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comparison edger-repenrich.xml @ 13:530626b0757c draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit df6b9491ad06e8a85e67c663b68db3cce3eb0115
author artbio
date Tue, 02 Apr 2024 21:16:37 +0000
parents 6bba3e33c2e7
children
comparison
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12:89e05f831259 13:530626b0757c
1 <tool id="edger-repenrich" name="edgeR-repenrich" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> 1 <tool id="edger-repenrich" name="edgeR-repenrich" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>Determines differentially expressed features from RepEnrich counts</description> 2 <description>Determines differentially expressed features from RepEnrich counts</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="edgeR_requirements"/>
7 <stdio> 7 <stdio>
8 <regex match="Execution halted" 8 <regex match="Execution halted"
9 source="both" 9 source="both"
10 level="fatal" 10 level="fatal"
11 description="Execution halted." /> 11 description="Execution halted." />
44 $factorlevelsB.append(str($file)) 44 $factorlevelsB.append(str($file))
45 #end for 45 #end for
46 $factorlevelsB.reverse() 46 $factorlevelsB.reverse()
47 --levelBfiles '#echo json.dumps(factorlevelsB)#' 47 --levelBfiles '#echo json.dumps(factorlevelsB)#'
48 48
49 #set $alignedA = list()
50 #for file in $alignmentFiles_A:
51 $alignedA.append(str($file))
52 #end for
53 $alignedA.reverse()
54 --alignmentA '#echo json.dumps(alignedA)#'
55
56 #set $alignedB = list()
57 #for file in $alignmentFiles_B:
58 $alignedB.append(str($file))
59 #end for
60 $alignedB.reverse()
61 --alignmentB '#echo json.dumps(alignedB)#'
62
63 -o 'edger_out' 49 -o 'edger_out'
64 50
65 -p '$plots' 51 -p '$plots'
66 #if $normCounts: 52 #if $normCounts:
67 -n '$counts_out' 53 -n '$counts_out'
81 <sanitizer> 67 <sanitizer>
82 <valid initial="string.letters,string.digits"><add value="_" /></valid> 68 <valid initial="string.letters,string.digits"><add value="_" /></valid>
83 </sanitizer> 69 </sanitizer>
84 </param> 70 </param>
85 <param name="countsFiles_A" type="data" format="tabular" multiple="true" label="Counts file(s)" help="Count files must have been generated by repenrich" /> 71 <param name="countsFiles_A" type="data" format="tabular" multiple="true" label="Counts file(s)" help="Count files must have been generated by repenrich" />
86 <param name="alignmentFiles_A" type="data" format="tabular" multiple="true" label="Number of aligned reads file(s)" help="files of total aligned reads generated by repenrich"/>
87 <param name="factorLevel_B" type="text" value="FactorLevel2" label="Specify a factor level, typical values could be 'wildtype' or 'control'" 72 <param name="factorLevel_B" type="text" value="FactorLevel2" label="Specify a factor level, typical values could be 'wildtype' or 'control'"
88 help="Only letters, numbers and underscores will be retained in this field"> 73 help="Only letters, numbers and underscores will be retained in this field">
89 <sanitizer> 74 <sanitizer>
90 <valid initial="string.letters,string.digits"><add value="_" /></valid> 75 <valid initial="string.letters,string.digits"><add value="_" /></valid>
91 </sanitizer> 76 </sanitizer>
92 </param> 77 </param>
93 <param name="countsFiles_B" type="data" format="tabular" multiple="true" label="Counts file(s)" help="Count files must have been generated by repenrich tool" /> 78 <param name="countsFiles_B" type="data" format="tabular" multiple="true" label="Counts file(s)" help="Count files must have been generated by repenrich tool" />
94 <param name="alignmentFiles_B" type="data" format="tabular" multiple="true" label="Number of aligned reads file(s)" help="files of total aligned reads generated by repenrich"/>
95 <param name="normCounts" type="boolean" truevalue="1" falsevalue="0" checked="false" 79 <param name="normCounts" type="boolean" truevalue="1" falsevalue="0" checked="false"
96 label="Output normalized counts table" /> 80 label="Output normalized counts table" />
97 </inputs> 81 </inputs>
98 <outputs> 82 <outputs>
99 <data format="tabular" name="edger_out" label="edgeR: ${factorLevel_A} compared to ${factorLevel_B}"> 83 <data format="tabular" name="edger_out" label="edgeR: ${factorLevel_A} compared to ${factorLevel_B}">
109 <tests> 93 <tests>
110 <test expect_num_outputs="3"> 94 <test expect_num_outputs="3">
111 <param name="factorName" value="Genotype"/> 95 <param name="factorName" value="Genotype"/>
112 <param name="factorLevel_A" value="Mutant"/> 96 <param name="factorLevel_A" value="Mutant"/>
113 <param name="countsFiles_A" value="355_fraction_counts.tab,356_fraction_counts.tab"/> 97 <param name="countsFiles_A" value="355_fraction_counts.tab,356_fraction_counts.tab"/>
114 <param name="alignmentFiles_A" value="aligned_355.tab,aligned_356.tab"/>
115 <param name="factorLevel_B" value="Wildtype"/> 98 <param name="factorLevel_B" value="Wildtype"/>
116 <param name="countsFiles_B" value="353_fraction_counts.tab,354_fraction_counts.tab"/> 99 <param name="countsFiles_B" value="353_fraction_counts.tab,354_fraction_counts.tab"/>
117 <param name="alignmentFiles_B" value="aligned_353.tab,aligned_354.tab"/>
118 <param name="normCounts" value="True"/> 100 <param name="normCounts" value="True"/>
119 <output name="counts_out" file="Normalized_counts_file.tab"/> 101 <output name="counts_out" file="Normalized_counts_file.tab"/>
120 <output name="plots" file="edgeR_plots.pdf"/> 102 <output name="plots" file="edgeR_plots.pdf"/>
121 <output name="edger_out" file="edgeR_result_file.tab"/> 103 <output name="edger_out" file="edgeR_result_file.tab"/>
122 104
162 BEL_I-int LTR Pao 23757 144 BEL_I-int LTR Pao 23757
163 -------------- ---------- ---------- ---------- 145 -------------- ---------- ---------- ----------
164 Gypsy6_I-int LTR Gypsy 7489 146 Gypsy6_I-int LTR Gypsy 7489
165 ============== ========== ========== ========== 147 ============== ========== ========== ==========
166 148
167 Count tables must be 149 Count tables must be generated for each sample individually. Here, edgeR_ is handling a
168 generated for each sample individually. Here, edgeR_ is handling a single factor 150 single factor (genotype, age, treatment, etc) that effect your experiment. This factor has
169 (genotype, age, treatment, etc) that effect your experiment. This factor has two 151 two levels/states (for instance, "wild-type" and "mutant". You need to select appropriate
170 levels/states (for instance, "wild-type" and "mutant". 152 count table from your history for each factor level.
171 You need to select appropriate count table from your history for each factor level.
172 153
173 The following table gives some examples of factors and their levels: 154 The following table gives some examples of factors and their levels:
174 155
175 ========= ============== =============== 156 ========= ============== ===============
176 Factor Factorlevel1 Factorlevel2 157 Factor Factorlevel1 Factorlevel2
187 *Note*: Output log2 fold changes are based on primary factor level 1 vs. factor level2. 168 *Note*: Output log2 fold changes are based on primary factor level 1 vs. factor level2.
188 Here the order of factor levels is important. For example, for the factor 'Treatment' given 169 Here the order of factor levels is important. For example, for the factor 'Treatment' given
189 in above table, edgeR computes fold changes of 'Treated' samples against 'Untreated', 170 in above table, edgeR computes fold changes of 'Treated' samples against 'Untreated',
190 i.e. the values correspond to up or down regulations of genes in Treated samples. 171 i.e. the values correspond to up or down regulations of genes in Treated samples.
191 172
192 *Number of aligned reads*:
193
194 A file containing the number of reads aligned to transposons by repenrich must me provided
195 to edger-repenrich. This file is a single-column tabular file containing a single value.
196
197 **Output** 173 **Output**
198 174
199 edgeR_ generates a tabular file containing the different columns and results visualized in a PDF: 175 edgeR_ generates a tabular file containing the different columns and results visualized in
176 a PDF:
200 177
201 ====== ============================================================================= 178 ====== =============================================================================
202 Column Description 179 Column Description
203 ------ ----------------------------------------------------------------------------- 180 ------ -----------------------------------------------------------------------------
204 1 Tag (transposon element ID) 181 1 Tag (transposon element ID)
210 ====== ============================================================================= 187 ====== =============================================================================
211 188
212 .. _edgeR: http://www.bioconductor.org/packages/release/bioc/html/edgeR.html 189 .. _edgeR: http://www.bioconductor.org/packages/release/bioc/html/edgeR.html
213 ]]> 190 ]]>
214 191
215 **Note**: This edgeR_ wrapper was adapted from code available at https://github.com/nskvir/RepEnrich 192 **Note**: This edgeR_ wrapper was adapted from code available at
193 https://github.com/nskvir/RepEnrich
216 194
217 </help> 195 </help>
218 <citations> 196 <citations>
219 <citation type="doi">10.1093/bioinformatics/btp616</citation> 197 <citation type="doi">10.1093/bioinformatics/btp616</citation>
220 </citations> 198 </citations>