Mercurial > repos > lecorguille > xcms_retcor
annotate abims_xcms_retcor.xml @ 3:3b44991a8e05 draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
author | lecorguille |
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date | Mon, 25 Apr 2016 11:14:51 -0400 |
parents | 54cc3edfe35c |
children | ac93ed26e4e1 |
rev | line source |
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54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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1 <tool id="abims_xcms_retcor" name="xcms.retcor" version="2.0.6"> |
0 | 2 |
3 <description>Retention Time Correction using retcor function from xcms R package </description> | |
4 | |
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54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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5 <macros> |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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6 <import>macros.xml</import> |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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7 </macros> |
0 | 8 |
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54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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9 <expand macro="requirements"/> |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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10 <expand macro="stdio"/> |
0 | 11 |
1 | 12 <command><![CDATA[ |
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54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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13 @COMMAND_XCMS_SCRIPT@ |
1 | 14 image $image |
15 xfunction retcor | |
16 | |
17 xsetRdataOutput $xsetRData | |
18 ticspdf $ticsCorPdf | |
19 bicspdf $bpcsCorPdf | |
20 rplotspdf $rplotsPdf | |
21 | |
22 method $methods.method | |
0 | 23 #if $methods.method == "obiwarp": |
24 profStep $methods.profStep | |
25 #else | |
26 smooth $methods.smooth | |
27 extra $methods.extra | |
28 missing $methods.missing | |
29 #if $methods.options.option == "show": | |
30 span $methods.options.span | |
31 family $methods.options.family | |
32 plottype $methods.options.plottype | |
33 #end if | |
34 #end if | |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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35 #if $zip_file: |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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36 zipfile $zip_file |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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37 #end if |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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38 @COMMAND_LOG_EXIT@ |
1 | 39 ]]></command> |
0 | 40 |
41 <inputs> | |
42 <param name="image" type="data" format="rdata.xcms.raw,rdata.xcms.group,rdata" label="xset RData file" help="output file from another function xcms (xcmsSet, retcor etc.)" /> | |
43 <conditional name="methods"> | |
44 <param name="method" type="select" label="Method to use for retention time correction" help="[method] See the help section below" > | |
45 <option value="obiwarp" >obiwarp</option> | |
46 <option value="peakgroups" selected="peakgroups">peakgroups</option> | |
47 </param> | |
48 <when value="obiwarp"> | |
49 <param name="profStep" type="float" value="1" label="Step size (in m/z)" help="[profStep] to use for profile generation from the raw data files" /> | |
50 </when> | |
51 <when value="peakgroups"> | |
52 <param name="smooth" type="select" label="Smooth method" help="[smooth] either 'loess’ for non-linear alignment or ‘linear’ for linear alignment" > | |
53 <option value="loess">loess</option> | |
54 <option value="linear">linear</option> | |
55 </param> | |
56 <param name="extra" type="integer" value="1" label="Number of extra peaks to allow in retention time correction correction groups" help="[extra]" /> | |
57 <param name="missing" type="integer" value="1" label="Number of missing samples to allow in retention time correction groups" help="[missing]" /> | |
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54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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58 |
0 | 59 <conditional name="options"> |
60 <param name="option" type="select" label="Advanced options"> | |
61 <option value="show">show</option> | |
62 <option value="hide" selected="true">hide</option> | |
63 </param> | |
64 <when value="show"> | |
65 <param name="span" type="float" value="0.2" label="Degree of smoothing for local polynomial regression fitting" help="[span]"/> | |
66 | |
1 | 67 <param name="family" type="select" label="Family" help="[family] if gaussian fitting is by least-squares with no outlier removal, and if symmetric a re descending M estimator is used with Tukey's biweight function, allowing outlier removal"> |
68 <option value="gaussian" selected="true">gaussian</option> | |
69 <option value="symmetric">symmetric</option> | |
70 </param> | |
0 | 71 |
1 | 72 <param name="plottype" type="select" help="[plottype] if deviation plot retention time deviation points and regression fit, and if mdevden also plot peak overall peak density and retention time correction peak density"> |
0 | 73 <option value="none" selected="true">none</option> |
74 <option value="deviation">deviation</option> | |
75 <option value="mdevden">mdevden</option> | |
76 </param> | |
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54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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77 |
0 | 78 </when> |
1 | 79 <when value="hide"> |
80 </when> | |
0 | 81 </conditional> |
82 </when> | |
83 </conditional> | |
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54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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84 <!-- To pass planemo test --> |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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85 <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" help="Use only if you get a message which say that your original zip file have been deleted on the server." /> |
0 | 86 </inputs> |
87 | |
88 <outputs> | |
89 <data name="xsetRData" format="rdata.xcms.retcor" label="${image.name[:-6]}.retcor.RData" /> | |
90 <data name="rplotsPdf" format="pdf" label="${image.name[:-6]}.retcor.Rplots.pdf"> | |
91 <filter>(methods['method'] == 'peakgroups')</filter> | |
92 <filter>(options['option'] == 'show')</filter> | |
93 <filter>(family == 'symmetric')</filter> | |
94 <filter>(plottype != 'none')</filter> | |
95 </data> | |
96 <data name="ticsCorPdf" format="pdf" label="${image.name[:-6]}.retcor.TICs_corrected.pdf" /> | |
97 <data name="bpcsCorPdf" format="pdf" label="${image.name[:-6]}.retcor.BPCs_corrected.pdf" /> | |
1 | 98 <data name="log" format="txt" label="xset.log.txt" hidden="true" /> |
0 | 99 </outputs> |
100 | |
101 <tests> | |
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3b44991a8e05
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
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102 <!--<test> |
0 | 103 <param name="image" value="xset.group.RData"/> |
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54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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104 <param name="methods|method" value="peakgroups"/> |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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105 <param name="methods|smooth" value="loess"/> |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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106 <param name="methods|extra" value="1"/> |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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107 <param name="methods|missing" value="1"/> |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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108 <param name="methods|options|option" value="show"/> |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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109 <param name="methods|options|span" value="0.2"/> |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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110 <param name="methods|options|family" value="gaussian"/> |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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111 <param name="methods|options|plottype" value="deviation"/> |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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112 <param name="zip_file" value="sacuri_dir_root.zip" ftype="zip" /> |
1 | 113 <output name="log"> |
114 <assert_contents> | |
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54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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115 <has_text text="object with 4 samples" /> |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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116 <has_text text="Time range: 0.2-1140.1 seconds (0-19 minutes)" /> |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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117 <has_text text="Mass range: 50.0021-999.9863 m/z" /> |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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118 <has_text text="Peaks: 59359 (about 14840 per sample)" /> |
1 | 119 <has_text text="Peak Groups: 0" /> |
120 <has_text text="Sample classes: bio, blank" /> | |
121 </assert_contents> | |
122 </output> | |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
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123 </test>--> |
3b44991a8e05
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
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124 <test> |
3b44991a8e05
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
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125 <param name="image" value="faahKO.xset.group.RData"/> |
3b44991a8e05
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
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126 <param name="methods|method" value="peakgroups"/> |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
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127 <param name="methods|smooth" value="loess"/> |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
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128 <param name="methods|extra" value="1"/> |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
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129 <param name="methods|missing" value="1"/> |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
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130 <param name="methods|options|option" value="show"/> |
3b44991a8e05
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
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131 <param name="methods|options|span" value="0.2"/> |
3b44991a8e05
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
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132 <param name="methods|options|family" value="gaussian"/> |
3b44991a8e05
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
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133 <param name="methods|options|plottype" value="deviation"/> |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
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134 <param name="zip_file" value="faahKO_reduce.zip" ftype="zip" /> |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
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135 <output name="log"> |
3b44991a8e05
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
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136 <assert_contents> |
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137 <has_text text="object with 4 samples" /> |
3b44991a8e05
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
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138 <has_text text="Time range: 2507.7-4481.7 seconds (41.8-74.7 minutes)" /> |
3b44991a8e05
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
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139 <has_text text="Mass range: 200.1-600 m/z" /> |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
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140 <has_text text="Peaks: 9251 (about 2313 per sample)" /> |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
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141 <has_text text="Peak Groups: 0" /> |
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142 <has_text text="Sample classes: KO, WT" /> |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
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143 </assert_contents> |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
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144 </output> |
0 | 145 </test> |
146 </tests> | |
147 | |
1 | 148 <help><![CDATA[ |
0 | 149 |
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150 @HELP_AUTHORS@ |
0 | 151 |
152 =========== | |
153 Xcms.retcor | |
154 =========== | |
155 | |
156 ----------- | |
157 Description | |
158 ----------- | |
159 | |
160 After matching peaks into groups, xcms can use those groups to identify and correct | |
161 correlated drifts in retention time from run to run. The aligned peaks can then be | |
162 used for a second pass of peak grouping which will be more accurate than the first. | |
163 The whole process can be repeated in an iterative fashion. Not all peak groups will be helpful | |
164 for identifying retention time drifts. Some groups may be missing peaks from a large | |
165 fraction of samples and thus provide an incomplete picture of the drift at that time point. | |
166 Still others may contain multiple peaks from the same sample, which is a sign of impropper grouping. | |
167 | |
168 .. class:: warningmark | |
169 | |
170 **After an retcor step, it is mandatory to do a group step, otherwise the rest of the workflow will not work with the RData file. (the initial peak grouping becomes invalid and is | |
171 discarded)** | |
172 | |
173 | |
174 | |
175 ----------------- | |
176 Workflow position | |
177 ----------------- | |
178 | |
179 | |
180 **Upstream tools** | |
181 | |
182 ========================= ================= ======= ========== | |
183 Name output file format parameter | |
184 ========================= ================= ======= ========== | |
185 xcms.group xset.group.RData RData RData file | |
186 ========================= ================= ======= ========== | |
187 | |
188 | |
189 **Downstream tools** | |
190 | |
191 +---------------------------+------------------+--------+ | |
192 | Name | Output file | Format | | |
193 +===========================+==================+========+ | |
194 |xcms.group | xset.retcor.RData| RData | | |
195 +---------------------------+------------------+--------+ | |
196 | |
197 The output file **xset.retcor.RData** is an RData file. You can continue your analysis using it in **xcms.group** tool as an next step. | |
198 | |
199 | |
200 **General schema of the metabolomic workflow** | |
201 | |
202 .. image:: xcms_retcor_workflow.png | |
203 | |
204 | |
205 ----------- | |
206 Input files | |
207 ----------- | |
208 | |
209 +---------------------------+----------------------+ | |
210 | Parameter : num + label | Format | | |
211 +===========================+======================+ | |
212 | 1 : RData file | rdata.xcms.group | | |
213 +---------------------------+----------------------+ | |
214 | |
215 | |
216 ---------- | |
217 Parameters | |
218 ---------- | |
219 | |
220 Method | |
221 ------ | |
222 | |
223 **peakgroups** | |
224 | |
225 | xcms ignores those groups by only considering well-behaved peak groups which are missing at most one sample and have at most one extra peak. (Those values can be changed with the **missing** and **extra** arguments.) | |
226 | For each of those well-behaved groups, the algorithm calculates a median retention time and, for every sample, a deviation from that median. Within a sample, the observed deviation generally changes over time in a nonlinear fashion. Those changes are approximated using a local polynomial regression technique implemented in the **loess** function. By default, the curve fitting is done using least-squares on all data points. | |
227 | However, it is possible to enable outlier detection and removal by setting the **family** argument to **symmetric**. | |
228 | |
229 **obiwarp** | |
230 | |
231 | Calculate retention time deviations for each sample using the obiwarp code at "http://obi-warp.sourceforge.net/". This function is able to align multiple samples by a center-star strategy. Ordered Bijective Interpolated Warping (OBI-Warp) aligns matrices along a single axis using Dynamic Time Warping (DTW) and a one-to-one (bijective) interpolated warp function. OBI-Warp harnesses the non-linear, comprehensive alignment power of DTW and builds on the discrete, non-bijective output of DTW to give natural interpolants that can be used across multiple datasets. | |
232 | For the original publication see :**Chromatographic Alignment of ESI-LC-MS Proteomics Data Sets by Ordered Bijective Interpo-lated Warping John T. Prince and, Edward M. Marcotte Analytical Chemistry 2006 78 (17), 6140-6152.** | |
233 | |
234 | |
235 ------------ | |
236 Output files | |
237 ------------ | |
238 | |
239 xset.group.retcor.TICs_corrected.pdf | |
240 | |
241 | "Total Ion Chromatograms" graph in pdf format,corrected after a retcor step. | |
242 | |
243 xset.group.retcor.BPCs_corrected.pdf | |
244 | |
245 | "Total Io"Base Peak Chromatograms" graph in pdf format,corrected after a retcor step | |
246 | |
247 xset.group.retcor.RData: rdata.xcms.retcor format | |
248 | |
249 | Rdata file that will be necessary in the **xcms.group** step of the workflow. | |
250 | |
251 | |
252 ------ | |
253 | |
254 .. class:: infomark | |
255 | |
256 The output file is an xset.retcor.RData file. You can continue your analysis using it in **xcms.fillPeaks** tool. | |
257 | |
258 | |
259 --------------------------------------------------- | |
260 | |
261 --------------- | |
262 Working example | |
263 --------------- | |
264 | |
265 Input files | |
266 ----------- | |
267 | |
268 | RData file -> **xset.group.RData** | |
269 | |
270 Parameters | |
271 ---------- | |
272 | |
273 | Method: -> **peakgroups** | |
274 | smooth: -> **loess** | |
275 | extra: -> **1** | |
276 | missing -> **1** | |
277 | Advanced options: -> **show** | |
278 | span -> **0.2** | |
279 | family -> **gaussian** | |
280 | plottype -> **deviation** | |
281 | |
282 | |
283 Output files | |
284 ------------ | |
285 | |
286 | **1) xset.group.retcor.RData: RData file** | |
287 | |
288 | **2) Example of an xset.group.retcor.TICs_corrected pdf file** | |
289 | |
290 .. image:: xcms_retcor.png | |
291 | |
1 | 292 |
293 --------------------------------------------------- | |
294 | |
295 Changelog/News | |
296 -------------- | |
297 | |
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298 **Version 2.0.6 - 04/04/2016** |
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299 |
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300 - TEST: refactoring to pass planemo test using conda dependencies |
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301 |
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302 |
1 | 303 **Version 2.0.5 - 10/02/2016** |
304 | |
305 - BUGFIX: better management of errors. Datasets remained green although the process failed | |
306 | |
307 - BUGFIX: some pdf remained empty even when the process succeed | |
308 | |
309 - UPDATE: refactoring of internal management of inputs/outputs | |
310 | |
311 - UPDATE: refactoring to feed the new report tool | |
312 | |
313 | |
314 **Version 2.0.2 - 02/06/2015** | |
315 | |
316 - IMPROVEMENT: new datatype/dataset formats (rdata.xcms.raw, rdata.xcms.group, rdata.xcms.retcor ...) will facilitate the sequence of tools and so avoid incompatibility errors. | |
317 | |
318 - IMPROVEMENT: parameter labels have changed to facilitate their reading. | |
319 | |
320 | |
321 ]]></help> | |
0 | 322 |
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323 |
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324 <expand macro="citation" /> |
0 | 325 |
326 </tool> |