Mercurial > repos > mvdbeek > damidseq_findpeaks

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 11875bd02ef0c27b5efa25ba5e256c530117e80a-dirty
author mvdbeek
date Fri, 20 Apr 2018 05:11:06 -0400
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29f82a5c7966 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 11875bd02ef0c27b5efa25ba5e256c530117e80a-dirty
mvdbeek
parents:
diff changeset
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
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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:
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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
4 Options:
29f82a5c7966 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 11875bd02ef0c27b5efa25ba5e256c530117e80a-dirty
mvdbeek
parents:
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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:
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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:
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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:
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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:
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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:
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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:
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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:
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