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comparison plotdexseq.xml @ 11:577d1c8baab4 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
author iuc
date Mon, 14 Jan 2019 05:01:42 -0500
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children e5fe98b50c21
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10:6f684b3b0a6d 11:577d1c8baab4
1 <tool id="plotdexseq" name="plotDEXSeq" version="@VERSION@.0">
2 <description>Visualization of the per gene DEXSeq results</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements">
7 <requirement type="package" version="1.20.2">r-getopt</requirement>
8 </expand>
9 <version_command><![CDATA[
10 echo $(R --version | grep version | grep -v GNU)", DEXSeq version" $(R --vanilla --slave -e "library(DEXSeq); cat(sessionInfo()\$otherPkgs\$DEXSeq\$Version)" 2> /dev/null | grep -v -i "WARNING: ")" (depends on DESeq2 "$(R --vanilla --slave -e "library(DESeq2); cat(sessionInfo()\$otherPkgs\$DESeq2\$Version)" 2> /dev/null | grep -v -i "WARNING: ")")"
11 ]]></version_command>
12 <command detect_errors="exit_code"><![CDATA[
13 Rscript '$__tool_directory__/plotdexseq.R'
14 -r '$rdata'
15 -p '$primaryfactor'
16 #if $genes.genes_select == 'list':
17 -f '$genes.genefile'
18 #else:
19 -g '$genes.geneid'
20 #end if
21 -c $fdr_cutoff
22 -t $transcripts
23 -a $names
24 -n $normcounts
25 -s $splicing
26 ]]></command>
27 <inputs>
28 <param name="rdata" type="data" format="rdata" label="DEXSeqResults object" help="A DEXSeqResults object in RDS format. This can be output from the DEXSeq tool"/>
29 <param name="primaryfactor" type="text" value="FactorName" label="Specify the primary factor name in the DEXSeqResults object" help="Only letters, numbers and underscores will be retained in this field">
30 <sanitizer>
31 <valid initial="string.letters,string.digits"><add value="_" /></valid>
32 </sanitizer>
33 </param>
34 <conditional name="genes">
35 <param name="genes_select" type="select" label="Genes to plot" help="Select to input a single gene ID or a list of IDs. Default: single gene ID">
36 <option value="single" selected="True">single</option>
37 <option value="list">list</option>
38 </param>
39 <when value="single">
40 <param name="geneid" type="text" label="Gene identifier" help="Gene identifier to visualize">
41 <sanitizer>
42 <valid initial="string.letters,string.digits"><add value="_" /></valid>
43 </sanitizer>
44 </param>
45 </when>
46 <when value="list">
47 <param name="genefile" type="data" format="tabular" label="List of gene IDs" help="This should be a single tabular column with one gene per row and no header." />
48 </when>
49 </conditional>
50 <param name="fdr_cutoff" type="float" min="0.0" max="1.0" value="0.1" label="False Discovery Rate"/>
51 <param name="transcripts" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Display transcripts" help="If Yes, the transcripts are displayed in the plot. Default: No"/>
52 <param name="names" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Display transcript names" help="If Yes, the names of the transcripts are shown. Default: No"/>
53 <param name="normcounts" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Plot count values from the individual samples" help="If yes, provides a plot of the counts normalized by the size factors. Default: No"/>
54 <param name="splicing" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Plot exon usage" help="If yes, the samples gene expression effects are averaged out, leaving only exon usage coefficients. Default: No" />
55 </inputs>
56
57 <outputs>
58 <data name="dexseq_plot" format="pdf" from_work_dir="plot.pdf" label="${tool.name} on ${on_string}" />
59 </outputs>
60 <tests>
61 <!-- Ensure default output works-->
62 <test expect_num_outputs="1">
63 <param name="rdata" ftype="rdata" value="dexseq.rds"/>
64 <param name="primaryfactor" value="condition"/>
65 <param name="geneid" value="FBgn0000053"/>
66 <param name="fdr_cutoff" value="1"/>
67 <output name="dexseq_plot" ftype="pdf" file="plotdexseq.pdf" compare="sim_size"/>
68 </test>
69 <!-- Ensure plotting multiple genes works-->
70 <test expect_num_outputs="1">
71 <param name="rdata" ftype="rdata" value="dexseq.rds"/>
72 <param name="primaryfactor" value="condition"/>
73 <param name="genefile" ftype="tabular" value="plotdexseq_genes.tab"/>
74 <param name="fdr_cutoff" value="1"/>
75 <output name="dexseq_plot" ftype="pdf" file="plotdexseq_multi.pdf" compare="sim_size"/>
76 </test>
77 </tests>
78 <help><![CDATA[
79 .. class:: infomark
80
81 **What it does**
82
83 This tool enables visualization of DEXSeq results for individual genes. The input is a DEXSeqResults rds file, which can be output from the DEXSeq tool, and a single gene ID or list of IDs to plot.
84
85 .. _DEXSeq: http://master.bioconductor.org/packages/release/bioc/html/DEXSeq.html
86 ]]></help>
87 <citations>
88 <citation type="doi">10.1101/gr.133744.111</citation>
89 </citations>
90 </tool>