Mercurial > repos > lecorguille > xcms_merge
comparison xcms_merge.xml @ 6:5c7a7484dc51 draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298
author | lecorguille |
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date | Tue, 13 Feb 2018 04:42:48 -0500 |
parents | 945652915244 |
children | dca722aecb67 |
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5:a4d1b79479a5 | 6:5c7a7484dc51 |
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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> |