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comparison ipo4retgroup.xml @ 7:dd0a593dded1 draft

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planemo upload commit c3ffcc9ea76a0e143e11613e6841ee59a28578fd
author lecorguille
date Wed, 12 Apr 2017 08:53:04 -0400
parents 03fdfbd914ab
children 364756ea5f42
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6:03fdfbd914ab 7:dd0a593dded1
2 2
3 <description>IPO optimization process for xcms.group and xcms.retcor</description> 3 <description>IPO optimization process for xcms.group and xcms.retcor</description>
4 4
5 <macros> 5 <macros>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
7
8 <macro name="group_density_bw_fixed">
9 <param name="bw" type="integer" value="30" label="Bandwidth" help="[bw] bandwidth (standard deviation or half width at half maximum) of gaussian smoothing kernel to apply to the peak density chromatogram" />
10 </macro>
11
12 <macro name="group_density_mzwid_fixed">
13 <param name="mzwid" type="float" value="0.25" label="Width of overlapping m/z slices" help="[mzwid] to use for creating peak density chromatograms and grouping peaks across samples " />
14 </macro>
7 </macros> 15 </macros>
8 16
9 <expand macro="requirements"/> 17 <expand macro="requirements"/>
10 <expand macro="stdio"/> 18 <expand macro="stdio"/>
11 19
22 30
23 ## group methods 31 ## group methods
24 32
25 sleep 0.001 33 sleep 0.001
26 #if $group.methods.method == "density": 34 #if $group.methods.method == "density":
27 bw "c($group.methods.bw)" 35 bw "c($group.methods.section_group_density_optiomizable.conditional_parameter.bw)"
28 minfrac "c($group.methods.minfrac)" 36 mzwid "c($group.methods.section_group_density_optiomizable.conditional_parameter.mzwid)"
29 mzwid "c($group.methods.mzwid)" 37
30 ## minsamp "c($group.methods.minsamp)" 38 minfrac $group.methods.section_group_density_non_optimizable.minfrac
31 #if $group.methods.density_options.option == "show": 39 max $group.methods.section_group_density_non_optimizable.max
32 max "c($group.methods.density_options.max)"
33 #end if
34 #end if 40 #end if
35
36
37 41
38 ## retcor methods 42 ## retcor methods
39 43
40 #if $retcor.methods.method == "obiwarp": 44 #if $retcor.methods.method == "obiwarp":
41 retcorMethod obiwarp 45 retcorMethod obiwarp
42 profStep "c($methods.profStep)" 46 profStep $methods.section_retcor_obiwarp_non_optimizable.profStep
43
44 ## $distFunc [1] "cor_opt"
45 ## $gapInit [1] 0.0 0.4
46 ## $gapExtend [1] 2.1 2.7
47 ## $$plottype [1] "none"
48 ## $response [1] 1
49 ## $factorDiag [1] 2
50 ## $factorGap [1] 1
51 ## $localAlignment [1] 0
52 47
53 #elif $retcor.methods.method == "peakgroups": 48 #elif $retcor.methods.method == "peakgroups":
54 ## smooth loess
55 retcorMethod loess 49 retcorMethod loess
56 smooth loess 50 smooth $retcor.methods.section_retcor_peakgroups_non_optimizable.smooth
57 extra "c($retcor.methods.extra)" 51 extra $retcor.methods.section_retcor_peakgroups_non_optimizable.extra
58 missing "c($retcor.methods.missing)" 52 missing $retcor.methods.section_retcor_peakgroups_non_optimizable.missing
59 #if $retcor.methods.options.option == "show": 53 span $retcor.methods.section_retcor_peakgroups_non_optimizable.span
60 span "c($retcor.methods.options.span)" 54 family $retcor.methods.section_retcor_peakgroups_non_optimizable.family
61 family "$retcor.methods.options.family" 55 plottype $retcor.methods.section_retcor_peakgroups_non_optimizable.plottype
62 plottype "$retcor.methods.options.plottype"
63 #end if
64 #elif $retcor.methods.method == "none": 56 #elif $retcor.methods.method == "none":
65 retcorMethod none 57 retcorMethod none
66 #end if 58 #end if
67 59
68 @COMMAND_FILE_LOAD@ 60 @COMMAND_FILE_LOAD@
74 66
75 <param name="image" type="data" format="rdata.xcms.raw,rdata.xcms.group,rdata.xcms.retcor,rdata" label="xset RData file" help="output file from another function xcms (xcmsSet, retcor etc.)" /> 67 <param name="image" type="data" format="rdata.xcms.raw,rdata.xcms.group,rdata.xcms.retcor,rdata" label="xset RData file" help="output file from another function xcms (xcmsSet, retcor etc.)" />
76 68
77 <param name="samplebyclass" type="integer" value="2" label="Number of samples used per class to estimate the best parameters" help="Set to 0 to use the whole dataset. To save time, reduce this number" /> 69 <param name="samplebyclass" type="integer" value="2" label="Number of samples used per class to estimate the best parameters" help="Set to 0 to use the whole dataset. To save time, reduce this number" />
78 70
79 <section name="group" title="Group Options" expanded="False"> 71 <section name="group" title="Group Options" expanded="True">
80
81 <conditional name="methods"> 72 <conditional name="methods">
82 <param name="method" type="select" label="Method to use for grouping" help="[method] See the help section below"> 73 <param name="method" type="select" label="Method to use for grouping" help="[method] See the help section below. Only the density method is available so far">
83 <option value="density" selected="true">density</option> 74 <option value="density" selected="true">density</option>
84 </param> 75 </param>
85 <when value="density"> 76 <when value="density">
86 <param name="bw" type="text" value="22,38" label="Range for Bandwidth" help="[bw] bandwidth (standard deviation or half width at half maximum) of gaussian smoothing kernel to apply to the peak density chromatogram (ex: 30 or 22,38)" /> 77 <section name="section_group_density_optiomizable" title="Optimizable parameters" expanded="True">
87 <param name="minfrac" type="text" value="0.3,0.7" label="Range for Minimum fraction of samples necessary" help="[minfrac] in at least one of the sample groups for it to be a valid group (ex: 0.5 or 0.3,0.7)" /> 78 <conditional name="conditional_parameter">
88 <param name="mzwid" type="text" value="0.015,0.035" label="Range for Width of overlapping m/z slices" help="[mzwid] to use for creating peak density chromatograms and grouping peaks across samples (ex: 0.25 or 0.015,0.035)" /> 79 <param name="select_parameter" type="select" label="Which parameter do you want to optimize?" help="Only one paramter can be optimized at once. The other will require fixed values">
89 <!-- 80 <option value="bw">Bandwidth [bw]</option>
90 <param name="minsamp" type="hidden" value="1" label="Range for Minimum number of samples necessary in at least one of the sample groups for it to be a valid group" help="[minsamp] (ex: 1 or 0,5" /> 81 <option value="mzwid">Width of overlapping m/z slices [mzwid]</option>
91 --> 82 </param>
92 <conditional name="density_options"> 83 <when value="bw">
93 <param name="option" type="select" label="Advanced options"> 84 <param name="bw" type="text" value="22,38" label="Range for Bandwidth" help="[bw] bandwidth (standard deviation or half width at half maximum) of gaussian smoothing kernel to apply to the peak density chromatogram (ex: 22,38)">
94 <option value="show">show</option> 85 <validator type="regex" message="Should be this format XX,YY">[0-9]+,[0-9]+</validator>
95 <option value="hide" selected="true">hide</option> 86 </param>
96 </param> 87 <expand macro="group_density_mzwid_fixed" />
97 <when value="show"> 88 </when>
98 <param name="max" type="text" value="50" label="Range for Maximum number of groups to identify in a single m/z slice" help="[max] (ex: 50 or 25,75)" /> 89 <when value="mzwid">
99 </when> 90 <param name="mzwid" type="text" value="0.015,0.035" label="Range for Width of overlapping m/z slices" help="[mzwid] to use for creating peak density chromatograms and grouping peaks across samples (ex: 0.015,0.035)" >
100 <when value="hide"> 91 <validator type="regex" message="Should be one combinaison of those format: XX,YY or -XX,YY or XX.XX,YY.YY">[\-]?[0-9]+[\.]?[0-9]*,[\-]?[0-9]+[\.]?[0-9]*</validator>
101 </when> 92 </param>
102 </conditional> 93 <expand macro="group_density_bw_fixed" />
103 94 </when>
95 </conditional>
96 </section>
97 <section name="section_group_density_non_optimizable" title="Non optimizable parameters" expanded="True">
98 <param name="minfrac" type="float" value="0.5" label="Minimum fraction of samples necessary" help="[minfrac] in at least one of the sample groups for it to be a valid group" />
99 <param name="max" type="integer" value="50" label="Maximum number of groups to identify in a single m/z slice" help="[max]" />
100 </section>
104 </when> 101 </when>
105 </conditional> 102 </conditional>
106
107
108 </section> 103 </section>
109 104
110 <section name="retcor" title="Retcor Options" expanded="False"> 105 <section name="retcor" title="Retcor Options" expanded="True">
111 <conditional name="methods"> 106 <conditional name="methods">
112 <param name="method" type="select" label="Method to use for retention time correction" help="[method] See the help section below" > 107 <param name="method" type="select" label="Method to use for retention time correction" help="[method] See the help section below" >
113 <option value="obiwarp">obiwarp</option> 108 <option value="obiwarp">obiwarp</option>
114 <option value="peakgroups">peakgroups</option> 109 <option value="peakgroups">peakgroups</option>
115 </param> 110 </param>
116 <when value="obiwarp"> 111 <when value="obiwarp">
117 <param name="profStep" type="text" value="0.7,1.0" label="Range for Step size (in m/z)" help="[profStep] to use for profile generation from the raw data files (ex: 1 or 0.7 1.0)" /> 112 <section name="section_retcor_obiwarp_non_optimizable" title="Non optimizable parameters" expanded="True">
118 <!-- 113 <param name="profStep" type="text" value="0.7,1.0" label="Range for Step size (in m/z)" help="[profStep] to use for profile generation from the raw data files (ex: 1 or 0.7 1.0)" />
119 ## $distFunc [1] "cor_opt" 114 </section>
120 ## $gapInit [1] 0.0 0.4
121 ## $gapExtend [1] 2.1 2.7
122 ## $$plottype [1] "none"
123 ## $response [1] 1
124 ## $factorDiag [1] 2
125 ## $factorGap [1] 1
126 ## $localAlignment [1] 0
127 -->
128 </when> 115 </when>
129 <when value="peakgroups"> 116 <when value="peakgroups">
130 <param name="smooth" type="select" label="Smooth method" help="[smooth] either 'loess’ for non-linear alignment or ‘linear’ for linear alignment" > 117 <section name="section_retcor_peakgroups_non_optimizable" title="Non optimizable parameters" expanded="True">
131 <option value="loess">loess</option> 118 <param name="smooth" type="select" label="Smooth method" help="[smooth] only the 'loess’ for non-linear alignment is available so far" >
132 </param> 119 <option value="loess">loess</option>
133 <param name="extra" type="text" value="1" label="Range for Number of extra peaks to allow in retention time correction correction groups" help="[extra] (ex: 1 or 1,3)" />
134 <param name="missing" type="text" value="1" label="Range for Number of missing samples to allow in retention time correction groups" help="[missing] (ex: 1or 1,3)" />
135
136 <conditional name="options">
137 <param name="option" type="select" label="Advanced options">
138 <option value="show">show</option>
139 <option value="hide" selected="true">hide</option>
140 </param> 120 </param>
141 <when value="show"> 121 <param name="extra" type="integer" value="1" label="Number of extra peaks to allow in retention time correction correction groups" help="[extra]" />
142 <param name="span" type="text" value="0.1,0.3" label="Range for Degree of smoothing for local polynomial regression fitting" help="[span] (ex: 0.2 or 0.1,0.3)"/> 122 <param name="missing" type="integer" value="1" label="Number of missing samples to allow in retention time correction groups" help="[missing]" />
143 <!-- @TODO multiple="true" --> 123 <param name="span" type="float" value="0.2" label="Degree of smoothing for local polynomial regression fitting" help="[span]"/>
144 <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"> 124 <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">
145 <option value="gaussian" selected="true">gaussian</option> 125 <option value="gaussian" selected="true">gaussian</option>
146 <option value="symmetric">symmetric</option> 126 <option value="symmetric">symmetric</option>
147 </param> 127 </param>
148 <!-- @TODO multiple="true" --> 128 <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">
149 <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"> 129 <option value="none" selected="true">none</option>
150 <option value="none" selected="true">none</option> 130 <option value="deviation">deviation</option>
151 <option value="deviation">deviation</option> 131 <option value="mdevden">mdevden</option>
152 <option value="mdevden">mdevden</option> 132 </param>
153 </param> 133 </section>
154
155 </when>
156 <when value="hide">
157 </when>
158 </conditional>
159 </when> 134 </when>
160 </conditional> 135 </conditional>
161 136
162 </section> 137 </section>
163 138
164 <expand macro="file_load"/> 139 <expand macro="input_file_load"/>
165 140
166 </inputs> 141 </inputs>
167 142
168 <outputs> 143 <outputs>
169 <data name="parametersOutput" format="tabular" label="IPO_parameters4xcmsSet.tsv" /> 144 <data name="parametersOutput" format="tabular" label="IPO_parameters4xcmsSet.tsv" />
180 <param name="group|methods|mzwid" value="0.15,0.35"/> 155 <param name="group|methods|mzwid" value="0.15,0.35"/>
181 <param name="retcor|methods|method" value="peakgroups"/> 156 <param name="retcor|methods|method" value="peakgroups"/>
182 <param name="retcor|methods|smooth" value="loess"/> 157 <param name="retcor|methods|smooth" value="loess"/>
183 <param name="retcor|methods|extra" value="1"/> 158 <param name="retcor|methods|extra" value="1"/>
184 <param name="retcor|methods|missing" value="1"/> 159 <param name="retcor|methods|missing" value="1"/>
185 <param name="file_load_conditional|file_load_select" value="yes" /> 160 <expand macro="test_file_load_zip"/>
186 <param name="file_load_conditional|inputs|zip_file" value="faahKO_reduce.zip" ftype="zip" />
187 <output name="parametersOutput" file="faahKO_IPO_parameters4retgroup.tsv" /> 161 <output name="parametersOutput" file="faahKO_IPO_parameters4retgroup.tsv" />
188 </test>--> 162 </test>-->
189 163
190 <test> 164 <test>
191 <param name="image" value="faahKO.xset.RData"/> 165 <param name="image" value="faahKO.xset.RData"/>
192 <param name="group|methods|method" value="density"/> 166 <section name="group">
193 <param name="group|methods|bw" value="28,32"/> 167 <conditional name="methods">
194 <param name="group|methods|minfrac" value="1"/> 168 <param name="method" value="density"/>
195 <param name="group|methods|mzwid" value="0.25"/> 169 <section name="section_group_density_optiomizable">
196 <param name="retcor|methods|method" value="peakgroups"/> 170 <conditional name="conditional_parameter">
197 <param name="retcor|methods|smooth" value="loess"/> 171 <param name="bw" value="28,32"/>
198 <param name="retcor|methods|extra" value="1"/> 172 <param name="mzwid" value="0.25"/>
199 <param name="retcor|methods|missing" value="1"/> 173 </conditional>
200 <param name="file_load_conditional|file_load_select" value="yes" /> 174 </section>
201 <param name="file_load_conditional|inputs|zip_file" value="faahKO_reduce.zip" ftype="zip" /> 175 <section name="section_group_density_non_optimizable">
176 <param name="minfrac" value="1"/>
177 </section>
178 </conditional>
179 </section>
180 <section name="retcor">
181 <conditional name="methods">
182 <param name="method" value="peakgroups"/>
183 <section name="section_retcor_peakgroups_non_optimizable">
184 <param name="smooth" value="loess"/>
185 <param name="rextra" value="1"/>
186 <param name="missing" value="1"/>
187 </section>
188 </conditional>
189 </section>
190 <expand macro="test_file_load_zip"/>
202 <output name="parametersOutput" file="faahKO_IPO_parameters4retgroup_bw.tsv" /> 191 <output name="parametersOutput" file="faahKO_IPO_parameters4retgroup_bw.tsv" />
203 </test> 192 </test>
204 193
205 <test> 194 <!--<test>
206 <param name="image" value="faahKO.xset.RData"/> 195 <param name="image" value="faahKO.xset.RData"/>
207 <param name="group|methods|method" value="density"/> 196 <param name="group|methods|method" value="density"/>
208 <param name="group|methods|bw" value="30"/> 197 <param name="group|methods|bw" value="30"/>
209 <param name="group|methods|minfrac" value="1"/> 198 <param name="group|methods|minfrac" value="1"/>
210 <param name="group|methods|mzwid" value="0.15,0.35"/> 199 <param name="group|methods|mzwid" value="0.15,0.35"/>
211 <param name="retcor|methods|method" value="peakgroups"/> 200 <param name="retcor|methods|method" value="peakgroups"/>
212 <param name="retcor|methods|smooth" value="loess"/> 201 <param name="retcor|methods|smooth" value="loess"/>
213 <param name="retcor|methods|extra" value="1"/> 202 <param name="retcor|methods|extra" value="1"/>
214 <param name="retcor|methods|missing" value="1"/> 203 <param name="retcor|methods|missing" value="1"/>
215 <param name="file_load_conditional|file_load_select" value="yes" /> 204 <expand macro="test_file_load_zip"/>
216 <param name="file_load_conditional|inputs|zip_file" value="faahKO_reduce.zip" ftype="zip" />
217 <output name="parametersOutput" file="faahKO_IPO_parameters4retgroup_mzmid.tsv" /> 205 <output name="parametersOutput" file="faahKO_IPO_parameters4retgroup_mzmid.tsv" />
218 </test> 206 </test>-->
219 207
220 <!--<test> 208 <!--<test>
221 <param name="image" value="MM-xset-merge.RData"/> 209 <param name="image" value="MM-xset-merge.RData"/>
222 <param name="group|methods|method" value="density"/> 210 <param name="group|methods|method" value="density"/>
223 <param name="group|methods|bw" value="22,38"/> 211 <param name="group|methods|bw" value="22,38"/>
226 <param name="retcor|methods|method" value="peakgroups"/> 214 <param name="retcor|methods|method" value="peakgroups"/>
227 <param name="retcor|methods|smooth" value="loess"/> 215 <param name="retcor|methods|smooth" value="loess"/>
228 <param name="retcor|methods|extra" value="1"/> 216 <param name="retcor|methods|extra" value="1"/>
229 <param name="retcor|methods|missing" value="1"/> 217 <param name="retcor|methods|missing" value="1"/>
230 <param name="file_load_conditional|file_load_select" value="yes" /> 218 <param name="file_load_conditional|file_load_select" value="yes" />
231 <param name="file_load_conditional|inputs|input" value="single_file" /> 219 <expand macro="test_file_load_single"/>
232 <param name="file_load_conditional|inputs|single_file" value="MM8.mzML,MM14.mzML" ftype="mzxml" />
233 <output name="parametersOutput" file="MM_IPO_parameters4retgroup.tsv" /> 220 <output name="parametersOutput" file="MM_IPO_parameters4retgroup.tsv" />
234 </test>--> 221 </test>-->
235 </tests> 222 </tests>
236 223
237 <help><![CDATA[ 224 <help><![CDATA[