annotate seacr.xml @ 1:66b7657f0bd6 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit f7c7e646aa289679a205cc8ce74a77608ce8f422"
author iuc
date Thu, 23 Apr 2020 04:30:14 -0400
parents c8ff96b9fb97
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
1 <?xml version="1.0"?>
1
66b7657f0bd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit f7c7e646aa289679a205cc8ce74a77608ce8f422"
iuc
parents: 0
diff changeset
2 <tool id="seacr" name="SEACR" version="@TOOL_VERSION@+@WRAPPER_VERSION@">
0
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
3 <description>for sparse enrichment analysis</description>
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
4 <macros>
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
5 <token name="@TOOL_VERSION@">1.3</token>
1
66b7657f0bd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit f7c7e646aa289679a205cc8ce74a77608ce8f422"
iuc
parents: 0
diff changeset
6 <token name="@WRAPPER_VERSION@">galaxy1</token>
0
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
7 </macros>
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
8 <requirements>
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
9 <requirement type="package" version="@TOOL_VERSION@">seacr</requirement>
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
10 <requirement type="package" version="2.29.2">bedtools</requirement>
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
11 </requirements>
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
12 <stdio></stdio>
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
13 <command detect_errors="exit_code"><![CDATA[
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
14 SEACR_@TOOL_VERSION@.sh
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
15 '$bedgraph'
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
16 #if $control_cond.control_sel == 'f'
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
17 '$control_cond.f'
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
18 #else if $control_cond.control_sel == 't'
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
19 '$control_cond.t'
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
20 #end if
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
21 '$normalize'
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
22 '$mode'
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
23 'results'
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
24 ]]></command>
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
25 <inputs>
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
26 <param argument="bedgraph" type="data" format="bedgraph" label="Select target bedgraph file" help="Target data bedgraph file in UCSC bedgraph format that omits regions containing 0 signal."/>
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
27 <conditional name="control_cond">
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
28 <param name="control_sel" type="select" label="Select control type">
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
29 <option value="f">Control bedgraph</option>
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
30 <option value="t">Threshold</option>
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
31 </param>
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
32 <when value="f">
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
33 <param argument="f" type="data" format="bedgraph" label="Select control bedgraph file" help="Control (IgG) data bedgraph file to generate an empirical threshold for peak calling."/>
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
34 </when>
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
35 <when value="t">
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
36 <param argument="t" type="float" value="" min="0.0" max="1.0" label="Set threshold" help="A numeric threshold n between 0 and 1 returns the top n fraction of peaks based on total signal within peaks."/>
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
37 </when>
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
38 </conditional>
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
39 <param name="normalize" type="boolean" truevalue="norm" falsevalue="non" checked="true" label="Normalize control to target data" help="'norm' denotes normalization of control to target data, 'non' skips this behavior. 'norm' is recommended unless experimental and control data are already rigorously normalized to each other (e.g. via spike-in)."/>
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
40 <param name="mode" type="select" label="Select mode" help="'relaxed' uses a total signal threshold between the knee and peak of the total signal curve, and corresponds to the 'relaxed' mode described in the text, whereas 'stringent' uses the peak of the curve, and corresponds to 'stringent' mode.">
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
41 <option value="relaxed">relaxed</option>
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
42 <option value="stringent">stringent</option>
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
43 </param>
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
44 </inputs>
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
45 <outputs>
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
46 <data name="out_s" format="tabular" from_work_dir="results.stringent.bed" label="${tool.name} on ${on_string}: stringent">
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
47 <filter>mode == 'stringent'</filter>
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
48 </data>
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
49 <data name="out_r" format="tabular" from_work_dir="results.relaxed.bed" label="${tool.name} on ${on_string}: relaxed">
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
50 <filter>mode == 'relaxed'</filter>
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
51 </data>
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
52 </outputs>
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
53 <tests>
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
54 <!-- #1 -->
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
55 <test expect_num_outputs="1">
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
56 <param name="bedgraph" value="test.bedgraph"/>
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
57 <conditional name="control_cond">
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
58 <param name="control_sel" value="t"/>
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
59 <param name="t" value="0.2"/>
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
60 </conditional>
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
61 <param name="normalize" value="norm"/>
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
62 <param name="mode" value="stringent"/>
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
63 <output name="out_s">
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
64 <assert_contents>
1
66b7657f0bd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit f7c7e646aa289679a205cc8ce74a77608ce8f422"
iuc
parents: 0
diff changeset
65 <has_n_lines n="46"/>
66b7657f0bd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit f7c7e646aa289679a205cc8ce74a77608ce8f422"
iuc
parents: 0
diff changeset
66 <has_line line="chr1&#009;10013&#009;10468&#009;549.991&#009;1.7156&#009;chr1:10346-10357"/>
66b7657f0bd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit f7c7e646aa289679a205cc8ce74a77608ce8f422"
iuc
parents: 0
diff changeset
67 <has_line line="chr1&#009;365935&#009;366920&#009;84.9934&#009;0.142966&#009;chr1:366191-366801"/>
0
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
68 </assert_contents>
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
69 </output>
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
70 </test>
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
71 <!-- #2 -->
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
72 <test expect_num_outputs="1">
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
73 <param name="bedgraph" value="test.bedgraph"/>
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
74 <conditional name="control_cond">
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
75 <param name="control_sel" value="t"/>
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
76 <param name="t" value="0.1"/>
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
77 </conditional>
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
78 <param name="normalize" value="non"/>
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
79 <param name="mode" value="relaxed"/>
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
80 <output name="out_r">
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
81 <assert_contents>
1
66b7657f0bd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit f7c7e646aa289679a205cc8ce74a77608ce8f422"
iuc
parents: 0
diff changeset
82 <has_n_lines n="200"/>
66b7657f0bd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit f7c7e646aa289679a205cc8ce74a77608ce8f422"
iuc
parents: 0
diff changeset
83 <has_line line="chr1&#009;10013&#009;10468&#009;549.991&#009;1.7156&#009;chr1:10346-10357"/>
66b7657f0bd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit f7c7e646aa289679a205cc8ce74a77608ce8f422"
iuc
parents: 0
diff changeset
84 <has_line line="chr1&#009;367832&#009;368025&#009;13.7963&#009;0.0714832&#009;chr1:367832-368025"/>
66b7657f0bd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit f7c7e646aa289679a205cc8ce74a77608ce8f422"
iuc
parents: 0
diff changeset
85 </assert_contents>
66b7657f0bd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit f7c7e646aa289679a205cc8ce74a77608ce8f422"
iuc
parents: 0
diff changeset
86 </output>
66b7657f0bd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit f7c7e646aa289679a205cc8ce74a77608ce8f422"
iuc
parents: 0
diff changeset
87 </test>
66b7657f0bd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit f7c7e646aa289679a205cc8ce74a77608ce8f422"
iuc
parents: 0
diff changeset
88 <!-- #3 -->
66b7657f0bd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit f7c7e646aa289679a205cc8ce74a77608ce8f422"
iuc
parents: 0
diff changeset
89 <test expect_num_outputs="1">
66b7657f0bd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit f7c7e646aa289679a205cc8ce74a77608ce8f422"
iuc
parents: 0
diff changeset
90 <param name="bedgraph" value="test.bedgraph"/>
66b7657f0bd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit f7c7e646aa289679a205cc8ce74a77608ce8f422"
iuc
parents: 0
diff changeset
91 <conditional name="control_cond">
66b7657f0bd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit f7c7e646aa289679a205cc8ce74a77608ce8f422"
iuc
parents: 0
diff changeset
92 <param name="control_sel" value="f"/>
66b7657f0bd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit f7c7e646aa289679a205cc8ce74a77608ce8f422"
iuc
parents: 0
diff changeset
93 <param name="f" value="control.bedgraph"/>
66b7657f0bd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit f7c7e646aa289679a205cc8ce74a77608ce8f422"
iuc
parents: 0
diff changeset
94 </conditional>
66b7657f0bd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit f7c7e646aa289679a205cc8ce74a77608ce8f422"
iuc
parents: 0
diff changeset
95 <param name="normalize" value="norm"/>
66b7657f0bd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit f7c7e646aa289679a205cc8ce74a77608ce8f422"
iuc
parents: 0
diff changeset
96 <param name="mode" value="relaxed"/>
66b7657f0bd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit f7c7e646aa289679a205cc8ce74a77608ce8f422"
iuc
parents: 0
diff changeset
97 <output name="out_r">
66b7657f0bd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit f7c7e646aa289679a205cc8ce74a77608ce8f422"
iuc
parents: 0
diff changeset
98 <assert_contents>
66b7657f0bd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit f7c7e646aa289679a205cc8ce74a77608ce8f422"
iuc
parents: 0
diff changeset
99 <has_n_lines n="7"/>
66b7657f0bd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit f7c7e646aa289679a205cc8ce74a77608ce8f422"
iuc
parents: 0
diff changeset
100 <has_line line="chr1&#009;10596&#009;11929&#009;430.615&#009;0.714832&#009;chr1:11036-11191"/>
66b7657f0bd6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit f7c7e646aa289679a205cc8ce74a77608ce8f422"
iuc
parents: 0
diff changeset
101 <has_line line="chr1&#009;251258&#009;252108&#009;384.65&#009;1.00076&#009;chr1:251347-251526"/>
0
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
102 </assert_contents>
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
103 </output>
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
104 </test>
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
105 </tests>
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
106 <help><![CDATA[
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
107 .. class:: infomark
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
108
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
109 **What it does**
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
110
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
111 SEACR (Sparse Enrichment Analysis for CUT&RUN) is intended to call peaks and enriched regions from sparse CUT&RUN or chromatin profiling data in which background is dominated by "zeroes" (i.e. regions with no read coverage).
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
112
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
113 CUT&RUN is an efficient epigenome profiling method that identifies sites of DNA binding protein enrichment genome-wide with high signal to noise and low sequencing requirements. Currently, the analysis of CUT&RUN data is complicated by its exceptionally low background, which renders programs designed for analysis of ChIP-seq data vulnerable to oversensitivity in identifying sites of protein binding.
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
114
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
115 SEACR is a highly selective peak caller that definitively validates the accuracy of CUT&RUN for datasets with known true negatives. SEACR uses the global distribution of background signal to calibrate a simple threshold for peak calling. SEACR discriminates between true and false-positive peaks with near-perfect specificity from gold standard CUT&RUN datasets and efficiently identifies enriched regions for several different protein targets.
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
116
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
117 **Input**
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
118
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
119 SEACR requires files in UCSC bedgraph format from paired-end sequencing as input, which can be generated from read pair BED files.
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
120
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
121 **Output**
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
122
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
123 Results are stored in BED files with the folowing format.
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
124
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
125 ::
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
126
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
127 <chr> <start> <end> <total signal> <max signal> <max signal region>
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
128
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
129 with
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
130
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
131 - <chr> Chromosome
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
132 - <start> Start coordinate
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
133 - <end> End coordinate
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
134 - <total signal> Total signal contained within denoted coordinates
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
135 - <max signal> Maximum bedgraph signal attained at any base pair within denoted coordinates
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
136 - <max signal region> Region representing the farthest upstream and farthest downstream bases within the denoted coordinates that are represented by the maximum bedgraph signal
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
137
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
138 .. class:: infomark
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
139
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
140 **References**
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
141
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
142 More information are available on `github <https://github.com/FredHutch/SEACR>`_. A web interface can be found `here <https://seacr.fredhutch.org>`_.
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
143 ]]></help>
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
144 <citations>
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
145 <citation type="doi">10.1186/s13072-019-0287-4</citation>
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
146 </citations>
c8ff96b9fb97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr commit 77e83ae050cdc9cbb8099a31375d1dbc004e15e8"
iuc
parents:
diff changeset
147 </tool>