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comparison sashimi_plot.xml @ 0:9304dd9a16a2 draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
author artbio
date Fri, 23 Aug 2019 11:38:29 -0400
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children 64aa67b5099f
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-1:000000000000 0:9304dd9a16a2
1 <tool id="sashimi_plot" name="Sashimi plot" version="0.1.0">
2 <description>: visualization of splicing events across multiple samples</description>
3 <requirements>
4 <requirement type="package" version="3">python</requirement>
5 <requirement type="package" version="1.3">samtools</requirement>
6 <requirement type="package" version="2.2.1=r3.4.1_0">r-ggplot2</requirement>
7 <requirement type="package" version="1.10.4=r3.4.1_0">r-data.table</requirement>
8 <requirement type="package" version="2.2.1=r3.4.1_0">r-gridextra</requirement>
9 </requirements>
10 <stdio>
11 <exit_code range="1:" level="fatal" description="Tool exception" />
12 </stdio>
13 <command detect_errors="exit_code"><![CDATA[
14 touch index_bams.tsv &&
15 #for $factor in $rep_factor:
16 #for $sample in $factor.rep_sample:
17 echo -e '${sample.sampleName}\t${sample.bamFile}\t${factor.factorName}' >> index_bams.tsv &&
18 samtools index ${sample.bamFile} &&
19 #end for
20 #end for
21
22 python $__tool_directory__/sashimi-plot.py
23 -b index_bams.tsv
24 -g ${gtf_file}
25 -c ${region}
26 #if $adv_opts.adv_opts_selector=="advanced":
27 -M ${adv_opts.min_coverage}
28 -C ${adv_opts.color_levels}
29 -O ${adv_opts.overlap.overlay}
30 #if $adv_opts.overlap.overlay=="3" and not $adv_opts.overlap.agg=="":
31 -A ${adv_opts.overlap.agg}
32 #end if
33 ${adv_opts.shrink}
34 --alpha ${adv_opts.alpha}
35 --base-size=${adv_opts.base_size}
36 --ann-height=${adv_opts.ann_height}
37 --height=${adv_opts.height}
38 --width=${adv_opts.width}
39 #end if
40 -o plot &&
41 mv plot.pdf ${plot}
42
43 ]]></command>
44 <inputs>
45 <param format="gtf" name="gtf_file" type="data" label="Genome annotation" help="" />
46 <repeat name="rep_factor" title="Genotype" min="1">
47 <param name="factorName" label="Factor name" type="text" help="Specify a factor level, typical values could be 'HOM', 'HET'" />
48 <repeat name="rep_sample" title="Bam file" min="1">
49 <param name="sampleName" type="text" label="Sample Name" help="Track name on plot"/>
50 <param name="bamFile" type="data" format="bam" multiple="false" label="Alignment File" help=""/>
51 </repeat>
52 </repeat>
53 <conditional name="adv_opts">
54 <param name="adv_opts_selector" type="select" label="Advanced Options">
55 <option value="basic" selected="True">Hide Advanced Options</option>
56 <option value="advanced">Show Advanced Options</option>
57 </param>
58 <when value="basic" />
59 <when value="advanced">
60 <param name="shrink" type="boolean" label="Intron shrinkage" truevalue="--shrink" falsevalue="" checked="false"
61 help="Shrink the introns by a factor for nicer display"/>
62 <param name="min_coverage" label="Minimum coverage" type="integer" value="1" help="Minimum number of reads supporting a junction to be drawn [default=1]"/>
63 <param name="color_levels" label="How to color samples ?" type="select">
64 <option value="3" selected="True">By Genotype</option>
65 <option value="1" >By Sample</option>
66 </param>
67 <conditional name="overlap">
68 <param name="overlay" label="Overlay sample by Genotype ?" type="boolean" truevalue="3" falsevalue="1" checked="false" />
69 <when value="3">
70 <param name="agg" label="Aggregate function for overlay" type="select" help="Use mean_j | median_j to keep density overlay but aggregate junction counts">
71 <option value="" selected="True">No aggregation</option>
72 <option value="mean" >Mean counts</option>
73 <option value="median" >Median counts</option>
74 <option value="mean_j" >Mean of counts supporting junctions</option>
75 <option value="median_j" >Median of counts supporting junctions</option>
76 </param>
77 </when>
78 <when value="1"/>
79 </conditional>
80 <param name="alpha" label="Transparency level for density histogram" type="float" value="0.5" help="default=0.5"/>
81 <param name="base_size" label="Base font size" type="float" value="14" help="Base font size of the plot in pch [default=14]"/>
82 <param name="ann_height" label="Height of annotation" type="float" value="1.5" help="Height of annotation plot (transcripts visualisation) in inches [default=1.5]"/>
83 <param name="height" label="Height of sashimi plot" type="float" value="2" help="Height of the individual signal plot (sashimi vizualisation) in inches [default=2]"/>
84 <param name="width" label="Width" type="float" value="10" help="Width of the plot in inches [default=10]"/>
85 </when>
86 </conditional>
87 <param name="region" type="text" help="Must be the following format : chromosome:start-end"/>
88 </inputs>
89 <outputs>
90 <data name="plot" format="pdf" label="Sashimi plot" />
91 </outputs>
92 <tests>
93 <test>
94 <param name="gtf_file" value="annotation.gtf" ftype="gtf" />
95 <repeat name="rep_factor">
96 <param name="factorName" value="Endothelial" />
97 <repeat name="rep_sample">
98 <param name="sampleName" value="sample1" />
99 <param name="bamFile" value="ENCFF450AIU.chr10_27035000_27050000.bam" ftype="bam" />
100 </repeat>
101 <repeat name="rep_sample">
102 <param name="sampleName" value="sample2" />
103 <param name="bamFile" value="ENCFF914GVK.chr10_27035000_27050000.bam" ftype="bam" />
104 </repeat>
105 </repeat>
106 <repeat name="rep_factor">
107 <param name="factorName" value="Epithelial" />
108 <repeat name="rep_sample">
109 <param name="sampleName" value="sample3" />
110 <param name="bamFile" value="ENCFF756PUW.chr10_27035000_27050000.bam" ftype="bam" />
111 </repeat>
112 <repeat name="rep_sample">
113 <param name="sampleName" value="sample4"/>
114 <param name="bamFile" value="ENCFF325HFX.chr10_27035000_27050000.bam" ftype="bam" />
115 </repeat>
116 </repeat>
117 <param name="region" value="chr10:27040584-27048100" />
118 <output name="plot" value="default.pdf" ftype="pdf" />
119 </test>
120 <test>
121 <param name="gtf_file" value="annotation.gtf" ftype="gtf" />
122 <repeat name="rep_factor">
123 <param name="factorName" value="Endothelial" />
124 <repeat name="rep_sample">
125 <param name="sampleName" value="sample1" />
126 <param name="bamFile" value="ENCFF450AIU.chr10_27035000_27050000.bam" ftype="bam" />
127 </repeat>
128 <repeat name="rep_sample">
129 <param name="sampleName" value="sample2" />
130 <param name="bamFile" value="ENCFF914GVK.chr10_27035000_27050000.bam" ftype="bam" />
131 </repeat>
132 </repeat>
133 <repeat name="rep_factor">
134 <param name="factorName" value="Epithelial" />
135 <repeat name="rep_sample">
136 <param name="sampleName" value="sample3" />
137 <param name="bamFile" value="ENCFF756PUW.chr10_27035000_27050000.bam" ftype="bam" />
138 </repeat>
139 <repeat name="rep_sample">
140 <param name="sampleName" value="sample4"/>
141 <param name="bamFile" value="ENCFF325HFX.chr10_27035000_27050000.bam" ftype="bam" />
142 </repeat>
143 </repeat>
144 <param name="region" value="chr10:27040584-27048100" />
145 <param name="adv_opts_selector" value="advanced" />
146 <param name="min_coverage" value="10" />
147 <param name="color_levels" value="3" />
148 <param name="alpha" value="0.25" />
149 <param name="base_size" value="20" />
150 <param name="ann_height" value="4" />
151 <param name="height" value="3" />
152 <param name="width" value="18" />
153 <param name="overlay" value="True" />
154 <output name="plot" file="overlay_without_aggregation.pdf" ftype="pdf" />
155 </test>
156 <test>
157 <param name="gtf_file" value="annotation.gtf" ftype="gtf" />
158 <repeat name="rep_factor">
159 <param name="factorName" value="Endothelial" />
160 <repeat name="rep_sample">
161 <param name="sampleName" value="sample1" />
162 <param name="bamFile" value="ENCFF450AIU.chr10_27035000_27050000.bam" ftype="bam" />
163 </repeat>
164 <repeat name="rep_sample">
165 <param name="sampleName" value="sample2" />
166 <param name="bamFile" value="ENCFF914GVK.chr10_27035000_27050000.bam" ftype="bam" />
167 </repeat>
168 </repeat>
169 <repeat name="rep_factor">
170 <param name="factorName" value="Epithelial" />
171 <repeat name="rep_sample">
172 <param name="sampleName" value="sample3" />
173 <param name="bamFile" value="ENCFF756PUW.chr10_27035000_27050000.bam" ftype="bam" />
174 </repeat>
175 <repeat name="rep_sample">
176 <param name="sampleName" value="sample4"/>
177 <param name="bamFile" value="ENCFF325HFX.chr10_27035000_27050000.bam" ftype="bam" />
178 </repeat>
179 </repeat>
180 <param name="region" value="chr10:27040584-27048100" />
181 <param name="adv_opts_selector" value="advanced" />
182 <param name="color_levels" value="3" />
183 <param name="ann_height" value="3" />
184 <param name="height" value="3" />
185 <param name="overlay" value="True" />
186 <param name="agg" value="mean" />
187 <param name="shrink" value="True" />
188 <output name="plot" file="overlay_with_aggregation.pdf" ftype="pdf" />
189 </test>
190 </tests>
191 <help>
192
193 .. class:: infomark
194
195 **What it does**
196
197 Generate a sashimi plot from bam files in order to visualize splicing events.
198 </help>
199 <citations>
200 <citation type="doi">10.1371/journal.pcbi.1006360</citation>
201 </citations>
202 </tool>
203