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comparison macs2_bdgdiff.xml @ 5:beb902da6e5f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
author iuc
date Sat, 08 Apr 2017 08:28:57 -0400
parents 56e104999978
children acbd3fb47f90
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4:56e104999978 5:beb902da6e5f
1 <tool id="macs2_bdgdiff" name="MACS2 bdgdiff" version="@VERSION_STRING@.0"> 1 <tool id="macs2_bdgdiff" name="MACS2 bdgdiff" version="@VERSION_STRING@.0">
2 <description>Differential peak detection based on paired four bedgraph files</description> 2 <description>Differential peak detection based on paired four bedgraph files</description>
3 <macros> 3 <macros>
4 <import>macs2_macros.xml</import> 4 <import>macs2_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements">
7 <requirement type="package" version="4.1.3">gawk</requirement>
8 </expand>
7 <expand macro="stdio" /> 9 <expand macro="stdio" />
8 <expand macro="version_command" /> 10 <expand macro="version_command" />
9 <command> 11 <command>
12 <![CDATA[
10 macs2 bdgdiff 13 macs2 bdgdiff
11 --t1 "${ infile_pileup_cond1 }" 14 --t1 '${ t1 }'
12 --t2 "${ infile_pileup_cond2 }" 15 --t2 '${ t2 }'
13 --c1 "${ infile_control_cond1 }" 16 --c1 '${ c1 }'
14 --c2 "${ infile_control_cond2 }" 17 --c2 '${ c2 }'
15 --cutoff "${ cutoff }" 18 --cutoff '${ cutoff }'
16 --min-len "${ minlen }" 19 --min-len '${ minlen }'
17 --depth1 "${ depth1 }" 20 --depth1 '${ depth.depth1 }'
18 --depth2 "${ depth2 }" 21 --depth2 '${ depth.depth2 }'
19 --max-gap "${ maxgap }" 22 --max-gap '${ maxgap }'
20 --o-prefix MACS2 23 -o c1.bed c2.bed both.bed &&
21 24
25 awk '!/^track name/' "c1.bed" > '${ output_cond1 }' &&
26 awk '!/^track name/' "c2.bed" > '${ output_cond1 }' &&
27 awk '!/^track name/' "both.bed" > '${ output_both }'
28
29 ]]>
22 </command> 30 </command>
23 <inputs> 31 <inputs>
24 <param name="infile_pileup_cond1" type="data" format="bedgraph" label="MACS pileup bedGraph for condition 1" /> 32 <param name="t1" type="data" format="bedgraph" label="BedGraph for Treatment experiment 1" />
25 <param name="infile_pileup_cond2" type="data" format="bedgraph" label="MACS pileup bedGraph for condition 2" /> 33 <param name="t2" type="data" format="bedgraph" label="BedGraph for Treatment experiment 2" />
26 34
27 <param name="infile_control_cond1" type="data" format="bedgraph" label="MACS control lambda bedGraph for condition 1" /> 35 <param name="c1" type="data" format="bedgraph" label="BedGraph for Control experiment 1" />
28 <param name="infile_control_cond2" type="data" format="bedgraph" label="MACS control lambda bedGraph for condition 2" /> 36 <param name="c2" type="data" format="bedgraph" label="Bedgraph for Control experiment 2" />
29 37
30 <param name="cutoff" type="float" label="Cutoff of log10 likelihood ratio cutoff" value="1.0" help="Default: 1.0 (likelihood ratio=10) (--cutoff)"/> 38 <param name="cutoff" type="float" label="Cutoff of log10 likelihood ratio cutoff" value="1.0" help="Default=1.0 correspoinding to likelihood ratio of 1,000 (--cutoff)"/>
31 <param name="minlen" type="integer" label="Minimum length of differential region" value="200"/> 39 <param name="minlen" type="integer" label="Minimum length of differential region" value="200" help=" Try bigger value to remove small regions. Default=200 (--min-len)"/>
32 <param name="depth1" type="integer" value="1" label="Sequence depth of condition 1 in million reads" help="default: 1 (--depth1)" />
33 <param name="depth2" type="integer" value="1" label="Sequence depth of condition 2 in million reads" help="default: 1 (--depth2)" />
34 <param name="maxgap" type="integer" value="100" label="Maximum gap to merge nearby differential regions" help="Consider a wider gap for broad marks. Maximum gap should be smaller than minimum length. Default: 100 (-g)." />
35 40
36 <param name="outputs" type="select" display="checkboxes" multiple="True" optional="false" label="Outputs"> 41 <section name="depth" title="Sequencing depth" expanded="True" help="Sequencing depths will be used to calculate scaling factor for each sample, to down-scale larger sample to the level of smaller one. For example, while comparing condition 1 (10 Million reads) and condition 2 (20 million reads), use --depth1 10 --depth2 20, then pileup value in bedGraph for condition 2 will be divided by 2.">
37 <option value="--ofile-cond1">Unique regions in condition 1</option> 42 <param name="depth1" type="integer" value="1" label="Sequence depth of condition 1 in million reads" help="Default=1 (--depth1)" />
38 <option value="--ofile-cond2">Unique regions in condition 2</option> 43 <param name="depth2" type="integer" value="1" label="Sequence depth of condition 2 in million reads" help="Default=1 (--depth2)" />
39 <option value="--ofile-both-conditions" selected="true">Common regions in both conditions</option> 44 </section>
40 </param> 45 <param name="maxgap" type="integer" value="100" label="Maximum gap to merge nearby differential regions" help="Consider a wider gap for broad marks. Maximum gap should be smaller than minimum length. Default=100 (--max-gap)." />
46
47
41 </inputs> 48 </inputs>
42 <outputs> 49 <outputs>
43 <data name="output_cond1" format="bed" from_work_dir="MACS2_cond1.bed" label="${tool.name} on ${on_string} (cond 1)"> 50 <data name="output_cond1" format="bed" label="${tool.name} on ${on_string} (Condition 1)"/>
44 <filter>'--ofile-cond1' in outputs</filter> 51 <data name="output_cond2" format="bed" label="${tool.name} on ${on_string} (Condition 2)"/>
45 </data> 52 <data name="output_both" format="bed" label="${tool.name} on ${on_string} (Common)"/>
46 <data name="output_cond2" format="bed" from_work_dir="MACS2_cond1.bed" label="${tool.name} on ${on_string} (cond 2)">
47 <filter>'--ofile-cond2' in outputs</filter>
48 </data>
49 <data name="output_both" format="bed" from_work_dir="MACS2_common.bed" label="${tool.name} on ${on_string} (both)">
50 <filter>'--ofile-both-conditions' in outputs</filter>
51 </data>
52 </outputs> 53 </outputs>
53 <tests> 54 <tests>
54 <!-- we need a second condition here -->
55 <!--
56 <test> 55 <test>
57 56
58 <param name="infile_control_cond1" value="Control_200K.bed" ftype="bed"/> 57 <param name="t1" value="bdgdiff_t1.bdg" ftype="bedgraph"/>
59 <param name="infile_control_cond2" value="Control_200K.bed" ftype="bed"/> 58 <param name="t2" value="bdgdiff_t2.bdg" ftype="bedgraph"/>
60 <param name="infile_pileup_cond1" value="ChIP_200K.bed" ftype="bed"/> 59 <param name="c1" value="bdgdiff_c1.bdg" ftype="bedgraph"/>
61 <param name="infile_pileup_cond2" value="ChIP_200K.bed" ftype="bed"/> 60 <param name="c2" value="bdgdiff_c2.bdg" ftype="bedgraph"/>
62 <param name="cutoff" value="1.0"/> 61 <param name="cutoff" value="1.0"/>
63 <param name="minlen" value="200"/> 62 <param name="minlen" value="200"/>
64 <param name="depth1" value="1"/> 63 <param name="depth1" value="10"/>
65 <param name="depth2" value="1"/> 64 <param name="depth2" value="1"/>
66 <param name="maxgap" value="100"/> 65 <param name="maxgap" value="100"/>
67 <param name="outputs" value="-ofile-cond1,-ofile-cond2,-ofile-both-conditions"/> 66 <output name="output_cond1">
68 <output name="output_cond1" file=""/> 67 <assert_contents>
69 <output name="output_cond2" file=""/> 68 <has_text text="c2.bed1" />
70 <output name="output_both" file=""/> 69 </assert_contents>
70 </output>
71 </test> 71 </test>
72 -->
73 </tests> 72 </tests>
74 <help> 73 <help>
74 <![CDATA[
75 **What it does** 75 **What it does**
76 76
77 bdgdiff from macs2 77 This is **bdgdiff** utility from the MACS2_ Package. It performs differential peak detection based on paired four bedgraph files.
78 78
79 .. _MACS2: https://github.com/taoliu/MACS
79 80
80 @citation@ 81 @citation@
82 ]]>
81 </help> 83 </help>
82 <expand macro="citations" /> 84 <expand macro="citations" />
83 </tool> 85 </tool>