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comparison mqppep_preproc.xml @ 5:b889e05ce77d draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit aa5f4a19e76ec636812865293b8ee9b196122121
author galaxyp
date Fri, 17 Feb 2023 22:38:40 +0000
parents b76c75521d91
children
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4:5c2beb4eb41c 5:b889e05ce77d
33 #end if 33 #end if
34 --phosphoCol '$phosphocol_script' 34 --phosphoCol '$phosphocol_script'
35 --startCol '$startcol_script' 35 --startCol '$startcol_script'
36 --intervalCol $intervalCol 36 --intervalCol $intervalCol
37 --localProbCutoff $localProbCutoff 37 --localProbCutoff $localProbCutoff
38 --collapse_func $collapse_func 38 --collapse_func $merge_function
39 -o '$phosphoPepIntensities' 39 -o '$phosphoPepIntensities'
40 --locProbCutoffGraph $locProbCutoffGraph 40 --locProbCutoffGraph $locProbCutoffGraph
41 --enrichGraph $enrichGraph 41 --enrichGraph $enrichGraph
42 --locProbCutoffGraph_svg $locProbCutoffGraph_svg 42 --locProbCutoffGraph_svg $locProbCutoffGraph_svg
43 --enrichGraph_svg $enrichGraph_svg 43 --enrichGraph_svg $enrichGraph_svg
119 help="Were samples enriched for pS and pT, or were they enriched for pY instead?" 119 help="Were samples enriched for pS and pT, or were they enriched for pY instead?"
120 > 120 >
121 <option value="st" selected="true">pST</option> 121 <option value="st" selected="true">pST</option>
122 <option value="y">pY</option> 122 <option value="y">pY</option>
123 </param> 123 </param>
124 <param name="collapse_func" type="select" 124 <param name="merge_function" type="select"
125 label="Intensity merge function" 125 label="Intensity merge function"
126 help="When a peptide is multiply phosphorylated, how should intensities be merged? [default: sum]" 126 help="When a peptide is multiply phosphorylated, how should intensities be merged? [default: sum]"
127 > 127 >
128 <option value="sum" selected="true">sum</option> 128 <option value="sum" selected="true">sum</option>
129 <option value="mean">average</option> 129 <option value="average">average</option>
130 </param> 130 </param>
131 <param name="localProbCutoff" type="float" value="0.75" min="0" max="1.0" 131 <param name="localProbCutoff" type="float" value="0.75" min="0" max="1.0"
132 label="Localization Probability Cutoff" 132 label="Localization Probability Cutoff"
133 help="See help below for an explanation." 133 help="See help below for an explanation."
134 /> 134 />
135 <param name="merge_function" type="select" label="intensity merge-function"
136 help="Specifies how intensities for identical phosphosites should be merged">
137 <option value="sum" selected="true">sum</option>
138 <option value="average">average</option>
139 </param>
140 <param name="protein_fasta" type="data" format="fasta" label="UniProtKB/SwissProt FASTA database" 135 <param name="protein_fasta" type="data" format="fasta" label="UniProtKB/SwissProt FASTA database"
141 help="Sequence database; supply the same FASTA file as you supplied to by MaxQuant" 136 help="Sequence database; supply the same FASTA file as you supplied to by MaxQuant"
142 /> 137 />
143 <param name="networkin" type="data" format="tabular" label="NetworKIN file" 138 <param name="networkin" type="data" format="tabular" label="NetworKIN file"
144 help="NetworKIN file; see help section below"/> 139 help="NetworKIN file; see help section below"/>
185 <param name="merge_function" value="sum"/> 180 <param name="merge_function" value="sum"/>
186 181
187 <param name="phosphoCol" value="^Number of Phospho [(][STY][STY]*[)]$"/> 182 <param name="phosphoCol" value="^Number of Phospho [(][STY][STY]*[)]$"/>
188 <param name="startCol" value="^Intensity[^_]"/> 183 <param name="startCol" value="^Intensity[^_]"/>
189 <param name="intervalCol" value="1"/> 184 <param name="intervalCol" value="1"/>
190 <param name="collapse_func" value="sum"/>
191 <param name="localProbCutoff" value="0.75"/> 185 <param name="localProbCutoff" value="0.75"/>
192 <param name="species" value="human"/> 186 <param name="species" value="human"/>
193 187
194 <output name="phosphoPepIntensities"> 188 <output name="phosphoPepIntensities">
195 <assert_contents> 189 <assert_contents>
250 <param name="merge_function" value="sum"/> 244 <param name="merge_function" value="sum"/>
251 245
252 <param name="phosphoCol" value="^Number of Phospho [(][STY][STY]*[)]$"/> 246 <param name="phosphoCol" value="^Number of Phospho [(][STY][STY]*[)]$"/>
253 <param name="startCol" value="^Intensity[^_]"/> 247 <param name="startCol" value="^Intensity[^_]"/>
254 <param name="intervalCol" value="1"/> 248 <param name="intervalCol" value="1"/>
255 <param name="collapse_func" value="sum"/>
256 <param name="localProbCutoff" value="0.75"/> 249 <param name="localProbCutoff" value="0.75"/>
257 <param name="species" value="human"/> 250 <param name="species" value="human"/>
258 251
259 <output name="phosphoPepIntensities"> 252 <output name="phosphoPepIntensities">
260 <assert_contents> 253 <assert_contents>
353 346
354 Localization probability cutoff 347 Localization probability cutoff
355 Minimum localization probability; see above. 348 Minimum localization probability; see above.
356 349
357 Intensity merge-function 350 Intensity merge-function
358 Specifies how intensities for identical phosphosites should be merged; see above. 351 Specifies how intensities for identical phosphosites should be merged. Choosing "sum" means that relative intensities reflect number of phospho-*residues*; choosing "average" means that relative intensities reflect number of phospho-*peptides*.
359 352
360 Output datasets 353 Output datasets
361 =============== 354 ===============
362 355
363 ``ppep_intensities`` 356 ``ppep_intensities``