94 <citations> |
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95 </citations> |
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96 </xml> |
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97 <xml name="gff3_input"> |
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98 <param label="GFF3 Annotations" name="gff3_data" type="data" format="gff3"/> |
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99 </xml> |
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100 <token name="@GENOME_SELECTOR_PRE@"> |
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101 #if $reference_genome.reference_genome_source == 'history': |
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102 ln -s $reference_genome.genome_fasta genomeref.fa; |
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103 #end if |
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104 </token> |
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105 <token name="@GENOME_SELECTOR@"> |
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106 #if $reference_genome.reference_genome_source == 'cached': |
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107 "${reference_genome.fasta_indexes.fields.path}" |
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108 #elif $reference_genome.reference_genome_source == 'history': |
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109 genomeref.fa |
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110 #end if |
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111 </token> |
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112 <token name="@REFERENCES@"> |
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113 <![CDATA[ |
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114 ------ |
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115 |
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116 **Citation** |
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117 |
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118 If you use this tool in Galaxy, please cite: |
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119 Eric Rasche (2016), `Galaxy wrapper <https://github.com/TAMU-CPT/galaxy-webapollo>`_ |
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120 ]]> |
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121 </token> |
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122 </macros> |