comparison manorm.xml @ 0:9cd4a30cb4f8 draft

planemo upload for repository https://github.com/shao-lab/MAnorm/tree/master/galaxy-tool
author haydensun
date Mon, 22 Jan 2018 04:03:44 -0500
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1 <tool id="manorm" name="MAnorm" version="1.0">
2 <description>Quantitative comparison of ChIP-Seq samples</description>
3 <requirements>
4 <requirement type="package" version="1.1.2">manorm</requirement>
5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[
7 manorm --p1 $p1 --p2 $p2 --r1 $r1 --r2 $r2 $s --name1 sample1 --name2 sample2 -o output_dir
8 #if $s1
9 --s1 $s1
10 #end if
11
12 #if $s2
13 --s2 $s2
14 #end if
15
16 #if $settings.advanced == "on"
17 #if $settings.w
18 -w $settings.w
19 #end if
20
21 #if $settings.d
22 -d $settings.d
23 #end if
24
25 #if $settings.n
26 -n $settings.n
27 #end if
28 #end if
29
30 #if $m
31 -m $m
32 #end if
33
34 #if $p
35 -p $p
36 #end if
37 ]]></command>
38 <inputs>
39 <param argument="--p1" type="data" format="tabular,bed" label="Peaks file of sample 1" />
40 <param argument="--p2" type="data" format="tabular,bed" label="Peaks file of sample 2" />
41 <param argument="--r1" type="data" format="bed" label="Reads file of sample 1" />
42 <param argument="--r2" type="data" format="bed" label="Reads file of sample 2" />
43 <param argument="--s1" type="integer" value="100" optional="true" label="Reads shift size of sample 1"
44 help="This value is used to shift reads towards 3' direction to determine the precise binding site. Set as half of the fragment length." />
45 <param argument="--s2" type="integer" value="100" optional="true" label="Reads shift size of sample 2"
46 help="Same as 'Reads shift size of sample 1'" />
47 <param argument="-m" type="float" value="1.0" optional="true" label="M-value (log2 fold change) cutoff" />
48 <param argument="-p" type="float" value="0.01" optional="true" label="P-value cutoff" />
49 <conditional name="settings">
50 <param name="advanced" type="select" label="Show advanced options">
51 <option value="on">Yes, show advanced options.</option>
52 <option value="off" selected="true">No</option>
53 </param>
54 <when value="on">
55 <param argument="-w" type="integer" value="1000" optional="true" label="Width of the window to calculate read densities"
56 help="Windows with unified length of 2*width centered at peak summit/midpoint are used to quantify the binding signal.
57 This should match the typical length of peaks, a value of 1000 is recommended for sharp histone marks like H3K4me3 and H3K9/27ac,
58 and 500 for transcription factors or DNase-Seq." />
59 <param argument="-d" type="integer" value="500" optional="true" label="Summit-to-summit distance cutoff for common peaks"
60 help="Only overlapped peaks with summit-to-summit distance less than than this value are considered as real common peaks of two samples when fitting M-A normalization model." />
61 <param argument="-n" type="integer" value="10" optional="true" label="Number of simulation to test the enrichment of peak overlap between two samples" />
62 </when>
63 <when value="off">
64 </when>
65 </conditional>
66 <param argument="-s" type="boolean" truevalue="-s" falsevalue="" optional="true" label="Full output"
67 help="By default, MAnorm will write the comparison results of unique and merged common peaks in a single output file.
68 With this option on, two extra files which contains the results of the original(unmerged) peaks will also be outputted." />
69 </inputs>
70 <outputs>
71 <data name="main_output" format="tabular" label="MAnorm (main result)" from_work_dir="output_dir/sample1_vs_sample2_all_MAvalues.xls" />
72 <data name="sample1_output" format="tabular" label="MAnorm (sample1 result)" from_work_dir="output_dir/sample1_MAvalues.xls">
73 <filter>s == True</filter>
74 </data>
75 <data name="sample2_output" format="tabular" label="MAnorm (sample2 result)" from_work_dir="output_dir/sample2_MAvalues.xls">
76 <filter>s == True</filter>
77 </data>
78 <data name="sample1_biased_peaks" format="bed" label="MAnorm (sample1 biased peaks)" from_work_dir="output_dir/output_filters/sample1_M_above_*_biased_peaks.bed" />
79 <data name="sample2_biased_peaks" format="bed" label="MAnorm (sample2 biased peaks)" from_work_dir="output_dir/output_filters/sample1_M_below_*_biased_peaks.bed" />
80 <data name="unbiased_peaks" format="bed" label="MAnorm (unbiased peaks)" from_work_dir="output_dir/output_filters/sample1_vs_sample2_unbiased_peaks.bed" />
81 <data name="m_value_track" format="wig" label="MAnorm (M values track)" from_work_dir="output_dir/output_tracks/sample1_vs_sample2_M_values.wig" />
82 <data name="a_value_track" format="wig" label="MAnorm (A values track)" from_work_dir="output_dir/output_tracks/sample1_vs_sample2_A_values.wig" />
83 <data name="p_value_track" format="wig" label="MAnorm (P values track)" from_work_dir="output_dir/output_tracks/sample1_vs_sample2_P_values.wig" />
84 <data name="ma_plot_before" format="png" label="MAnorm (MA plot before normalization)" from_work_dir="output_dir/output_figures/sample1_vs_sample2_MA_plot_before_normalization.png" />
85 <data name="ma_plot_after" format="png" label="MAnorm (MA plot after normalization)" from_work_dir="output_dir/output_figures/sample1_vs_sample2_MA_plot_after_normalization.png" />
86 <data name="ma_plot_with_p_value" format="png" label="MAnorm (MA plot with P values)" from_work_dir="output_dir/output_figures/sample1_vs_sample2_MA_plot_with_P-value.png" />
87 <data name="read_density_plot" format="png" label="MAnorm (Read density plot)" from_work_dir="output_dir/output_figures/sample1_vs_sample2_read_density_on_common_peaks.png" />
88 </outputs>
89 <tests>
90 <test>
91 <param name="p1" value="H1hescH3k4me3Rep1_peaks.xls" ftype="tabular" />
92 <param name="p2" value="K562H3k4me3Rep1_peaks.xls" ftype="tabular" />
93 <param name="r1" value="H1hescH3k4me3Rep1_reads.bed" ftype="bed" />
94 <param name="r2" value="K562H3k4me3Rep1_reads.bed" ftype="bed" />
95 <param name="s1" value="100" />
96 <param name="s2" value="100" />
97 <output name="main_output" file="H1_vs_K562_H3K4me3_all_MAvalues.xls"/>
98 </test>
99 </tests>
100 <help><![CDATA[
101 What it does?
102 -------------
103
104 MAnorm is a robust model for quantitative comparison of ChIP-Seq data sets. It uses the common peaks between two samples
105 to fit a rescaling model for normalization and infers the binding difference in all peak regions.
106
107 Workflow of MAnorm:
108 - Classify peaks from given samples into unique/common peaks
109 - Take common peaks to fit a robust linear model to reflect the rescaling relationship between two samples
110 - Normalize all peaks with the fitted model
111 - Infer differential binding events by M-value (log2 fold change)
112
113
114 Documentation
115 -------------
116 To see the full documentation of MAnorm, please refer to: http://manorm.readthedocs.io/en/latest/
117
118
119 Links
120 -----
121 The Python version of MAnorm is developed by ShaoLab_ at `CAS-MPG Partner Institute for Computational Biology, SIBS, CAS`_.
122
123 GitHub: https://github.com/shao-lab/MAnorm
124
125 .. _ShaoLab: http://bioinfo.sibs.ac.cn/shaolab/
126 .. _CAS-MPG Partner Institute for Computational Biology, SIBS, CAS: http://www.picb.ac.cn/picb/indexeng.jsp
127
128 ]]></help>
129 <citations>
130 <citation type="doi">10.1186/gb-2012-13-3-r16</citation>
131 </citations>
132 </tool>