Mercurial > repos > mvdbeek > damidseq_findpeaks

annotate damidseq_findpeaks.xml @ 7:d532111763ee 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 11875bd02ef0c27b5efa25ba5e256c530117e80a-dirty
author mvdbeek
date Fri, 20 Apr 2018 05:32:08 -0400
parents 300ef54bd35b
children 7efacf19bedc
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
mvdbeek
parents:
diff changeset
1 <tool id="damidseq_find_peaks" name="damidseq find peaks" version="0.1.3">
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
mvdbeek
parents:
diff changeset
2 <description>Simple FDR random permutation peak caller</description>
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
mvdbeek
parents:
diff changeset
3 <requirements>
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
mvdbeek
parents:
diff changeset
4 <requirement type="package" version="5.26">perl</requirement>
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
mvdbeek
parents:
diff changeset
5 </requirements>
3
61d383c9047a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 11875bd02ef0c27b5efa25ba5e256c530117e80a-dirty
mvdbeek
parents: 2
diff changeset
6 <version_command><![CDATA[perl '$__tool_directory__/find_peaks' --help 2>&1| grep find_peaks]]></version_command>
0
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
mvdbeek
parents:
diff changeset
7 <command detect_errors="aggressive"><![CDATA[
1
e726f7546561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 11875bd02ef0c27b5efa25ba5e256c530117e80a
mvdbeek
parents: 0
diff changeset
8 perl '$__tool_directory__/find_peaks'
0
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
mvdbeek
parents:
diff changeset
9 --fdr=$fdr
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
mvdbeek
parents:
diff changeset
10 --frac=$fdr
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
mvdbeek
parents:
diff changeset
11 --min_count=$min_count
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
mvdbeek
parents:
diff changeset
12 --min_quant=$min_quant
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
mvdbeek
parents:
diff changeset
13 --n=$n
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
mvdbeek
parents:
diff changeset
14 --step=$step
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
mvdbeek
parents:
diff changeset
15 --unified_peaks=$unified_peaks
6
300ef54bd35b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 11875bd02ef0c27b5efa25ba5e256c530117e80a-dirty
mvdbeek
parents: 5
diff changeset
16 '$input_file' 2>&1 | LC_ALL=C sed -e 's/[^A-Za-z0-9._-]/ /g' > log.txt &&
0
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
mvdbeek
parents:
diff changeset
17 mv peak_analysis*/*.gff peaks.gff &&
4
5a56b400df93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 11875bd02ef0c27b5efa25ba5e256c530117e80a-dirty
mvdbeek
parents: 3
diff changeset
18 cat peak_analysis*/*data >> log.txt
0
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
mvdbeek
parents:
diff changeset
19 ]]></command>
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
mvdbeek
parents:
diff changeset
20 <inputs>
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
mvdbeek
parents:
diff changeset
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."/>
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
mvdbeek
parents:
diff changeset
22 <param argument="--fdr" type="float" min="0" max="1" value="0.01" label="Set the False Discovery Rate (FDR)"/>
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
mvdbeek
parents:
diff changeset
23 <param argument="--frac" type="float" min="0" max="1" value="0.01" label="Number of random fragments to consider per iteration"/>
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
mvdbeek
parents:
diff changeset
24 <param argument="--min_count" type="integer" min="1" value="2" label="Minimum number of fragments to consider as a peak"/>
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
mvdbeek
parents:
diff changeset
25 <param argument="--min_quant" type="float" min="0" max="1" value="0.95" label="Minimum quantile for considering peaks"/>
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
mvdbeek
parents:
diff changeset
26 <param argument="--n" type="integer" min="1" value="100" label="Number of iterations"/>
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
mvdbeek
parents:
diff changeset
27 <param argument="--step" type="float" min="0" max="1" value="0.01" label="Stepping for quantiles"/>
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
mvdbeek
parents:
diff changeset
28 <param argument="--unified_peaks" type="select" label="Set the False Discovery Rate (FDR)">
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
mvdbeek
parents:
diff changeset
29 <option value="max">call maximum overlap as peak</option>
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
mvdbeek
parents:
diff changeset
30 <option value="min">call minimum overlap as peak</option>
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
mvdbeek
parents:
diff changeset
31 </param>
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
mvdbeek
parents:
diff changeset
32 </inputs>
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
mvdbeek
parents:
diff changeset
33 <outputs>
7
d532111763ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 11875bd02ef0c27b5efa25ba5e256c530117e80a-dirty
mvdbeek
parents: 6
diff changeset
34 <data name="peaks" format="gff3" from_work_dir="peaks.gff" label="${tool.name} GFF on ${on_string}"/>
0
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
mvdbeek
parents:
diff changeset
35 <data name="logs" format="txt" hidden="true" from_work_dir="log.txt" label="${tool.name} logs on ${on_string}"/>
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
mvdbeek
parents:
diff changeset
36 </outputs>
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
mvdbeek
parents:
diff changeset
37 <tests>
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
mvdbeek
parents:
diff changeset
38 <test>
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
mvdbeek
parents:
diff changeset
39 <param name="input_file" value="hp1.bed" ftype="bed"/>
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
mvdbeek
parents:
diff changeset
40 <param name="min_count" value="1"/>
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
mvdbeek
parents:
diff changeset
41 <param name="fdr" value="0.1"/>
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
mvdbeek
parents:
diff changeset
42 <output name="peaks" value="peaks.gff"/>
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
mvdbeek
parents:
diff changeset
43 </test>
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
mvdbeek
parents:
diff changeset
44 </tests>
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
mvdbeek
parents:
diff changeset
45 <help><![CDATA[
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
mvdbeek
parents:
diff changeset
46
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
mvdbeek
parents:
diff changeset
47 Options:
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
mvdbeek
parents:
diff changeset
48 --fdr False discovery rate value
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
mvdbeek
parents:
diff changeset
49 [Current value: 0.01]
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
mvdbeek
parents:
diff changeset
50 --frac Number of random fragments to consider per iteration
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
mvdbeek
parents:
diff changeset
51 --min_count Minimum number of fragments to consider as a peak
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
mvdbeek
parents:
diff changeset
52 [Current value: 2]
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
mvdbeek
parents:
diff changeset
53 --min_quant Minimum quantile for considering peaks
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
mvdbeek
parents:
diff changeset
54 [Current value: 0.95]
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
mvdbeek
parents:
diff changeset
55 --n Number of iterations
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
mvdbeek
parents:
diff changeset
56 [Current value: 100]
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
mvdbeek
parents:
diff changeset
57 --step Stepping for quantiles
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
mvdbeek
parents:
diff changeset
58 [Current value: 0.01]
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
mvdbeek
parents:
diff changeset
59 --unified_peaks Method for calling peak overlaps (two options):
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
mvdbeek
parents:
diff changeset
60 'min': call minimum overlapping peak area
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
mvdbeek
parents:
diff changeset
61 'max': call maximum overlap as peak
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
mvdbeek
parents:
diff changeset
62 [Current value: max]
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
mvdbeek
parents:
diff changeset
63
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
mvdbeek
parents:
diff changeset
64 ]]></help>
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
mvdbeek
parents:
diff changeset
65 <citations>
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
mvdbeek
parents:
diff changeset
66 <citation type="doi">10.1093/bioinformatics/btv386</citation>
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
mvdbeek
parents:
diff changeset
67 </citations>
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
mvdbeek
parents:
diff changeset
68 </tool>