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comparison ceas.xml @ 2:012afa77c724 draft default tip

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author nikhil-joshi
date Tue, 09 Dec 2014 06:54:34 -0500
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1:d59bf233d184 2:012afa77c724
1 <tool id="ceas" name="CEAS" version="1.0.2">
2 <description>Get stats on ChIP enrichment and infer genes regulated by binding factors</description>
3
4 <command>
5 mkdir -p "$pdf_out.files_path" &amp;&amp;
6 cd "$pdf_out.files_path" &amp;&amp;
7
8 ceas
9
10 -g "$refgene_table.fields.path"
11 #if $analysis_files.wig_or_bed == "bed" or $analysis_files.wig_or_bed == "both1" or $analysis_files.wig_or_bed == "both2":
12 -b $chip_bed
13 #end if
14
15 #if $analysis_files.wig_or_bed == "wig" or $analysis_files.wig_or_bed == "both1" or $analysis_files.wig_or_bed == "both2":
16 -w $chip_wig
17 #end if
18
19 #if $analysis_files.wig_or_bed == "both2":
20 --bg
21 #end if
22
23 #if str($extra_bed) != 'None':
24 -e $extra_bed
25 #end if
26
27 #if str($sizes) != "":
28 --sizes=$sizes
29 #end if
30
31 #if str($bisizes) != "":
32 --bisizes=$bisizes
33 #end if
34
35 #if str($span) != "":
36 --span=$span
37 #end if
38
39 #if str($pfres) != "":
40 --pf-res=$pfres
41 #end if
42
43 #if str($reldist) != "":
44 --rel-dist=$reldist
45 #end if
46
47 --name=ceas_out
48
49 2&gt; /dev/null
50
51 &amp;&amp;
52
53 #if $analysis_files.wig_or_bed != "wig":
54 mv $pdf_out.files_path/ceas_out.xls $annot_out &amp;&amp;
55 #end if
56 mv $pdf_out.files_path/ceas_out.R $r_out &amp;&amp;
57 mv $pdf_out.files_path/ceas_out.pdf $pdf_out &amp;&amp;
58
59 rm -r "$pdf_out.files_path"
60 </command>
61
62 <inputs>
63 <conditional name="analysis_files">
64 <param name="wig_or_bed" type="select" optional="false" label="Select the type of analysis">
65 <option value="bed" selected="true">Run only ChIP region and gene-centered annotation</option>
66 <option value="wig">Run only average signal profiling</option>
67 <option value="both1">Run both annotation and profiling</option>
68 <option value="both2">Run genome background annotation</option>
69 </param>
70
71 <when value="bed">
72 <param format="bed" name="chip_bed" type="data" label="BED file of ChIP regions"/>
73 </when>
74
75 <when value="wig">
76 <param format="wig" name="chip_wig" type="data" label="WIG file with ChiP enrichment signal"/>
77 </when>
78
79 <when value="both1">
80 <param format="bed" name="chip_bed" type="data" label="BED file of ChIP regions"/>
81 <param format="wig" name="chip_wig" type="data" label="WIG file with ChiP enrichment signal"/>
82 </when>
83
84 <when value="both2">
85 <param format="bed" name="chip_bed" type="data" label="BED file of ChIP regions"/>
86 <param format="wig" name="chip_wig" type="data" label="WIG file for genome background annotation"/>
87 </when>
88 </conditional>
89
90 <param name="refgene_table" label="Gene annotation table" type="select">
91 <options from_data_table="ceas_refgene_tables">
92 <filter type="sort_by" column="1"/>
93 <validator type="no_options" message="No indexes are available for the selected dataset"/>
94 </options>
95 </param>
96
97 <param format="bed" name="extra_bed" type="data" optional="true" label="BED file of extra regions of interest (e.g. non-coding regions)"/>
98
99 <param name="sizes" type="integer" optional="true" label="Promoter (also downstream) sizes for ChIP region annotation" help="Three comma-separated integers or a single integer. Leave blank for default."/>
100
101 <param name="bisizes" type="integer" optional="true" label="Bidirectional promoter sizes for ChIP region annotation" help="Two comma-separated integers or a single integer. Leave blank for default."/>
102
103 <param name="span" type="integer" optional="true" label="Span from TSS and TTS in the gene-centered annotation" help="Leave blank for default."/>
104 <param name="pfres" type="integer" optional="true" label="WIG profiling resolution" help="Leave blank for default."/>
105 <param name="reldist" type="integer" optional="true" label="Relative distance to TSS/TTS in wig profiling" help="Leave blank for default."/>
106
107 </inputs>
108
109 <outputs>
110 <data format="tabular" name="annot_out" label="Gene-centered annotation from ${tool.name} on ${on_string} (XLS)">
111 <filter>(analysis_files['wig_or_bed'] != 'wig')</filter>
112 </data>
113 <data format="txt" name="r_out" label="R script for graph results from ${tool.name} on ${on_string}" />
114 <data format="pdf" name="pdf_out" label="Graph results from ${tool.name} on ${on_string} (PDF)" />
115 </outputs>
116
117 <help>
118 Options:
119 -b BED, --bed=BED BED file of ChIP regions.
120 -w WIG, --wig=WIG WIG file for either wig profiling or genome background
121 annotation. WARNING: --bg flag must be set for genome
122 background re-annotation.
123 -e EBED, --ebed=EBED BED file of extra regions of interest (eg, non-coding
124 regions)
125 -g GDB, --gt=GDB Gene annotation table (eg, a refGene table in sqlite3
126 db format provided through the CEAS web,
127 http://liulab.dfci.harvard.edu/CEAS/download.html).
128 --sizes=SIZES Promoter (also dowsntream) sizes for ChIP region
129 annotation. Comma-separated three values or a single
130 value can be given. If a single value is given, it
131 will be segmented into three equal fractions (ie, 3000
132 is equivalent to 1000,2000,3000), DEFAULT:
133 1000,2000,3000. WARNING: Values > 10000bp are
134 automatically set to 10000bp.
135 --bisizes=BISIZES Bidirectional-promoter sizes for ChIP region
136 annotation Comma-separated two values or a single
137 value can be given. If a single value is given, it
138 will be segmented into two equal fractions (ie, 5000
139 is equivalent to 2500,5000) DEFAULT: 2500,5000bp.
140 WARNING: Values > 20000bp are automatically set to
141 20000bp.
142 --bg Run genome BG annotation again. WARNING: This flag is
143 effective only if a WIG file is given through -w
144 (--wig). Otherwise, ignored.
145 --span=SPAN Span from TSS and TTS in the gene-centered annotation.
146 ChIP regions within this range from TSS and TTS are
147 considered when calculating the coverage rates in
148 promoter and downstream, DEFAULT=3000bp
149 --pf-res=PF_RES Wig profiling resolution, DEFAULT: 50bp. WARNING:
150 Value smaller than the wig interval (resolution) may
151 cause aliasing error.
152 --rel-dist=REL_DIST Relative distance to TSS/TTS in wig profiling,
153 DEFAULT: 3000bp
154 </help>
155
156 </tool>