Mercurial > repos > rnateam > paralyzer

annotate test-data/input.ini @ 1:f880686a9194 draft default tip

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244"
author rnateam
date Wed, 23 Oct 2019 19:07:22 -0400
parents 4dbe81be8b81
children
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4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
rnateam
parents:
diff changeset
1 #all values are the default ones
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
rnateam
parents:
diff changeset
2 BANDWIDTH=3
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
rnateam
parents:
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3 CONVERSION=T>C
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
rnateam
parents:
diff changeset
4 MINIMUM_READ_COUNT_PER_GROUP=5
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
rnateam
parents:
diff changeset
5 MINIMUM_READ_COUNT_PER_CLUSTER=2
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
rnateam
parents:
diff changeset
6 MINIMUM_READ_COUNT_FOR_KDE=3
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
rnateam
parents:
diff changeset
7 MINIMUM_CLUSTER_SIZE=11
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
rnateam
parents:
diff changeset
8 MINIMUM_CONVERSION_LOCATIONS_FOR_CLUSTER=2
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
rnateam
parents:
diff changeset
9 MINIMUM_CONVERSION_COUNT_FOR_CLUSTER=2
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
rnateam
parents:
diff changeset
10 MINIMUM_READ_COUNT_FOR_CLUSTER_INCLUSION=1
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
rnateam
parents:
diff changeset
11 MINIMUM_READ_LENGTH=20
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
rnateam
parents:
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12 MAXIMUM_NUMBER_OF_NON_CONVERSION_MISMATCHES=1
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
rnateam
parents:
diff changeset
13
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
rnateam
parents:
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14 EXTEND_BY_READ
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
rnateam
parents:
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15
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
rnateam
parents:
diff changeset
16 GENOME_2BIT_FILE=input.2bit
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
rnateam
parents:
diff changeset
17 SAM_FILE=input.sam=COLLAPSED
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
rnateam
parents:
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18
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
rnateam
parents:
diff changeset
19 OUTPUT_DISTRIBUTIONS_FILE=out.distribution
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
rnateam
parents:
diff changeset
20 OUTPUT_GROUPS_FILE=out.groups
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
rnateam
parents:
diff changeset
21 OUTPUT_CLUSTERS_FILE=out.clusters
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
rnateam
parents:
diff changeset
22 #OUTPUT_READS_FILE=out_PARalyzer_Utilized.sam