annotate plotdexseq.xml @ 10:df929f257179 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 2ea27822b171dbf519509dc1da150c8ccee2a140
author iuc
date Tue, 04 Apr 2023 08:25:51 +0000
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1 <tool id="plotdexseq" name="plotDEXSeq" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>Visualization of the per gene DEXSeq results</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="xrefs"/>
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7 <expand macro="requirements"/>
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8 <version_command><![CDATA[
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9 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: ")")"
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10 ]]></version_command>
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11 <command detect_errors="exit_code"><![CDATA[
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12 Rscript '$__tool_directory__/plotdexseq.R'
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13 -r '$rdata'
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14 -p '$primaryfactor'
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15 #if $genes.genes_select == 'list':
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16 -f '$genes.genefile'
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17 #else:
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18 -g '$genes.geneid'
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19 #end if
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20 -c $fdr_cutoff
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21 -t $transcripts
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22 -a $names
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23 -n $normcounts
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24 -s $splicing
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25 ]]></command>
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26 <inputs>
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27 <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"/>
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28 <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">
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29 <sanitizer>
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30 <valid initial="string.letters,string.digits"><add value="_" /></valid>
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31 </sanitizer>
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32 </param>
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33 <conditional name="genes">
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34 <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">
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35 <option value="single" selected="True">single</option>
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36 <option value="list">list</option>
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37 </param>
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38 <when value="single">
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39 <param name="geneid" type="text" label="Gene identifier" help="Gene identifier to visualize">
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40 <sanitizer>
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41 <valid initial="string.letters,string.digits"><add value="_" /></valid>
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42 </sanitizer>
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43 </param>
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44 </when>
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45 <when value="list">
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46 <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." />
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47 </when>
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48 </conditional>
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49 <param name="fdr_cutoff" type="float" min="0.0" max="1.0" value="0.1" label="False Discovery Rate"/>
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50 <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"/>
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51 <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"/>
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52 <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"/>
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53 <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" />
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54 </inputs>
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55
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56 <outputs>
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57 <data name="dexseq_plot" format="pdf" from_work_dir="plot.pdf" label="${tool.name} on ${on_string}" />
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58 </outputs>
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59 <tests>
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60 <!-- Ensure default output works-->
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61 <test expect_num_outputs="1">
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62 <param name="rdata" ftype="rdata" value="dexseq.rds"/>
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63 <param name="primaryfactor" value="condition"/>
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64 <param name="geneid" value="FBgn0000053"/>
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65 <param name="fdr_cutoff" value="1"/>
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66 <output name="dexseq_plot" ftype="pdf" file="plotdexseq.pdf" compare="sim_size"/>
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67 </test>
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68 <!-- Ensure plotting multiple genes works-->
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69 <test expect_num_outputs="1">
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70 <param name="rdata" ftype="rdata" value="dexseq.rds"/>
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71 <param name="primaryfactor" value="condition"/>
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72 <param name="genefile" ftype="tabular" value="plotdexseq_genes.tab"/>
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73 <param name="fdr_cutoff" value="1"/>
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74 <output name="dexseq_plot" ftype="pdf" file="plotdexseq_multi.pdf" compare="sim_size"/>
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75 </test>
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76 </tests>
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77 <help><![CDATA[
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78 .. class:: infomark
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79
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80 **What it does**
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81
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82 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.
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83
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84 .. _DEXSeq: http://master.bioconductor.org/packages/release/bioc/html/DEXSeq.html
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85 ]]></help>
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86 <citations>
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87 <citation type="doi">10.1101/gr.133744.111</citation>
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88 </citations>
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89 </tool>