comparison xcms_merge.xml @ 6:5c7a7484dc51 draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298
author lecorguille
date Tue, 13 Feb 2018 04:42:48 -0500
parents 945652915244
children dca722aecb67
comparison
equal deleted inserted replaced
5:a4d1b79479a5 6:5c7a7484dc51
1 <tool id="xcms_merge" name="xcms.xcmsSet Merger" version="1.0.0"> 1 <tool id="xcms_merge" name="xcms.xcmsSet Merger" version="1.1.0">
2 <description>Merge xcms.xcmsSet xset in one to be used by group</description> 2 <description>Merge xcms.xcmsSet xset in one to be used by group</description>
3 3
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
58 print(error_message) 58 print(error_message)
59 stop(error_message) 59 stop(error_message)
60 } 60 }
61 61
62 sampclass(xset)=sampleMetadata\$V2[match(rownames(xset@phenoData),sampleMetadata\$V1)] 62 sampclass(xset)=sampleMetadata\$V2[match(rownames(xset@phenoData),sampleMetadata\$V1)]
63
64 if (any(is.na(sampclass(xset)))) {
65 sample_missing <- rownames(phenoData(xset))[is.na(sampclass(xset))]
66 error_message <- paste("Those samples are missing in your sampleMetadata:", paste(sample_missing, collapse=" "))
67 print(error_message)
68 stop(error_message)
69 }
63 #end if 70 #end if
64 71
65 72
66 73
67 cat("\tXSET OBJECT INFO\n") 74 cat("\tXSET OBJECT INFO\n")
121 <has_text text="Peaks: 236 (about 118 per sample)" /> 128 <has_text text="Peaks: 236 (about 118 per sample)" />
122 <has_text text="Peak Groups: 0" /> 129 <has_text text="Peak Groups: 0" />
123 <has_text text="Sample classes: ." /> 130 <has_text text="Sample classes: ." />
124 </assert_stdout> 131 </assert_stdout>
125 </test> 132 </test>
133 <test expect_failure="True">
134 <param name="images" value="ko15-xset.RData,ko16-xset.RData,wt15-xset.RData,wt16-xset.RData" />
135 <param name="sampleMetadata" value="sampleMetadata_missing.tab" />
136 <expand macro="test_file_load_single"/>
137 <assert_stderr>
138 <has_text text="Those samples are missing in your sampleMetadata: ko16" />
139 </assert_stderr>
140 </test>
126 </tests> 141 </tests>
127 142
128 <help><![CDATA[ 143 <help><![CDATA[
129 144
130 @HELP_AUTHORS@ 145 @HELP_AUTHORS@
213 --------------------------------------------------- 228 ---------------------------------------------------
214 229
215 Changelog/News 230 Changelog/News
216 -------------- 231 --------------
217 232
233 **Version 1.0.1 - 13/02/2017**
234
235 - IMPROVMENT: the tool will now raise an error if a sample isn't describe in the sampleMetadata file
236
237
218 **Version 1.0.0 - 03/02/2017** 238 **Version 1.0.0 - 03/02/2017**
219 239
220 - NEW: a new tool to merge individual xcmsSet outputs to be used by xcms.group 240 - NEW: a new tool to merge individual xcmsSet outputs to be used by xcms.group
221 241
222 ]]></help> 242 ]]></help>