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comparison plotdexseq.xml @ 12:74ec758e63a4 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit ed4091f895ae0f46323534ca42da290c6e103598
author iuc
date Fri, 31 Jan 2025 18:00:45 +0000
parents df929f257179
children
comparison
equal deleted inserted replaced
11:9a7c5b6d8f1e 12:74ec758e63a4
20 -c $fdr_cutoff 20 -c $fdr_cutoff
21 -t $transcripts 21 -t $transcripts
22 -a $names 22 -a $names
23 -n $normcounts 23 -n $normcounts
24 -s $splicing 24 -s $splicing
25 #if $pl_width:
26 -w $pl_width
27 #end if
28 #if $pl_height:
29 -h $pl_height
30 #end if
25 ]]></command> 31 ]]></command>
26 <inputs> 32 <inputs>
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"/> 33 <param name="rdata" type="data" format="rds" label="DEXSeqResults object" help="A DEXSeqResults object in RDS format. This can be output from the DEXSeq tool"/>
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"> 34 <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">
29 <sanitizer> 35 <sanitizer>
30 <valid initial="string.letters,string.digits"><add value="_" /></valid> 36 <valid initial="string.letters,string.digits"><add value="_" /></valid>
31 </sanitizer> 37 </sanitizer>
32 </param> 38 </param>
36 <option value="list">list</option> 42 <option value="list">list</option>
37 </param> 43 </param>
38 <when value="single"> 44 <when value="single">
39 <param name="geneid" type="text" label="Gene identifier" help="Gene identifier to visualize"> 45 <param name="geneid" type="text" label="Gene identifier" help="Gene identifier to visualize">
40 <sanitizer> 46 <sanitizer>
41 <valid initial="string.letters,string.digits"><add value="_" /></valid> 47 <valid initial="string.letters,string.digits,string.punctuation"><add value="_" /></valid>
42 </sanitizer> 48 </sanitizer>
43 </param> 49 </param>
44 </when> 50 </when>
45 <when value="list"> 51 <when value="list">
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." /> 52 <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." />
49 <param name="fdr_cutoff" type="float" min="0.0" max="1.0" value="0.1" label="False Discovery Rate"/> 55 <param name="fdr_cutoff" type="float" min="0.0" max="1.0" value="0.1" label="False Discovery Rate"/>
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"/> 56 <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"/>
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"/> 57 <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"/>
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"/> 58 <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"/>
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" /> 59 <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" />
60 <param name="pl_width" type="integer" optional="true" value="" label="Width of the plot" help="In inches, Default: 7" />
61 <param name="pl_height" type="integer" optional="true" value="" label="Height of the plot" help="In inches, Default: 7" />
54 </inputs> 62 </inputs>
55 63
56 <outputs> 64 <outputs>
57 <data name="dexseq_plot" format="pdf" from_work_dir="plot.pdf" label="${tool.name} on ${on_string}" /> 65 <data name="dexseq_plot" format="pdf" from_work_dir="plot.pdf" label="${tool.name} on ${on_string}" />
58 </outputs> 66 </outputs>
59 <tests> 67 <tests>
60 <!-- Ensure default output works--> 68 <!-- Ensure default output works-->
61 <test expect_num_outputs="1"> 69 <test expect_num_outputs="1">
62 <param name="rdata" ftype="rdata" value="dexseq.rds"/> 70 <param name="rdata" ftype="rdata" value="dexseq.rds"/>
63 <param name="primaryfactor" value="condition"/> 71 <param name="primaryfactor" value="condition"/>
64 <param name="geneid" value="FBgn0000053"/> 72 <conditional name="genes">
73 <param name="genes_select" value="single" />
74 <param name="geneid" value="FBgn0000053"/>
75 </conditional>
65 <param name="fdr_cutoff" value="1"/> 76 <param name="fdr_cutoff" value="1"/>
66 <output name="dexseq_plot" ftype="pdf" file="plotdexseq.pdf" compare="sim_size"/> 77 <output name="dexseq_plot" ftype="pdf" file="plotdexseq.pdf" compare="sim_size"/>
67 </test> 78 </test>
68 <!-- Ensure plotting multiple genes works--> 79 <!-- Ensure plotting multiple genes works-->
69 <test expect_num_outputs="1"> 80 <test expect_num_outputs="1">
70 <param name="rdata" ftype="rdata" value="dexseq.rds"/> 81 <param name="rdata" ftype="rdata" value="dexseq.rds"/>
71 <param name="primaryfactor" value="condition"/> 82 <param name="primaryfactor" value="condition"/>
72 <param name="genefile" ftype="tabular" value="plotdexseq_genes.tab"/> 83 <conditional name="genes">
84 <param name="genes_select" value="list" />
85 <param name="genefile" ftype="tabular" value="plotdexseq_genes.tab"/>
86 </conditional>
73 <param name="fdr_cutoff" value="1"/> 87 <param name="fdr_cutoff" value="1"/>
74 <output name="dexseq_plot" ftype="pdf" file="plotdexseq_multi.pdf" compare="sim_size"/> 88 <output name="dexseq_plot" ftype="pdf" file="plotdexseq_multi.pdf" compare="sim_size"/>
89 </test>
90 <!-- Ensure plotting with non-default dimensions works-->
91 <test expect_num_outputs="1">
92 <param name="rdata" ftype="rdata" value="dexseq.rds"/>
93 <param name="primaryfactor" value="condition"/>
94 <conditional name="genes">
95 <param name="genes_select" value="list" />
96 <param name="genefile" ftype="tabular" value="plotdexseq_genes.tab"/>
97 </conditional>
98 <param name="fdr_cutoff" value="1"/>
99 <param name="pl_width" value="5"/>
100 <param name="pl_height" value="3"/>
101 <output name="dexseq_plot" ftype="pdf" file="plotdexseq_multi_custom_dim.pdf" compare="sim_size"/>
75 </test> 102 </test>
76 </tests> 103 </tests>
77 <help><![CDATA[ 104 <help><![CDATA[
78 .. class:: infomark 105 .. class:: infomark
79 106