Mercurial > repos > mvdbeek > damidseq_findpeaks

comparison damidseq_findpeaks.xml @ 0:be830200e987 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
author mvdbeek
date Fri, 20 Apr 2018 04:34:17 -0400
parents
children e726f7546561
comparison
equal deleted inserted replaced
-1:000000000000 0:be830200e987
1 <tool id="damidseq_find_peaks" name="damidseq find peaks" version="0.1.3">
2 <description>Simple FDR random permutation peak caller</description>
3 <requirements>
4 <requirement type="package" version="5.26">perl</requirement>
5 </requirements>
6 <version_command><![CDATA['$__tool_directory__/find_peaks' --help 2>&1| grep find_peaks]]></version_command>
7 <command detect_errors="aggressive"><![CDATA[
8 '$__tool_directory__/find_peaks'
9 --fdr=$fdr
10 --frac=$fdr
11 --min_count=$min_count
12 --min_quant=$min_quant
13 --n=$n
14 --step=$step
15 --unified_peaks=$unified_peaks
16 '$input_file' &&
17 mv peak_analysis*/*.gff peaks.gff &&
18 mv peak_analysis*/*data log.txt
19 ]]></command>
20 <inputs>
21 <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."/>
22 <param argument="--fdr" type="float" min="0" max="1" value="0.01" label="Set the False Discovery Rate (FDR)"/>
23 <param argument="--frac" type="float" min="0" max="1" value="0.01" label="Number of random fragments to consider per iteration"/>
24 <param argument="--min_count" type="integer" min="1" value="2" label="Minimum number of fragments to consider as a peak"/>
25 <param argument="--min_quant" type="float" min="0" max="1" value="0.95" label="Minimum quantile for considering peaks"/>
26 <param argument="--n" type="integer" min="1" value="100" label="Number of iterations"/>
27 <param argument="--step" type="float" min="0" max="1" value="0.01" label="Stepping for quantiles"/>
28 <param argument="--unified_peaks" type="select" label="Set the False Discovery Rate (FDR)">
29 <option value="max">call maximum overlap as peak</option>
30 <option value="min">call minimum overlap as peak</option>
31 </param>
32 </inputs>
33 <outputs>
34 <data name="peaks" format="gff3" from_work_dir="peaks.gff" label="${tool.name} on ${on_string}"/>
35 <data name="logs" format="txt" hidden="true" from_work_dir="log.txt" label="${tool.name} logs on ${on_string}"/>
36 </outputs>
37 <tests>
38 <test>
39 <param name="input_file" value="hp1.bed" ftype="bed"/>
40 <param name="min_count" value="1"/>
41 <param name="fdr" value="0.1"/>
42 <output name="peaks" value="peaks.gff"/>
43 </test>
44 </tests>
45 <help><![CDATA[
46
47 Options:
48 --fdr False discovery rate value
49 [Current value: 0.01]
50 --frac Number of random fragments to consider per iteration
51 --min_count Minimum number of fragments to consider as a peak
52 [Current value: 2]
53 --min_quant Minimum quantile for considering peaks
54 [Current value: 0.95]
55 --n Number of iterations
56 [Current value: 100]
57 --step Stepping for quantiles
58 [Current value: 0.01]
59 --unified_peaks Method for calling peak overlaps (two options):
60 'min': call minimum overlapping peak area
61 'max': call maximum overlap as peak
62 [Current value: max]
63
64 ]]></help>
65 <citations>
66 <citation type="doi">10.1093/bioinformatics/btv386</citation>
67 </citations>
68 </tool>