Mercurial > repos > rhpvorderman > data_manager_select_index_by_path
annotate tool-data/rnastar_index2.loc.sample @ 39:ad5d85570342 draft default tip
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit a9b8c9549044fb951570d9c6cf88107d98800afb
| author | rhpvorderman |
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| date | Wed, 25 Jul 2018 10:34:49 -0400 |
| parents | 0a1afc109ad9 |
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| rev | line source |
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0a1afc109ad9
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
rhpvorderman
parents:
diff
changeset
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1 #This is a sample file distributed with Galaxy that enables tools |
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0a1afc109ad9
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
rhpvorderman
parents:
diff
changeset
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2 #to use a directory of rna-star indexed sequences data files. You will |
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0a1afc109ad9
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
rhpvorderman
parents:
diff
changeset
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3 #need to create these data files and then create a rnastar_index2.loc |
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0a1afc109ad9
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
rhpvorderman
parents:
diff
changeset
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4 #file similar to this one (store it in this directory) that points to |
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0a1afc109ad9
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
rhpvorderman
parents:
diff
changeset
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5 #the directories in which those files are stored. The rnastar_index2.loc |
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0a1afc109ad9
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
rhpvorderman
parents:
diff
changeset
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6 #file has this format (longer white space characters are TAB characters): |
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0a1afc109ad9
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
rhpvorderman
parents:
diff
changeset
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7 # |
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0a1afc109ad9
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
rhpvorderman
parents:
diff
changeset
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8 #<unique_build_id> <dbkey> <display_name> <file_base_path> <with-gtf> |
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0a1afc109ad9
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
rhpvorderman
parents:
diff
changeset
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9 # |
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0a1afc109ad9
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
rhpvorderman
parents:
diff
changeset
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10 #The <with-gtf> column should be 1 or 0, indicating whether the index was made |
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0a1afc109ad9
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
rhpvorderman
parents:
diff
changeset
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11 #with an annotation (i.e., --sjdbGTFfile and --sjdbOverhang were used) or not, |
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0a1afc109ad9
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
rhpvorderman
parents:
diff
changeset
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12 #respecively. |
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0a1afc109ad9
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
rhpvorderman
parents:
diff
changeset
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13 # |
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0a1afc109ad9
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
rhpvorderman
parents:
diff
changeset
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14 #Note that STAR indices can become quite large. Consequently, it is only |
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0a1afc109ad9
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
rhpvorderman
parents:
diff
changeset
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15 #advisable to create indices with annotations if it's known ahead of time that |
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0a1afc109ad9
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
rhpvorderman
parents:
diff
changeset
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16 #(A) the annotations won't be frequently updated and (B) the read lengths used |
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0a1afc109ad9
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
rhpvorderman
parents:
diff
changeset
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17 #will also rarely vary. If either of these is not the case, it's advisable to |
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0a1afc109ad9
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
rhpvorderman
parents:
diff
changeset
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18 #create indices without annotations and then specify an annotation file and |
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0a1afc109ad9
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
rhpvorderman
parents:
diff
changeset
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19 #maximum read length (minus 1) when running STAR. |
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0a1afc109ad9
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
rhpvorderman
parents:
diff
changeset
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20 # |
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0a1afc109ad9
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
rhpvorderman
parents:
diff
changeset
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21 #hg19 hg19 hg19 full /mnt/galaxyIndices/genomes/hg19/rnastar 0 |
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0a1afc109ad9
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
rhpvorderman
parents:
diff
changeset
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22 #hg19Ensembl hg19Ensembl hg19 full with Ensembl annotation /mnt/galaxyIndices/genomes/hg19Ensembl/rnastar 1 |
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0a1afc109ad9
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
rhpvorderman
parents:
diff
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23 |