Mercurial > repos > artbio > sashimi_plot

annotate sashimi_plot.xml @ 1:64aa67b5099f draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit acaadd44d1b24de272ea5cf31c2645570aa8fde9"
author artbio
date Mon, 26 Aug 2019 05:05:23 -0400
parents 9304dd9a16a2
children 964b974a5348
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9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
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1 <tool id="sashimi_plot" name="Sashimi plot" version="0.1.0">
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
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2 <description>: visualization of splicing events across multiple samples</description>
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
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3 <requirements>
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4 <requirement type="package" version="3">python</requirement>
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5 <requirement type="package" version="1.3">samtools</requirement>
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
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6 <requirement type="package" version="2.2.1=r3.4.1_0">r-ggplot2</requirement>
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
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7 <requirement type="package" version="1.10.4=r3.4.1_0">r-data.table</requirement>
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
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8 <requirement type="package" version="2.2.1=r3.4.1_0">r-gridextra</requirement>
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
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9 </requirements>
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
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10 <stdio>
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11 <exit_code range="1:" level="fatal" description="Tool exception" />
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
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12 </stdio>
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
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13 <command detect_errors="exit_code"><![CDATA[
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
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14 touch index_bams.tsv &&
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15 #for $factor in $rep_factor:
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
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16 #for $sample in $factor.rep_sample:
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
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17 echo -e '${sample.sampleName}\t${sample.bamFile}\t${factor.factorName}' >> index_bams.tsv &&
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18 samtools index ${sample.bamFile} &&
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19 #end for
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20 #end for
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21
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
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22 python $__tool_directory__/sashimi-plot.py
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
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23 -b index_bams.tsv
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
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24 -g ${gtf_file}
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
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25 -c ${region}
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
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26 #if $adv_opts.adv_opts_selector=="advanced":
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
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27 -M ${adv_opts.min_coverage}
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
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28 -C ${adv_opts.color_levels}
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
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29 -O ${adv_opts.overlap.overlay}
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
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30 #if $adv_opts.overlap.overlay=="3" and not $adv_opts.overlap.agg=="":
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
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31 -A ${adv_opts.overlap.agg}
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
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32 #end if
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
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33 ${adv_opts.shrink}
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34 --alpha ${adv_opts.alpha}
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35 --base-size=${adv_opts.base_size}
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36 --ann-height=${adv_opts.ann_height}
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
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37 --height=${adv_opts.height}
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38 --width=${adv_opts.width}
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
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39 #end if
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
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40 -o plot &&
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
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41 mv plot.pdf ${plot}
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42
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
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43 ]]></command>
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44 <inputs>
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45 <param format="gtf" name="gtf_file" type="data" label="Genome annotation" help="" />
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
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46 <repeat name="rep_factor" title="Genotype" min="1">
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47 <param name="factorName" label="Factor name" type="text" help="Specify a factor level, typical values could be 'HOM', 'HET'" />
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48 <repeat name="rep_sample" title="Bam file" min="1">
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49 <param name="sampleName" type="text" label="Sample Name" help="Track name on plot"/>
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
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50 <param name="bamFile" type="data" format="bam" multiple="false" label="Alignment File" help=""/>
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51 </repeat>
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52 </repeat>
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53 <conditional name="adv_opts">
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54 <param name="adv_opts_selector" type="select" label="Advanced Options">
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55 <option value="basic" selected="True">Hide Advanced Options</option>
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
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56 <option value="advanced">Show Advanced Options</option>
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57 </param>
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58 <when value="basic" />
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59 <when value="advanced">
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60 <param name="shrink" type="boolean" label="Intron shrinkage" truevalue="--shrink" falsevalue="" checked="false"
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61 help="Shrink the introns by a factor for nicer display"/>
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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]"/>
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63 <param name="color_levels" label="How to color samples ?" type="select">
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64 <option value="3" selected="True">By Genotype</option>
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65 <option value="1" >By Sample</option>
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66 </param>
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67 <conditional name="overlap">
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68 <param name="overlay" label="Overlay sample by Genotype ?" type="boolean" truevalue="3" falsevalue="1" checked="false" />
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69 <when value="3">
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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">
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71 <option value="" selected="True">No aggregation</option>
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72 <option value="mean" >Mean counts</option>
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73 <option value="median" >Median counts</option>
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74 <option value="mean_j" >Mean of counts supporting junctions</option>
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75 <option value="median_j" >Median of counts supporting junctions</option>
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76 </param>
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77 </when>
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78 <when value="1"/>
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79 </conditional>
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80 <param name="alpha" label="Transparency level for density histogram" type="float" value="0.5" help="default=0.5"/>
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81 <param name="base_size" label="Base font size" type="float" value="14" help="Base font size of the plot in pch [default=14]"/>
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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]"/>
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
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parents:
diff changeset
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]"/>
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
84 <param name="width" label="Width" type="float" value="10" help="Width of the plot in inches [default=10]"/>
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
85 </when>
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
86 </conditional>
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
87 <param name="region" type="text" help="Must be the following format : chromosome:start-end"/>
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
88 </inputs>
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
89 <outputs>
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
90 <data name="plot" format="pdf" label="Sashimi plot" />
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
91 </outputs>
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
92 <tests>
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
93 <test>
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
94 <param name="gtf_file" value="annotation.gtf" ftype="gtf" />
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
95 <repeat name="rep_factor">
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
96 <param name="factorName" value="Endothelial" />
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
97 <repeat name="rep_sample">
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
98 <param name="sampleName" value="sample1" />
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
99 <param name="bamFile" value="ENCFF450AIU.chr10_27035000_27050000.bam" ftype="bam" />
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
100 </repeat>
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
101 <repeat name="rep_sample">
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
102 <param name="sampleName" value="sample2" />
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
103 <param name="bamFile" value="ENCFF914GVK.chr10_27035000_27050000.bam" ftype="bam" />
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
104 </repeat>
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
105 </repeat>
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
106 <repeat name="rep_factor">
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
107 <param name="factorName" value="Epithelial" />
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
108 <repeat name="rep_sample">
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
109 <param name="sampleName" value="sample3" />
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
110 <param name="bamFile" value="ENCFF756PUW.chr10_27035000_27050000.bam" ftype="bam" />
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
111 </repeat>
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
112 <repeat name="rep_sample">
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
113 <param name="sampleName" value="sample4"/>
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
114 <param name="bamFile" value="ENCFF325HFX.chr10_27035000_27050000.bam" ftype="bam" />
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
115 </repeat>
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
116 </repeat>
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
117 <param name="region" value="chr10:27040584-27048100" />
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
118 <output name="plot" value="default.pdf" ftype="pdf" />
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
119 </test>
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
120 <test>
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
121 <param name="gtf_file" value="annotation.gtf" ftype="gtf" />
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
122 <repeat name="rep_factor">
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
123 <param name="factorName" value="Endothelial" />
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
124 <repeat name="rep_sample">
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
125 <param name="sampleName" value="sample1" />
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
126 <param name="bamFile" value="ENCFF450AIU.chr10_27035000_27050000.bam" ftype="bam" />
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
127 </repeat>
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
128 <repeat name="rep_sample">
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
129 <param name="sampleName" value="sample2" />
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
130 <param name="bamFile" value="ENCFF914GVK.chr10_27035000_27050000.bam" ftype="bam" />
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
131 </repeat>
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
132 </repeat>
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
133 <repeat name="rep_factor">
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
134 <param name="factorName" value="Epithelial" />
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
135 <repeat name="rep_sample">
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
136 <param name="sampleName" value="sample3" />
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
137 <param name="bamFile" value="ENCFF756PUW.chr10_27035000_27050000.bam" ftype="bam" />
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
138 </repeat>
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
139 <repeat name="rep_sample">
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
140 <param name="sampleName" value="sample4"/>
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
141 <param name="bamFile" value="ENCFF325HFX.chr10_27035000_27050000.bam" ftype="bam" />
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
142 </repeat>
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
143 </repeat>
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
144 <param name="region" value="chr10:27040584-27048100" />
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
145 <param name="adv_opts_selector" value="advanced" />
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
146 <param name="min_coverage" value="10" />
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
147 <param name="color_levels" value="3" />
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
148 <param name="alpha" value="0.25" />
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
149 <param name="base_size" value="20" />
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
150 <param name="ann_height" value="4" />
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
151 <param name="height" value="3" />
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
152 <param name="width" value="18" />
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
153 <param name="overlay" value="True" />
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
154 <output name="plot" file="overlay_without_aggregation.pdf" ftype="pdf" />
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
155 </test>
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
156 <test>
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
157 <param name="gtf_file" value="annotation.gtf" ftype="gtf" />
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
158 <repeat name="rep_factor">
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
159 <param name="factorName" value="Endothelial" />
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
160 <repeat name="rep_sample">
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
161 <param name="sampleName" value="sample1" />
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
162 <param name="bamFile" value="ENCFF450AIU.chr10_27035000_27050000.bam" ftype="bam" />
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
163 </repeat>
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
164 <repeat name="rep_sample">
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
165 <param name="sampleName" value="sample2" />
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
166 <param name="bamFile" value="ENCFF914GVK.chr10_27035000_27050000.bam" ftype="bam" />
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
167 </repeat>
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
artbio
parents:
diff changeset
168 </repeat>
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
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169 <repeat name="rep_factor">
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
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170 <param name="factorName" value="Epithelial" />
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
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171 <repeat name="rep_sample">
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
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172 <param name="sampleName" value="sample3" />
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
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173 <param name="bamFile" value="ENCFF756PUW.chr10_27035000_27050000.bam" ftype="bam" />
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
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174 </repeat>
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
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175 <repeat name="rep_sample">
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
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176 <param name="sampleName" value="sample4"/>
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
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177 <param name="bamFile" value="ENCFF325HFX.chr10_27035000_27050000.bam" ftype="bam" />
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
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178 </repeat>
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
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179 </repeat>
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
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180 <param name="region" value="chr10:27040584-27048100" />
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
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181 <param name="adv_opts_selector" value="advanced" />
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
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182 <param name="color_levels" value="3" />
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
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183 <param name="ann_height" value="3" />
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
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184 <param name="height" value="3" />
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
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185 <param name="overlay" value="True" />
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
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186 <param name="agg" value="mean" />
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
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187 <param name="shrink" value="True" />
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
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188 <output name="plot" file="overlay_with_aggregation.pdf" ftype="pdf" />
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
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189 </test>
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
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190 </tests>
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
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191 <help>
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
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192
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
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193 .. class:: infomark
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194
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
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195 **What it does**
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
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196
1
64aa67b5099f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit acaadd44d1b24de272ea5cf31c2645570aa8fde9"
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197 Generate a sashimi plot from bam files in order to visualize splicing events using ggsashimi.
0
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
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198 </help>
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
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199 <citations>
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
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200 <citation type="doi">10.1371/journal.pcbi.1006360</citation>
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
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201 </citations>
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
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202 </tool>
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"
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203