Mercurial > repos > mvdbeek > damidseq_findpeaks
annotate log @ 8:7efacf19bedc draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 8dccd750ac2057caa6495636153250bdd4ecf549
author | mvdbeek |
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date | Fri, 20 Apr 2018 06:14:28 -0400 |
parents | 29f82a5c7966 |
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rev | line source |
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5
29f82a5c7966
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 11875bd02ef0c27b5efa25ba5e256c530117e80a-dirty
mvdbeek
parents:
diff
changeset
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1 Simple FDR random permutation peak caller |
29f82a5c7966
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 11875bd02ef0c27b5efa25ba5e256c530117e80a-dirty
mvdbeek
parents:
diff
changeset
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2 Usage: [options] [files in bedgraph or GFF format] |
29f82a5c7966
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 11875bd02ef0c27b5efa25ba5e256c530117e80a-dirty
mvdbeek
parents:
diff
changeset
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3 |
29f82a5c7966
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 11875bd02ef0c27b5efa25ba5e256c530117e80a-dirty
mvdbeek
parents:
diff
changeset
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4 Options: |
29f82a5c7966
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 11875bd02ef0c27b5efa25ba5e256c530117e80a-dirty
mvdbeek
parents:
diff
changeset
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5 --fdr False discovery rate value |
29f82a5c7966
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 11875bd02ef0c27b5efa25ba5e256c530117e80a-dirty
mvdbeek
parents:
diff
changeset
|
6 [Current value: 0.01] |
29f82a5c7966
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 11875bd02ef0c27b5efa25ba5e256c530117e80a-dirty
mvdbeek
parents:
diff
changeset
|
7 --frac Number of random fragments to consider per iteration |
29f82a5c7966
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 11875bd02ef0c27b5efa25ba5e256c530117e80a-dirty
mvdbeek
parents:
diff
changeset
|
8 --min_count Minimum number of fragments to consider as a peak |
29f82a5c7966
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 11875bd02ef0c27b5efa25ba5e256c530117e80a-dirty
mvdbeek
parents:
diff
changeset
|
9 [Current value: 2] |
29f82a5c7966
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 11875bd02ef0c27b5efa25ba5e256c530117e80a-dirty
mvdbeek
parents:
diff
changeset
|
10 --min_quant Minimum quantile for considering peaks |
29f82a5c7966
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 11875bd02ef0c27b5efa25ba5e256c530117e80a-dirty
mvdbeek
parents:
diff
changeset
|
11 [Current value: 0.95] |
29f82a5c7966
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 11875bd02ef0c27b5efa25ba5e256c530117e80a-dirty
mvdbeek
parents:
diff
changeset
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12 --n Number of iterations |
29f82a5c7966
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 11875bd02ef0c27b5efa25ba5e256c530117e80a-dirty
mvdbeek
parents:
diff
changeset
|
13 [Current value: 100] |
29f82a5c7966
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 11875bd02ef0c27b5efa25ba5e256c530117e80a-dirty
mvdbeek
parents:
diff
changeset
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14 --step Stepping for quantiles |
29f82a5c7966
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 11875bd02ef0c27b5efa25ba5e256c530117e80a-dirty
mvdbeek
parents:
diff
changeset
|
15 [Current value: 0.01] |
29f82a5c7966
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 11875bd02ef0c27b5efa25ba5e256c530117e80a-dirty
mvdbeek
parents:
diff
changeset
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16 --unified_peaks Method for calling peak overlaps (two options): |
29f82a5c7966
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 11875bd02ef0c27b5efa25ba5e256c530117e80a-dirty
mvdbeek
parents:
diff
changeset
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17 'min': call minimum overlapping peak area |
29f82a5c7966
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 11875bd02ef0c27b5efa25ba5e256c530117e80a-dirty
mvdbeek
parents:
diff
changeset
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18 'max': call maximum overlap as peak |
29f82a5c7966
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 11875bd02ef0c27b5efa25ba5e256c530117e80a-dirty
mvdbeek
parents:
diff
changeset
|
19 [Current value: max] |
29f82a5c7966
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 11875bd02ef0c27b5efa25ba5e256c530117e80a-dirty
mvdbeek
parents:
diff
changeset
|
20 |