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comparison run_de_analysis.xml @ 20:8d0bf0fceec1 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
author iuc
date Tue, 11 Apr 2023 19:41:06 +0000
parents ecc9243ba0f7
children 522092f3dfa4
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19:30a7f47090e2 20:8d0bf0fceec1
1 <tool id="trinity_run_de_analysis" name="Differential expression analysis" version="@WRAPPER_VERSION@"> 1 <tool id="trinity_run_de_analysis" name="Differential expression analysis" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
2 <description>using a Trinity assembly</description> 2 <description>using a Trinity assembly</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="bio_tools"/> 6 <expand macro="bio_tools"/>
7 <expand macro="requirements"> 7 <expand macro="requirements"/>
8 <requirement type="package" version="3.20.7">bioconductor-edger</requirement>
9 <requirement type="package" version="3.34.9">bioconductor-limma</requirement>
10 <requirement type="package" version="1.18.1">bioconductor-deseq2</requirement>
11 </expand>
12 <command detect_errors="aggressive"><![CDATA[ 8 <command detect_errors="aggressive"><![CDATA[
13 9
14 ln -f -s '${matrix}' "input.matrix" 10 ln -f -s '${matrix}' input.matrix
15
16 && 11 &&
17
18 run_DE_analysis.pl 12 run_DE_analysis.pl
19 13 --matrix input.matrix
20 --matrix "input.matrix" 14 --samples_file '${samples_file}'
21
22 --samples_file '${samples}'
23
24 --method ${method_choice.method} 15 --method ${method_choice.method}
25 16
26 #if $method_choice.method == "edgeR": 17 #if $method_choice.method == "edgeR":
27 --dispersion ${method_choice.edger_dispersion} 18 --dispersion ${method_choice.dispersion}
28 #end if 19 #end if
29 20
30 #if $method_choice.method == "ROTS": 21 #if $method_choice.method == "ROTS":
31 --ROTS_B ${method_choice.rots_b} 22 --ROTS_B ${method_choice.rots_b}
32 --ROTS_K ${method_choice.rots_k} 23 --ROTS_K ${method_choice.rots_k}
44 35
45 --output results 36 --output results
46 37
47 ]]></command> 38 ]]></command>
48 <inputs> 39 <inputs>
49 <param format="tabular" name="matrix" argument="--matrix" type="data" label="Expression matrix" help="output of Build expression matrix - matrix of raw read counts (not normalized!)"/> 40 <param argument="--matrix" format="tabular" type="data" label="Expression matrix" help="output of Build expression matrix - matrix of raw read counts (not normalized!)"/>
50 <param format="tabular" name="samples" argument="--samples_file" type="data" label="Sample description" help="file describing samples and replicates"/> 41 <param argument="--samples_file" format="tabular" type="data" label="Sample description" help="file describing samples and replicates"/>
51 42
52 <conditional name="method_choice"> 43 <conditional name="method_choice">
53 <param type="select" name="method" argument="--method" label="Differential analysis method"> 44 <param type="select" argument="--method" label="Differential analysis method">
54 <option value="edgeR">edgeR</option> 45 <option value="edgeR">edgeR</option>
55 <option value="DESeq2">DESeq2</option> 46 <option value="DESeq2">DESeq2</option>
56 <option value="voom">voom</option> 47 <option value="voom">voom</option>
57 <option value="ROTS">ROTS</option> 48 <option value="ROTS">ROTS</option>
58 </param> 49 </param>
59 <when value="edgeR"> 50 <when value="edgeR">
60 <param name="edger_dispersion" argument="--dispersion" type="float" value="0.1" label="edgeR dispersion value" help="Read edgeR manual to guide your value choice" /> 51 <param argument="--dispersion" type="float" value="0.1" label="edgeR dispersion value" help="Read edgeR manual to guide your value choice" />
61 </when> 52 </when>
62 <when value="ROTS"> 53 <when value="ROTS">
63 <param name="rots_b" argument="--ROTS_B" type="integer" value="500" label="number of bootstraps and permutation resampling" /> 54 <param name="rots_b" argument="--ROTS_B" type="integer" value="500" label="Number of bootstraps and permutation resampling" />
64 <param name="rots_k" argument="--ROTS_K" type="integer" value="5000" label="largest top genes size" /> 55 <param name="rots_k" argument="--ROTS_K" type="integer" value="5000" label="Largest top genes size" />
65 </when> 56 </when>
66 <when value="voom"> 57 <when value="voom"/>
67 </when> 58 <when value="DESeq2" />
68 <when value="DESeq2">
69 </when>
70 </conditional> 59 </conditional>
71 60
72 <section name="additional_params" title="Additional Options" expanded="False"> 61 <section name="additional_params" title="Additional Options" expanded="False">
73 <param name="min_cpm" type="integer" value="1" label="Minimum count per replicate" help="Only those rows of matrix meeting requirement will be tested"/> 62 <param name="min_cpm" type="integer" value="1" label="Minimum count per replicate" help="Only those rows of matrix meeting requirement will be tested"/>
74 <param name="min_reps" type="integer" value="2" label="Minimum number of replicates meeting minimum count per replicate" help="Only those rows of matrix meeting requirement will be tested"/> 63 <param name="min_reps" type="integer" value="2" label="Minimum number of replicates meeting minimum count per replicate" help="Only those rows of matrix meeting requirement will be tested"/>
75 <param name="reference_sample" argument="--reference_sample" type="text" optional="true" value="" label="Name of a sample to which all other samples should be compared" help="default is doing all pairwise-comparisons among samples"/> 64 <param argument="--reference_sample" type="text" optional="true" value="" label="Name of a sample to which all other samples should be compared" help="default is doing all pairwise-comparisons among samples"/>
76 <param format="tabular" name="contrasts" argument="--contrasts" optional="true" type="data" label="Pairs of sample comparisons to perform" help="A 2-column tabular with lists of pairs of samples to compare"/> 65 <param argument="--contrasts" optional="true" type="data" format="tabular" label="Pairs of sample comparisons to perform" help="A 2-column tabular with lists of pairs of samples to compare"/>
77 </section> 66 </section>
78 </inputs> 67 </inputs>
79 <outputs> 68 <outputs>
80 <collection name="DE_results" type="list" label="Differential expression results on ${on_string}"> 69 <collection name="DE_results" type="list" label="Differential expression results on ${on_string}">
81 <discover_datasets pattern="(?P&lt;name&gt;.+)\.DE_results$" ext="tabular" directory="results" /> 70 <discover_datasets pattern="(?P&lt;name&gt;.+)\.DE_results$" ext="tabular" directory="results" />
88 </collection> 77 </collection>
89 </outputs> 78 </outputs>
90 <tests> 79 <tests>
91 <test> 80 <test>
92 <param name="matrix" value="count/qcheck/matrix.counts.matrix"/> 81 <param name="matrix" value="count/qcheck/matrix.counts.matrix"/>
93 <param name="samples" value="count/samples.txt"/> 82 <param name="samples_file" value="count/samples.txt"/>
94 <param name="method" value="DESeq2"/> 83 <param name="method" value="DESeq2"/>
95 <output_collection name="DE_results"> 84 <output_collection name="DE_results">
96 <element name="input.matrix.wt_37_vs_wt_GSNO.DESeq2" compare="sim_size" file="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results"/> 85 <element name="input.matrix.wt_37_vs_wt_GSNO.DESeq2" compare="sim_size" file="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results"/>
97 <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2" compare="sim_size" file="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results"/> 86 <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2" compare="sim_size" file="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results"/>
98 <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2" compare="sim_size" file="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results"/> 87 <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2" compare="sim_size" file="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results"/>
108 <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf"/> 97 <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf"/>
109 </output_collection> 98 </output_collection>
110 </test> 99 </test>
111 <test> 100 <test>
112 <param name="matrix" value="count/qcheck/matrix.counts.matrix"/> 101 <param name="matrix" value="count/qcheck/matrix.counts.matrix"/>
113 <param name="samples" value="count/samples.txt"/> 102 <param name="samples_file" value="count/samples.txt"/>
114 <param name="method" value="edgeR"/> 103 <param name="method" value="edgeR"/>
115 <output_collection name="DE_results"> 104 <output_collection name="DE_results">
116 <element name="input.matrix.wt_37_vs_wt_GSNO.edgeR" compare="sim_size" file="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results"/> 105 <element name="input.matrix.wt_37_vs_wt_GSNO.edgeR" compare="sim_size" file="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results"/>
117 <element name="input.matrix.wt_37_vs_wt_ph8.edgeR" compare="sim_size" file="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.DE_results"/> 106 <element name="input.matrix.wt_37_vs_wt_ph8.edgeR" compare="sim_size" file="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.DE_results"/>
118 <element name="input.matrix.wt_GSNO_vs_wt_ph8.edgeR" compare="sim_size" file="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results"/> 107 <element name="input.matrix.wt_GSNO_vs_wt_ph8.edgeR" compare="sim_size" file="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results"/>
128 <element name="input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results.MA_n_Volcano.pdf"/> 117 <element name="input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results.MA_n_Volcano.pdf"/>
129 </output_collection> 118 </output_collection>
130 </test> 119 </test>
131 <test> 120 <test>
132 <param name="matrix" value="count/qcheck/matrix.counts.matrix"/> 121 <param name="matrix" value="count/qcheck/matrix.counts.matrix"/>
133 <param name="samples" value="count/samples.txt"/> 122 <param name="samples_file" value="count/samples.txt"/>
134 <param name="method" value="voom"/> 123 <param name="method" value="voom"/>
135 <output_collection name="DE_results"> 124 <output_collection name="DE_results">
136 <element name="input.matrix.wt_37_vs_wt_GSNO.voom" compare="sim_size" file="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.DE_results"/> 125 <element name="input.matrix.wt_37_vs_wt_GSNO.voom" compare="sim_size" file="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.DE_results"/>
137 <element name="input.matrix.wt_37_vs_wt_ph8.voom" compare="sim_size" file="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.DE_results"/> 126 <element name="input.matrix.wt_37_vs_wt_ph8.voom" compare="sim_size" file="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.DE_results"/>
138 <element name="input.matrix.wt_GSNO_vs_wt_ph8.voom" compare="sim_size" file="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results"/> 127 <element name="input.matrix.wt_GSNO_vs_wt_ph8.voom" compare="sim_size" file="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results"/>