Mercurial > repos > lecorguille > msnbase_readmsdata

comparison msnbase_readmsdata.xml @ 4:df53d666da13 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
author lecorguille
date Wed, 05 Sep 2018 05:56:03 -0400
parents fa17ee3bc9ce
children 8705b9de3e6c
comparison
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3:9581705d6578 4:df53d666da13
114 Workflow position 114 Workflow position
115 ----------------- 115 -----------------
116 116
117 **Upstream tools** 117 **Upstream tools**
118 118
119 ========================= ================= ======= ========= 119 ========================= ==========================================
120 Name output file format parameter 120 Name Format
121 ========================= ================= ======= ========= 121 ========================= ==========================================
122 NA NA zip NA 122 Upload File mzxml,mzml,mzdata,netcdf,no_unzip.zip,zip
123 ========================= ================= ======= ========= 123 ========================= ==========================================
124 124
125 The easier way to process is to create a Dataset Collection of the type List
125 126
126 **Downstream tools** 127 **Downstream tools**
127 128
128 =========================== ==================== ==================== 129 =========================== ==================== ====================
129 Name Output file Format 130 Name Output file Format
130 =========================== ==================== ==================== 131 =========================== ==================== ====================
131 xcms.findChromPeaks xset.RData rdata.msnbase.raw 132 xcms.findChromPeaks ``*``.raw.RData rdata.msnbase.raw
132 --------------------------- -------------------- --------------------
133 PCA ellipsoid by factors sampleMetadata.tsv Tabular
134 --------------------------- -------------------- --------------------
135 Anova sampleMetadata.tsv Tabular
136 =========================== ==================== ==================== 133 =========================== ==================== ====================
137 134
138 135
139 136
140 **Example of a metabolomic workflow** 137 **Example of a metabolomic workflow**
141 138
142 .. image:: mnsbase_readmsdata_workflow.png 139 .. image:: msnbase_readmsdata_workflow.png
143 140
144 --------------------------------------------------- 141 ---------------------------------------------------
145 142
146 143
147 144
216 213
217 ------------ 214 ------------
218 Output files 215 Output files
219 ------------ 216 ------------
220 217
221 sampleMetadata.tsv 218 xset.RData: rdata.msnbase.raw format
219
220 | Rdata file that is necessary in the second step of the workflow "xcms.findChromPeaks".
221
222 sampleMetadata.tsv (only when a zip is used)
222 223
223 | Tabular file that contains for each sample, it's associated class and polarity (positive,negative and mixed). 224 | Tabular file that contains for each sample, it's associated class and polarity (positive,negative and mixed).
224 | This file is necessary in the Anova and PCA step of the workflow. 225 | This file is necessary in the Anova and PCA step of the workflow.
225 226 | You get a sampleMetadata.tsv only if you use a zip. Otherwise, you have to provide one for the findChromPeaks Merger step
226 xset.RData: rdata.msnbase.raw format
227
228 | Rdata file that is necessary in the second step of the workflow "xcms.findChromPeaks".
229 227
230 --------------------------------------------------- 228 ---------------------------------------------------
231 229
232 Changelog/News 230 Changelog/News
233 -------------- 231 --------------