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/tools/peakcalling/MMChIP-seq.xml

https://bitbucket.org/cistrome/cistrome-harvard/
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  1<tool name="MMChIP-seq" id="peakcalling_MMChIP-seq">
  2  <description>can combine ChIP-seq libraries from different batches with different fragment sizes.</description>
  3  <command interpreter="command">/bin/bash $shscript</command>
  4  <inputs>
  5    <conditional name="genome_size_cond">
  6      <param name="genome_size" type="select" label="mappable genome size">
  7        <option value="2770000000">Human (hg18)</option>
  8        <option value="2790000000">Human (hg19)</option>
  9        <option value="1870000000">Mouse (mm8)</option>
 10        <option value="1910000000">Mouse (mm9)</option>
 11        <option value="90300000">C elegans (ce4)</option>
 12        <option value="90300000">C elegans (ce6)</option>
 13        <option value="119000000">Drosophila (dm2)</option>
 14        <option value="152000000">Drosophila (dm3)</option>
 15        <option value="OTHER">Other</option>
 16      </param>
 17      <when value="OTHER">
 18        <param name="genome_size_other" type="text" label="Custom Genome Size"/>
 19      </when>
 20      <when value="2770000000"/>
 21      <when value="2790000000"/>
 22      <when value="1870000000"/>
 23      <when value="1910000000"/>
 24      <when value="90300000"/>
 25      <when value="90300000"/>
 26      <when value="119000000"/>
 27      <when value="152000000"/>
 28    </conditional>
 29    <param name="pvalue" type="float" label="p-value cutoff for peak detection" value="0.00001">
 30      <validator type="in_range" max="1" min="0" message="Pvalue is out of range, Pvalue has to be between 0 to 1" />
 31    </param>
 32    <repeat name="more" title="more bed file">
 33      <param format="bed" name="tfile" type="data" label="select treat file"/>
 34      <param format="bed" name="cfile" type="data" label="select control file" />
 35      <param name="frag" type="integer" label="fragment size" value="0" />
 36    </repeat>
 37  </inputs>
 38  <outputs>
 39    <data format="bed" name="peakfile" label="MMChIP-seq peaks output" />
 40    <data format="txt" name="xlsfile" label="MMChIP-seq xls output" />
 41    <data format="wig" name="wigfile" label="MMChIP-seq wig output" />
 42    <data format="txt" name="log" label="MMChIP-seq log" />
 43  </outputs>
 44  <configfiles>
 45    <configfile name="shscript">
 46#!/bin/bash
 47#import os
 48
 49#set $ad = chr(38)
 50#set $gt = chr(62)
 51#set $dollar = chr(36)
 52
 53#set $genomeSize = $genome_size_cond.genome_size
 54#if $genome_size_cond.genome_size == "OTHER"
 55#set $genomeSize = $genome_size_cond.genome_size_other
 56#end if
 57
 58#set $files = ""
 59#for $m in $more
 60
 61#set $path = os.path.abspath($__app__.config.tool_path)
 62
 63format=`$path/validation/fcfunc.py $m.tfile`
 64if [[ ${dollar}format != "passed" ]]; then
 65   echo ${dollar}format ${gt}${ad}2
 66   exit;
 67fi
 68format=`$path/validation/fcfunc.py $m.cfile`
 69if [[ ${dollar}format != "passed" ]]; then
 70   echo ${dollar}format ${gt}${ad}2
 71   exit;
 72fi
 73
 74#set $temp = str($m.tfile)+","+str($m.cfile)+","+str($m.frag)
 75#set $files = $files + " " + str($temp)
 76#end for
 77
 78paths=`python $path/peakcalling/GetPath.py $files`
 79echo ${dollar}paths 
 80MMChIP-seq ${dollar}paths $genomeSize $pvalue ${ad}${gt} $log
 81mv MMChIP-seq_peaks.bed $peakfile
 82mv MMChIP-seq_peaks.xls $xlsfile
 83zcat MMChIP-seq_MACS_wiggle/treat/*.gz ${gt} $wigfile
 84###mv MMChIP-seq_peaks.wig $wigfile
 85    </configfile>
 86  </configfiles>
 87  <help>
 88For ChIP-seq data, it is recommended to use MM-ChIP when inter-library
 89size difference is comparatively large. Otherwise, one can simply uses
 90MACS on the merged tag data (see more details in our paper, entitled
 91"MM-ChIP enables integrative analysis of cross-platform and
 92between-laboratory ChIP-chip or ChIP-seq data" published in Genome
 93Biology.
 94
 95**TIP:** CAUTIONS: For ChIP-seq data,MM-ChIP was only tested on Illumina data
 96because of the lack of public ChIP-seq datasets for the same protein of
 97interest under similar biological conditions from technical platforms
 98other than Ilumina. For cross-platform data, different statistical models
 99may be needed to account for inter-platform variations besides variation
100in inter-library size (see the discussion part in our paper).
101
102This tool is for integrative analysis of ChIP-seq datasets. Original code is
103written by Yiwen Chen. 
104
105.. class:: warningmark
106
107**NEED IMPROVEMENT**
108
109-----
110
111**Parameters**
112
113- **mappable genome size** Effective genome size. It can be 1.0e+9 or 1000000000
114- **P-VALUE** the p-value cutoff for peak detection
115- **Add More BED file** click the *Add new More BED files* to add
116  more. 
117- **select treat file** the name of mapped read files for ChIP samples.
118- **select control file** the name of the mapped read file for input samples.
119  If there is no control sample, the 2nd column can be ommitted. 
120- **fragment size** the fragment size(d) of individual datasets, which 
121  is estimated by MACS program. 
122
123
124-----
125
126**Outputs**
127
128- *bed file* This file contains the peak information.
129- *xls file* This file contains peaks' detail information.
130- *wig file* This file contains the score for each region.
131  </help>
132</tool>