Mercurial > repos > iuc > data_manager_star_index_builder
annotate data_manager/rna_star_index_builder.xml @ 5:f5eb9afa8f8a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 9b68f6ae375aed38493f8399b8572347c750336d
author | iuc |
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date | Thu, 15 Aug 2019 11:30:16 -0400 |
parents | 6ef6520f14fc |
children | 64deddb6a8ec |
rev | line source |
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5
f5eb9afa8f8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 9b68f6ae375aed38493f8399b8572347c750336d
iuc
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1 <tool id="rna_star_index_builder_data_manager" name="rnastar index2" tool_type="manage_data" version="2.7.1a" profile="17.01"> |
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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
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2 <description>builder</description> |
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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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3 |
1
cdc4d8a998e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
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4 <macros> |
cdc4d8a998e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
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5 <import>macros.xml</import> |
cdc4d8a998e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
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6 </macros> |
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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7 |
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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
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8 <expand macro="requirements" /> |
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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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9 |
1
cdc4d8a998e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
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10 <command><![CDATA[ |
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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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11 if [ -z "\$GALAXY_MEMORY_MB" ] ; then |
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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12 GALAXY_MEMORY_BYTES=31000000000 ; |
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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13 else |
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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14 GALAXY_MEMORY_BYTES=\$((GALAXY_MEMORY_MB * 1000000)) ; |
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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15 fi ; |
1
cdc4d8a998e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
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16 |
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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17 #import json, os |
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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18 #set params = json.loads(open(str($out_file)).read()) |
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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19 #set target_directory = $params['output_data'][0]['extra_files_path'].encode('ascii', 'replace') |
6ef6520f14fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 39b9b154845ecf517f7d9e9d76c386b473c3ebd2
iuc
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20 #set subdir = os.path.basename(target_directory) |
6ef6520f14fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 39b9b154845ecf517f7d9e9d76c386b473c3ebd2
iuc
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21 |
6ef6520f14fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 39b9b154845ecf517f7d9e9d76c386b473c3ebd2
iuc
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22 mkdir -p '${target_directory}/${subdir}' && |
1
cdc4d8a998e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
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23 |
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6ef6520f14fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 39b9b154845ecf517f7d9e9d76c386b473c3ebd2
iuc
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24 STAR |
6ef6520f14fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 39b9b154845ecf517f7d9e9d76c386b473c3ebd2
iuc
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25 --runMode genomeGenerate |
6ef6520f14fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 39b9b154845ecf517f7d9e9d76c386b473c3ebd2
iuc
parents:
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26 --genomeFastaFiles '${all_fasta_source.fields.path}' |
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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27 --genomeDir '${target_directory}/${subdir}' |
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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28 --limitGenomeGenerateRAM \${GALAXY_MEMORY_BYTES} |
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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29 #if $GTFconditional.GTFselect == "withGTF": |
6ef6520f14fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 39b9b154845ecf517f7d9e9d76c386b473c3ebd2
iuc
parents:
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30 --sjdbGTFfile '${GTFconditional.sjdbGTFfile}' |
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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31 --sjdbOverhang ${GTFconditional.sjdbOverhang} |
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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32 #end if |
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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33 #if $advanced_options.advanced_options_selector == "advanced": |
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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34 --genomeSAindexNbases ${advanced_options.genomeSAindexNbases} |
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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35 --genomeChrBinNbits ${advanced_options.genomeChrBinNbits} |
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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36 --genomeSAsparseD ${advanced_options.genomeSAsparseD} |
6ef6520f14fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 39b9b154845ecf517f7d9e9d76c386b473c3ebd2
iuc
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37 #end if |
6ef6520f14fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 39b9b154845ecf517f7d9e9d76c386b473c3ebd2
iuc
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38 --runThreadN \${GALAXY_SLOTS:-2} && |
1
cdc4d8a998e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
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39 |
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6ef6520f14fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 39b9b154845ecf517f7d9e9d76c386b473c3ebd2
iuc
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40 python '${__tool_directory__}/rna_star_index_builder.py' |
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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41 --config-file '${out_file}' |
6ef6520f14fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 39b9b154845ecf517f7d9e9d76c386b473c3ebd2
iuc
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42 --value '${all_fasta_source.fields.value}' |
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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43 --dbkey '${all_fasta_source.fields.dbkey}' |
5
f5eb9afa8f8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 9b68f6ae375aed38493f8399b8572347c750336d
iuc
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44 --index-version '@IDX_VERSION@' |
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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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45 #if $name: |
6ef6520f14fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 39b9b154845ecf517f7d9e9d76c386b473c3ebd2
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46 --name '$name' |
6ef6520f14fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 39b9b154845ecf517f7d9e9d76c386b473c3ebd2
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47 #else |
6ef6520f14fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 39b9b154845ecf517f7d9e9d76c386b473c3ebd2
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48 --name '${all_fasta_source.fields.name}' |
6ef6520f14fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 39b9b154845ecf517f7d9e9d76c386b473c3ebd2
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49 #end if |
6ef6520f14fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 39b9b154845ecf517f7d9e9d76c386b473c3ebd2
iuc
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50 #if str($GTFconditional.GTFselect) == "withGTF": |
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f5eb9afa8f8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 9b68f6ae375aed38493f8399b8572347c750336d
iuc
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51 --with-gene-model |
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6ef6520f14fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 39b9b154845ecf517f7d9e9d76c386b473c3ebd2
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52 #end if |
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f5eb9afa8f8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 9b68f6ae375aed38493f8399b8572347c750336d
iuc
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53 --data-table rnastar_index2_versioned |
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6ef6520f14fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 39b9b154845ecf517f7d9e9d76c386b473c3ebd2
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54 --subdir '${subdir}' |
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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
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55 ]]></command> |
cdc4d8a998e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
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56 <inputs> |
cdc4d8a998e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
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57 <param name="all_fasta_source" type="select" label="Source FASTA Sequence"> |
cdc4d8a998e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
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58 <options from_data_table="all_fasta"/> |
cdc4d8a998e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
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59 </param> |
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6ef6520f14fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 39b9b154845ecf517f7d9e9d76c386b473c3ebd2
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60 <param name="name" type="text" value="" label="Informative name for sequence index" |
6ef6520f14fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 39b9b154845ecf517f7d9e9d76c386b473c3ebd2
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61 help="By using different settings, you may have several indices per reference genome. Give an appropriate description to the index to distinguish between indices"/> |
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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
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62 <conditional name="GTFconditional"> |
cdc4d8a998e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
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63 <param name="GTFselect" type="select" label="Reference genome with or without an annotation" help="Must the index have been created WITH a GTF file (if not you can specify one afterward)."> |
cdc4d8a998e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
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64 <option value="withoutGTF">use genome reference without builtin gene-model</option> |
cdc4d8a998e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
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65 <option value="withGTF">use genome reference with builtin gene-model</option> |
cdc4d8a998e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
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66 </param> |
cdc4d8a998e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
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67 <when value="withGTF"> |
cdc4d8a998e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
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68 <param argument="--sjdbGTFfile" type="data" format="gff3,gtf" label="Gene model (gff3,gtf) file for splice junctions" optional="false" 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
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69 <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
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70 </when> |
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71 <when value="withoutGTF" /> |
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72 </conditional> |
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73 <conditional name="advanced_options"> |
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74 <param name="advanced_options_selector" type="select" label="Advanced options"> |
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75 <option value="default" selected="true">Use default options</option> |
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76 <option value="advanced">Set advanced options</option> |
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77 </param> |
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78 <when value="default" /> |
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79 <when value="advanced"> |
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80 <param argument="--genomeSAindexNbases" type="integer" min="1" value="14" |
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81 label="Length (bases) of the SA pre-indexing string" |
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82 help="Typically between 10 and 15. Longer strings will use much more memory, but allow |
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83 faster searches. For small genomes, the parameter –genomeSAindexNbases must be scaled |
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84 down to min(14, log2(GenomeLength)/2 - 1). For example, for 1 megaBase genome, this is |
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85 equal to 9, for 100 kiloBase genome, this is equal to 7."/> |
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86 <param argument="--genomeChrBinNbits" type="integer" min="1" value="18" |
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87 label="Log2(chrBin), where chrBin is the size of the bins for genome storage" |
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88 help="Each chromosome will occupy an integer number of bins. For a genome with large number |
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89 of contigs, it is recommended to scale this parameter as min(18, |
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90 log2[max(GenomeLength/NumberOfReferences,ReadLength)]). For example, for 3 gigaBase |
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91 genome with 100,000 chromosomes/scaffolds, this is equal to 15."/> |
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92 <param argument="--genomeSAsparseD" type="integer" min="1" value="1" label="Suffix array sparsity" |
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93 help="The distance between indices: use bigger numbers to decrease needed RAM at the cost of |
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94 mapping speed reduction"/> |
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95 </when> |
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96 </conditional> |
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97 </inputs> |
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98 |
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99 <outputs> |
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100 <data name="out_file" format="data_manager_json"/> |
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101 </outputs> |
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102 |
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103 <!-- not available in planemo at the moment of writing |
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104 <tests> |
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105 <test> |
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106 <param name="all_fasta_source" value="phiX.fa"/> |
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107 <param name="sequence_name" value="phiX"/> |
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108 <param name="sequence_id" value="minimal-settings"/> |
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109 <param name="modelformat" value="None"/> |
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110 |
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111 <output name="out_file" file="test_star_01.data_manager_json"/> |
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112 </test> |
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113 </tests> |
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114 --> |
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115 |
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116 <help><![CDATA[ |
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117 .. class:: infomark |
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118 |
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119 *What it does* |
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120 |
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121 This is a Galaxy datamanager for the rna STAR gap-aware RNA aligner. |
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122 |
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123 Please read the fine manual - that and the google group are the places to learn about the options above. |
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124 |
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125 *Memory requirements* |
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126 |
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127 To run efficiently, RNA-STAR requires enough free memory to |
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128 hold the SA-indexed reference genome in RAM. For Human Genome hg19 this |
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129 index is about 27GB and running RNA-STAR requires approximately ~30GB of RAM. |
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130 For custom genomes, the rule of thumb is to multiply the size of the |
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131 reference FASTA file by 9 to estimated required amount of RAM. |
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132 |
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133 *Note on sjdbOverhang* |
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134 |
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135 From https://groups.google.com/forum/#!topic/rna-star/h9oh10UlvhI:: |
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136 |
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137 James is right, using large enough --sjdbOverhang is safer and should not generally cause any problems with reads of varying length. If your reads are very short, <50b, then I would strongly recommend using optimum --sjdbOverhang=mateLength-1 |
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138 By mate length I mean the length of one of the ends of the read, i.e. it's 100 for 2x100b PE or 1x100b SE. For longer reads you can simply use generic --sjdbOverhang 100. |
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139 It is a bit confusing because of the way I named this parameter. --sjdbOverhang Noverhang is only used at the genome generation step for constructing the reference sequence out of the annotations. |
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140 Basically, the Noverhang exonic bases from the donor site and Noverhang exonic bases from the acceptor site are spliced together for each of the junctions, and these spliced sequences are added to the genome sequence. |
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141 |
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142 At the mapping stage, the reads are aligned to both genomic and splice sequences simultaneously. If a read maps to one of spliced sequences and crosses the "junction" in the middle of it, the coordinates of two pspliced pieces are translated back to genomic space and added to the collection of mapped pieces, which are then all "stitched" together to form the final alignment. Since in the process of "maximal mapped length" search the read is split into pieces of no longer than --seedSearchStartLmax (=50 by default) bases, even if the read (mate) is longer than --sjdbOverhang, it can still be mapped to the spliced reference, as long as --sjdbOverhang > --seedSearchStartLmax. |
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143 |
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144 Cheers |
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145 Alex |
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146 |
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147 *Note on gene model requirements for splice junctions* |
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148 |
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149 From https://groups.google.com/forum/#!msg/rna-star/3Y_aaTuzBrE/lUylTB8h5vMJ:: |
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150 |
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151 When you generate a genome with annotations, you need to specify --sjdbOverhang value, which ideally should be equal to (oneMateLength-1), or you could use a generic value of ~100. |
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152 |
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153 Your gtf lines look fine to me. STAR needs 3 features from a GTF file: |
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154 1. Chromosome names in col.1 that agree with chromosome names in genome .fasta files. If you have "chr2L" names in the genome .fasta files, and "2L" in the .gtf file, then you need to use --sjdbGTFchrPrefix chr option. |
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155 2. 'exon' in col.3 for the exons of all transcripts (this name can be changed with --sjdbGTFfeatureExon) |
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156 3. 'transcript_id' attribute that assigns each exon to a transcript (--this name can be changed with --sjdbGTFtagExonParentTranscript) |
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157 |
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158 Cheers |
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159 Alex |
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160 |
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161 **Notice:** If you leave name, description, or id blank, it will be generated automatically. |
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162 ]]></help> |
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163 <expand macro="citations" /> |
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164 </tool> |