Mercurial > repos > mvdbeek > damidseq_findpeaks

changeset 9:8fd3191302d0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 5bf4f4dbd82988d1612d951d69125bc5f5b439be
author mvdbeek
date Wed, 13 Jun 2018 12:41:00 -0400
parents 7efacf19bedc
children 48d9c6f9ef41
files damidseq_findpeaks.xml log
diffstat 2 files changed, 1 insertions(+), 21 deletions(-) [+]
line wrap: on
line diff
--- a/damidseq_findpeaks.xml	Fri Apr 20 06:14:28 2018 -0400
+++ b/damidseq_findpeaks.xml	Wed Jun 13 12:41:00 2018 -0400
@@ -20,7 +20,7 @@
     <inputs>
         <param name="input_file" type="data" format="gff,bed,bedgraph" label="Select dam-fusion/dam ratio files" help="You can use damidseq_core to produce this file."/>
         <param argument="--fdr" type="float" min="0" max="1" value="0.01" label="Set the False Discovery Rate (FDR)"/>
-        <param argument="--frac" type="float" min="0" max="1" value="0.01" label="Number of random fragments to consider per iteration"/>
+        <param argument="--frac" type="float" min="0" max="1" value="0" label="Number of random fragments to consider per iteration"/>
         <param argument="--min_count" type="integer" min="1" value="2" label="Minimum number of fragments to consider as a peak"/>
         <param argument="--min_quant" type="float" min="0" max="1" value="0.95" label="Minimum quantile for considering peaks"/>
         <param argument="--n" type="integer" min="1" value="100" label="Number of iterations"/>
--- a/log	Fri Apr 20 06:14:28 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,20 +0,0 @@
-Simple FDR random permutation peak caller
-Usage: [options] [files in bedgraph or GFF format]
-	
-Options:
- --fdr            False discovery rate value
-                    [Current value: 0.01]
- --frac           Number of random fragments to consider per iteration
- --min_count      Minimum number of fragments to consider as a peak
-                    [Current value: 2]
- --min_quant      Minimum quantile for considering peaks
-                    [Current value: 0.95]
- --n              Number of iterations
-                    [Current value: 100]
- --step           Stepping for quantiles
-                    [Current value: 0.01]
- --unified_peaks  Method for calling peak overlaps (two options):
-                    'min': call minimum overlapping peak area
-                    'max': call maximum overlap as peak
-                    [Current value: max]
-