Mercurial > repos > iuc > data_manager_star_index_builder
annotate data_manager/macros.xml @ 4:6ef6520f14fc draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 39b9b154845ecf517f7d9e9d76c386b473c3ebd2
author | iuc |
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date | Wed, 18 Jul 2018 13:26:12 -0400 |
parents | cdc4d8a998e1 |
children | f5eb9afa8f8a |
rev | line source |
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cdc4d8a998e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
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changeset
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1 <macros> |
cdc4d8a998e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
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2 <xml name="requirements"> |
cdc4d8a998e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
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changeset
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3 <requirements> |
4
6ef6520f14fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 39b9b154845ecf517f7d9e9d76c386b473c3ebd2
iuc
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4 <requirement type="package" version="2.6.0b">star</requirement> |
6ef6520f14fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 39b9b154845ecf517f7d9e9d76c386b473c3ebd2
iuc
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5 <requirement type="package" version="1.8">samtools</requirement> |
1
cdc4d8a998e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
diff
changeset
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6 </requirements> |
cdc4d8a998e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
diff
changeset
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7 </xml> |
cdc4d8a998e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
diff
changeset
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8 <token name="@FASTQ_GZ_OPTION@"> |
cdc4d8a998e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
diff
changeset
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9 --readFilesCommand zcat |
cdc4d8a998e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
diff
changeset
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10 </token> |
cdc4d8a998e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
diff
changeset
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11 <xml name="citations"> |
cdc4d8a998e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
diff
changeset
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12 <citations> |
cdc4d8a998e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
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changeset
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13 <citation type="doi">10.1093/bioinformatics/bts635</citation> |
cdc4d8a998e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
diff
changeset
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14 </citations> |
cdc4d8a998e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
diff
changeset
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15 </xml> |
cdc4d8a998e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
diff
changeset
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16 <xml name="@SJDBOPTIONS@"> |
cdc4d8a998e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
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changeset
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17 <param argument="--sjdbGTFfile" type="data" format="gff3,gtf" label="Gene model (gff3,gtf) file for splice junctions" optional="true" help="Exon junction information for mapping splices"/> |
cdc4d8a998e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
diff
changeset
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18 <param argument="--sjdbOverhang" type="integer" min="1" value="100" label="Length of the genomic sequence around annotated junctions" help="Used in constructing the splice junctions database. Ideal value is ReadLength-1"/> |
cdc4d8a998e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
diff
changeset
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19 </xml> |
4
6ef6520f14fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 39b9b154845ecf517f7d9e9d76c386b473c3ebd2
iuc
parents:
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20 <xml name="dbKeyActions"> |
6ef6520f14fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 39b9b154845ecf517f7d9e9d76c386b473c3ebd2
iuc
parents:
1
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changeset
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21 <actions> |
6ef6520f14fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 39b9b154845ecf517f7d9e9d76c386b473c3ebd2
iuc
parents:
1
diff
changeset
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22 <conditional name="refGenomeSource.geneSource"> |
6ef6520f14fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 39b9b154845ecf517f7d9e9d76c386b473c3ebd2
iuc
parents:
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changeset
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23 <when value="indexed"> |
6ef6520f14fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 39b9b154845ecf517f7d9e9d76c386b473c3ebd2
iuc
parents:
1
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changeset
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24 <action type="metadata" name="dbkey"> |
6ef6520f14fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 39b9b154845ecf517f7d9e9d76c386b473c3ebd2
iuc
parents:
1
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25 <option type="from_data_table" name="rnastar_index2" column="1" offset="0"> |
6ef6520f14fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 39b9b154845ecf517f7d9e9d76c386b473c3ebd2
iuc
parents:
1
diff
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26 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> |
6ef6520f14fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 39b9b154845ecf517f7d9e9d76c386b473c3ebd2
iuc
parents:
1
diff
changeset
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27 <filter type="param_value" ref="refGenomeSource.GTFconditional.genomeDir" column="0"/> |
6ef6520f14fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 39b9b154845ecf517f7d9e9d76c386b473c3ebd2
iuc
parents:
1
diff
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28 </option> |
6ef6520f14fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 39b9b154845ecf517f7d9e9d76c386b473c3ebd2
iuc
parents:
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diff
changeset
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29 </action> |
6ef6520f14fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 39b9b154845ecf517f7d9e9d76c386b473c3ebd2
iuc
parents:
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30 </when> |
6ef6520f14fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 39b9b154845ecf517f7d9e9d76c386b473c3ebd2
iuc
parents:
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31 <when value="history"> |
6ef6520f14fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 39b9b154845ecf517f7d9e9d76c386b473c3ebd2
iuc
parents:
1
diff
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32 <action type="metadata" name="dbkey"> |
6ef6520f14fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 39b9b154845ecf517f7d9e9d76c386b473c3ebd2
iuc
parents:
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33 <option type="from_param" name="refGenomeSource.genomeFastaFiles" param_attribute="dbkey" /> |
6ef6520f14fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 39b9b154845ecf517f7d9e9d76c386b473c3ebd2
iuc
parents:
1
diff
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34 </action> |
6ef6520f14fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 39b9b154845ecf517f7d9e9d76c386b473c3ebd2
iuc
parents:
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35 </when> |
6ef6520f14fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 39b9b154845ecf517f7d9e9d76c386b473c3ebd2
iuc
parents:
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36 </conditional> |
6ef6520f14fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 39b9b154845ecf517f7d9e9d76c386b473c3ebd2
iuc
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37 </actions> |
6ef6520f14fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 39b9b154845ecf517f7d9e9d76c386b473c3ebd2
iuc
parents:
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38 </xml> |
1
cdc4d8a998e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
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39 </macros> |