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comparison deseq2.xml @ 6:4939397c4706 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
author iuc
date Wed, 09 Nov 2016 17:00:31 -0500
parents d38fd393402e
children cb23006f34ff
comparison
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5:d38fd393402e 6:4939397c4706
1 <tool id="deseq2" name="DESeq2" version="2.1.8.4"> 1 <tool id="deseq2" name="DESeq2" version="2.11.38">
2 <description>Determines differentially expressed features from count tables</description> 2 <description>Determines differentially expressed features from count tables</description>
3 <requirements> 3 <requirements>
4 <!-- odering is crucial, otherwise R will override the ENV variables from deseq2 --> 4 <requirement type="package" version="1.12.4">bioconductor-deseq2</requirement>
5 <requirement type="package" version="1.20.0">r-getopt</requirement>
6 <requirement type="package" version="2.17.0">r-gplots</requirement>
7 <requirement type="package" version="0.2.15">r-rjson</requirement>
8 <requirement type="package" version="1.10.1">bioconductor-deseq2</requirement>
9 </requirements> 5 </requirements>
10 <stdio> 6 <stdio>
11 <regex match="Execution halted" 7 <regex match="Execution halted"
12 source="both" 8 source="both"
13 level="fatal" 9 level="fatal"
26 echo $(R --version | grep version | grep -v GNU)", DESeq2 version" $(R --vanilla --slave -e "library(DESeq2); cat(sessionInfo()\$otherPkgs\$DESeq2\$Version)" 2> /dev/null | grep -v -i "WARNING: ") 22 echo $(R --version | grep version | grep -v GNU)", DESeq2 version" $(R --vanilla --slave -e "library(DESeq2); cat(sessionInfo()\$otherPkgs\$DESeq2\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
27 ]]> 23 ]]>
28 </version_command> 24 </version_command>
29 <command> 25 <command>
30 <![CDATA[ 26 <![CDATA[
31 R -e 'library(DESeq2); sink("DESEQ2_ROOT_PATH"); cat(file.path(find.package("DESeq2"),"script","deseq2.R"))' && 27
28 #if $tximport.tximport_selector == 'tximport':
29 #if $tximport.mapping_format.mapping_format_selector == 'gtf':
30 ln -s '$tximport.mapping_format.gtf_file' mapping.gtf &&
31 #else:
32 ln -s '$tximport.mapping_format.tabular_file' mapping.txt &&
33 #end if
34 #end if
32 35
33 #import json 36 #import json
34 Rscript \$(cat DESEQ2_ROOT_PATH) 37 Rscript '${__tool_directory__}/deseq2.R'
35 -o "$deseq_out" 38 -o '$deseq_out'
36 #if $pdf: 39 #if $pdf:
37 -p "$plots" 40 -p '$plots'
41 #end if
42 #if $normCounts:
43 -n '$counts_out'
38 #end if 44 #end if
39 #set $temp_factor_names = list() 45 #set $temp_factor_names = list()
40 #for $factor in $rep_factorName: 46 #for $factor in $rep_factorName:
41 #set $temp_factor = list() 47 #set $temp_factor = list()
42 #for $level in $factor.rep_factorLevel: 48 #for $level in $factor.rep_factorLevel:
48 #end for 54 #end for
49 $temp_factor.reverse() 55 $temp_factor.reverse()
50 $temp_factor_names.append([str($factor.factorName), $temp_factor]) 56 $temp_factor_names.append([str($factor.factorName), $temp_factor])
51 #end for 57 #end for
52 -f '#echo json.dumps(temp_factor_names)#' 58 -f '#echo json.dumps(temp_factor_names)#'
53 -t "$fit_type" 59 -t '$fit_type'
54 #if $outlier_replace_off: 60 #if $outlier_replace_off:
55 -a 61 -a
56 #end if 62 #end if
57 #if $outlier_filter_off: 63 #if $outlier_filter_off:
58 -b 64 -b
60 #if $auto_mean_filter_off: 66 #if $auto_mean_filter_off:
61 -c 67 -c
62 #end if 68 #end if
63 #if $many_contrasts: 69 #if $many_contrasts:
64 -m 70 -m
71 #end if
72 #if $tximport.tximport_selector == 'tximport':
73 -i
74 #if $tximport.mapping_format.mapping_format_selector == 'gtf':
75 -x mapping.gtf
76 #else:
77 -x mapping.txt
78 #end if
79
65 #end if 80 #end if
66 ]]> 81 ]]>
67 </command> 82 </command>
68 <inputs> 83 <inputs>
69 <repeat name="rep_factorName" title="Factor" min="1"> 84 <repeat name="rep_factorName" title="Factor" min="1">
70 <param name="factorName" type="text" value="FactorName" label="Specify a factor name" 85 <param name="factorName" type="text" value="FactorName" label="Specify a factor name, e.g. effects_drug_x or cancer_markers"
71 help="Only letters, numbers and underscores will be retained in this field"> 86 help="Only letters, numbers and underscores will be retained in this field">
72 <sanitizer> 87 <sanitizer>
73 <valid initial="string.letters,string.digits"><add value="_" /></valid> 88 <valid initial="string.letters,string.digits"><add value="_" /></valid>
74 </sanitizer> 89 </sanitizer>
75 </param> 90 </param>
76 <repeat name="rep_factorLevel" title="Factor level" min="2" default="2"> 91 <repeat name="rep_factorLevel" title="Factor level" min="2" default="2">
77 <param name="factorLevel" type="text" value="FactorLevel" label="Specify a factor level" 92 <param name="factorLevel" type="text" value="FactorLevel" label="Specify a factor level, typical values could be 'tumor', 'normal', 'treated' or 'control'"
78 help="Only letters, numbers and underscores will be retained in this field"> 93 help="Only letters, numbers and underscores will be retained in this field">
79 <sanitizer> 94 <sanitizer>
80 <valid initial="string.letters,string.digits"><add value="_" /></valid> 95 <valid initial="string.letters,string.digits"><add value="_" /></valid>
81 </sanitizer> 96 </sanitizer>
82 </param> 97 </param>
83 <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts file(s)"/> 98 <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts file(s)"/>
84 </repeat> 99 </repeat>
85 </repeat> 100 </repeat>
101
102 <conditional name="tximport">
103 <param name="tximport_selector" type="select" label="Choice of Input data">
104 <option value="count" selected="True">Count data (e.g. from htseq-count or feature-count)</option>
105 <option value="tximport">TPM values (e.g. from sailfish or salmon)</option>
106 </param>
107 <when value="tximport">
108 <conditional name="mapping_format">
109 <param name="mapping_format_selector" type="select" label="Gene mapping format">
110 <option value="gtf" selected="True">GTF</option>
111 <option value="tabular">Transcript-ID and Gene-ID mapping file</option>
112 </param>
113 <when value="gtf">
114 <param name="gtf_file" type="data" format="gtf" label="GTF file with Transcript - Gene mapping"/>
115 </when>
116 <when value="tabular">
117 <param name="tabular_file" type="data" format="tabular" label="Tabular file with Transcript - Gene mapping"/>
118 </when>
119 </conditional>
120 </when>
121 <when value="count" />
122 </conditional>
86 <param name="pdf" type="boolean" truevalue="1" falsevalue="0" checked="true" 123 <param name="pdf" type="boolean" truevalue="1" falsevalue="0" checked="true"
87 label="Visualising the analysis results" 124 label="Visualising the analysis results"
88 help="output an additional PDF files" /> 125 help="output an additional PDF files" />
126 <param name="normCounts" type="boolean" truevalue="1" falsevalue="0" checked="false"
127 label="Output normalized counts table" />
89 <param name="many_contrasts" type="boolean" truevalue="1" falsevalue="0" checked="false" 128 <param name="many_contrasts" type="boolean" truevalue="1" falsevalue="0" checked="false"
90 label="Output all levels vs all levels of primary factor (use when you have >2 levels for primary factor)" 129 label="Output all levels vs all levels of primary factor (use when you have >2 levels for primary factor)"
91 help=" DESeq2 performs independent filtering by default using the mean of normalized counts as a filter statistic" /> 130 help=" DESeq2 performs independent filtering by default using the mean of normalized counts as a filter statistic" />
92 <param name="fit_type" type="select" label="Fit type"> 131 <param name="fit_type" type="select" label="Fit type">
93 <option value="1" selected="true">parametric</option> 132 <option value="1" selected="true">parametric</option>
108 help=" DESeq2 performs independent filtering by default using the mean of normalized counts as a filter statistic" /> 147 help=" DESeq2 performs independent filtering by default using the mean of normalized counts as a filter statistic" />
109 </inputs> 148 </inputs>
110 <outputs> 149 <outputs>
111 <data format="tabular" name="deseq_out" label="DESeq2 result file on ${on_string}"> 150 <data format="tabular" name="deseq_out" label="DESeq2 result file on ${on_string}">
112 <filter>many_contrasts is False</filter> 151 <filter>many_contrasts is False</filter>
152 <actions>
153 <action name="column_names" type="metadata" default="GeneID,Base mean,log2(FC),StdErr,Wald-Stats,P-value,P-adj" />
154 </actions>
113 </data> 155 </data>
114 <collection name="split_output" type="list" label="DESeq2 result files on ${on_string}"> 156 <collection name="split_output" type="list" label="DESeq2 result files on ${on_string}">
115 <filter>many_contrasts is True</filter> 157 <filter>many_contrasts is True</filter>
116 <discover_datasets pattern="None.(?P&lt;designation&gt;.+_vs_.+)" format="tabular" directory="." visible="false"/> 158 <discover_datasets pattern="None.(?P&lt;designation&gt;.+_vs_.+)" format="tabular" directory="." visible="false"/>
117 </collection> 159 </collection>
118 <data format="pdf" name="plots" label="DESeq2 plots on ${on_string}"> 160 <data format="pdf" name="plots" label="DESeq2 plots on ${on_string}">
119 <filter>pdf == True</filter> 161 <filter>pdf == True</filter>
120 </data> 162 </data>
163 <data format="tabular" name="counts_out" label="Normalized counts file on ${on_string}">
164 <filter>normCounts == True</filter>
165 </data>
121 </outputs> 166 </outputs>
122 <tests> 167 <tests>
123 <test> 168 <test>
124 <repeat name="rep_factorName"> 169 <repeat name="rep_factorName">
125 <param name="factorName" value="Treatment"/> 170 <param name="factorName" value="Treatment"/>
130 <repeat name="rep_factorLevel"> 175 <repeat name="rep_factorLevel">
131 <param name="factorLevel" value="Untreated"/> 176 <param name="factorLevel" value="Untreated"/>
132 <param name="countsFile" value="GSM461176_untreat_single.counts,GSM461177_untreat_paired.counts,GSM461178_untreat_paired.counts,GSM461182_untreat_single.counts"/> 177 <param name="countsFile" value="GSM461176_untreat_single.counts,GSM461177_untreat_paired.counts,GSM461178_untreat_paired.counts,GSM461182_untreat_single.counts"/>
133 </repeat> 178 </repeat>
134 </repeat> 179 </repeat>
135 <param name="pdf" value="no"/> 180 <param name="pdf" value="False"/>
136 <output name="deseq_out" file="deseq2_out.tab" compare="sim_size" delta="1000"/> 181 <param name="normCounts" value="True"/>
137 <output name="deseq_out_filtered" file="deseq2_out_filtered.tab" compare="sim_size" delta="1000"/> 182 <output name="counts_out" file="normalized_readcounts.tab"/>
183 <output name="deseq_out" file="deseq2_out.tab"/>
184 </test>
185 <test>
186 <repeat name="rep_factorName">
187 <param name="factorName" value="Treatment"/>
188 <repeat name="rep_factorLevel">
189 <param name="factorLevel" value="Treated"/>
190 <param name="countsFile" value="sailfish_quant_result1.tab,sailfish_quant_result2.tab"/>
191 </repeat>
192 <repeat name="rep_factorLevel">
193 <param name="factorLevel" value="Untreated"/>
194 <param name="countsFile" value="sailfish_quant_result3.tab,sailfish_quant_result4.tab"/>
195 </repeat>
196 </repeat>
197 <param name="pdf" value="False"/>
198 <param name="tximport_selector" value="tximport"/>
199 <param name="mapping_format_selector" value="gtf"/>
200 <param name="gtf_file" value="genes_sub.gtf"/>
201 <output name="deseq_out" file="deseq2_tximport_out.tab"/>
138 </test> 202 </test>
139 </tests> 203 </tests>
140 <help> 204 <help>
141 <![CDATA[ 205 <![CDATA[
142 .. class:: infomark 206 .. class:: infomark