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comparison groupCorr.xml @ 0:cb57be5de070 draft default tip

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planemo upload commit 24d44ee26b7c23380c2b42fae2f7f6e58472100d
author workflow4metabolomics
date Sun, 24 Nov 2024 21:29:48 +0000
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1 <tool id="CAMERA_groupCorr" name="CAMERA.groupCorr" version="0.1.0+camera@TOOL_VERSION@-galaxy@VERSION_SUFFIX@" profile="23.0">
2
3 <description>EIC correlation grouping of LC/ESI-MS data</description>
4
5 <macros>
6 <import>macros.xml</import>
7 </macros>
8
9 <expand macro="requirements"/>
10
11 <required_files>
12 <include type="literal" path="CAMERA_groupCorr.R"/>
13 <include type="literal" path="lib.r"/>
14 </required_files>
15
16 <command detect_errors="exit_code"><![CDATA[
17 @COMMAND_RSCRIPT@CAMERA_groupCorr.R
18 image '$image'
19 cor_eic_th $cor_eic_th
20 pval $pval
21 graphMethod $graphMethod
22 calcIso $calcIso
23 calcCiS $calcCiS
24 calcCaS $calcCaS
25
26 #if $psg_list_block.psg_list_select == "FALSE":
27 psg_list NULL
28 #else
29 psg_list $psg_list
30 #end if
31
32 cor_exp_th $cor_exp_th
33 intval $intval
34 numDigitsMZ $numDigitsMZ
35 numDigitsRT $numDigitsRT
36 convertRTMinute $convertRTMinute
37
38 @COMMAND_FILE_LOAD@
39 ]]>
40 </command>
41
42 <inputs>
43 <param name="image" type="data" label="RData file" format="rdata" help="output file from another function xcms (fillPeaks)" />
44 <param name="cor_eic_th" type="float" value="0.75" max="1" min="0" label="Correlation threshold (0..1)" />
45 <param name="pval" type="float" value="0.05" max="1" min="0" label="Significant correlation threshold" />
46 <param name="graphMethod" type="select" label="Method selection for grouping peaks after correlation analysis into pseudospectra">
47 <option value="hcs" selected="true">hcs</option>
48 <option value="lpc">lpc</option>
49 </param>
50 <param name="calcIso" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Use isotopic relationship for peak grouping" />
51 <param name="calcCiS" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Use correlation inside samples for peak grouping" />
52 <param name="calcCaS" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Use correlation across samples for peak grouping" />
53 <param name="cor_exp_th" type="float" value="0.75" max="1" min="0" label="Threshold for intensity correlations across samples (0..1)" />
54 <param name="intval" type="select" label="Method selection for grouping peaks after correlation analysis into pseudospectra">
55 <option value="into" selected="true">into</option>
56 <option value="maxo">maxo</option>
57 <option value="intb">intb</option>
58 <!-- <option value="intf">intf</option>
59 <option value="maxf">maxf</option>
60 <option value="area">area</option> -->
61 </param>
62 <conditional name="psg_list_block">
63 <param name="psg_list_select" type="select" label="Use a personal psg_list">
64 <option value="TRUE">TRUE</option>
65 <option value="FALSE" selected="true">FALSE</option>
66 </param>
67 <when value="FALSE">
68 <!--<param name="psg_list" type="text" value="NULL" label="No psg_list" optional="true" />-->
69 </when>
70 <when value="TRUE">
71 <param name="psg_list" type="text" optional="true" label="Pseudospectra indices (optional)" help="Provide a comma-separated list of pseudospectra indices (e.g. 1,2,3)." />
72 </when>
73 </conditional>
74 <param name="convertRTMinute" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Convert seconds to minutes when exporting tsv" />
75 <param name="numDigitsMZ" type="integer" value="4" max="4" min="0" label="Number of digits for MZ values (namecustom)" />
76 <param name="numDigitsRT" type="integer" value="4" max="4" min="0" label="Number of digits for RT values (namecustom)" />
77 <expand macro="input_file_load"/>
78 </inputs>
79 <outputs>
80 <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.groupCorr.variableMetadata.tsv" from_work_dir="variableMetadata.tsv" />
81 <data name="camera_groupCorr_rdata" format="rdata" label="${image.name[:-6]}.groupCorr.RData" from_work_dir="camera_groupCorr.RData" />
82 </outputs>
83 <tests>
84 <test expect_num_outputs="2">
85 <param name="image" value="xset.merged.group.retcor.group.fillPeaks.fwhm.RData" />
86 <!--<param name="cor_eic_th" value="0.75" />
87 <param name="pval" value="0.05" />
88 <param name="graphMethod" value="hcs" />
89 <param name="calcIso" value="FALSE" />
90 <param name="calcCiS" value="TRUE" />
91 <param name="calcCaS" value="FALSE" />
92 <param name="cor_exp_th" value="0.75" />
93 <param name="intval" value="into" />-->
94 <expand macro="test_file_load_faahKO_15"/>
95 <output name="variableMetadata" file="xset.merged.group.retcor.group.fillPeaks.fwhm.groupCorr.variableMetadata.tsv" />
96 <output name="camera_groupCorr_rdata" value="xset.merged.group.retcor.group.fillPeaks.fwhm.groupCorr.RData" compare="sim_size" delta="5000" />
97 </test>
98 </tests>
99 <help><![CDATA[
100
101 ================
102 CAMERA.groupCorr
103 ================
104
105 -----------
106 Description
107 -----------
108
109 .. _link: https://bioconductor.org/packages/release/bioc/manuals/CAMERA/man/CAMERA.pdf
110
111 Peak grouping after correlation information into pseudospectrum groups for an xsAnnotate object.
112 Return an xsAnnotate object with grouping information. Click on the link to see the "Reference Manual" : link_ .
113
114 ---------------------------------------------------
115
116 ---------
117 Arguments
118 ---------
119
120 +----------------+---------------------------------------------------------------------------------------------------------------------------------------------+
121 | Variables | Descriptions |
122 +================+=============================================================================================================================================+
123 | object | the xsAnnotate object |
124 +----------------+---------------------------------------------------------------------------------------------------------------------------------------------+
125 | cor_eic_th | Correlation threshold for EIC correlation |
126 +----------------+---------------------------------------------------------------------------------------------------------------------------------------------+
127 | pval | p-value threshold for testing correlation of significance |
128 +----------------+---------------------------------------------------------------------------------------------------------------------------------------------+
129 | graphMethod | Clustering method for resulting correlation graph. See calcPC for more details. |
130 +----------------+---------------------------------------------------------------------------------------------------------------------------------------------+
131 | calcIso | Include isotope detection information for graph clustering |
132 +----------------+---------------------------------------------------------------------------------------------------------------------------------------------+
133 | calcCiS | Calculate correlation inside samples |
134 +----------------+---------------------------------------------------------------------------------------------------------------------------------------------+
135 | calcCaS | Calculate correlation across samples |
136 +----------------+---------------------------------------------------------------------------------------------------------------------------------------------+
137 | psg_list | Vector of pseudospectra indices. The correlation analysis will be only done for those groups |
138 +----------------+---------------------------------------------------------------------------------------------------------------------------------------------+
139 | xraw | Optional xcmsRaw object, which should be used for raw data extraction |
140 +----------------+---------------------------------------------------------------------------------------------------------------------------------------------+
141 | cor_exp_th | Threshold for intensity correlations across samples |
142 +----------------+---------------------------------------------------------------------------------------------------------------------------------------------+
143 | intval | Selection of the intensity values (such as "into") that should be used in the correlation analysis. See getPeaklist for all allowed values. |
144 +----------------+---------------------------------------------------------------------------------------------------------------------------------------------+
145
146 ---------------------------------------------------
147
148 ------------------------------------------
149 General schema of the metabolomic workflow
150 ------------------------------------------
151
152 .. image:: groupCorr.png
153
154 ---------------------------------------------------
155
156 -------
157 Details
158 -------
159
160 The algorithm calculates different informations for group peaks into so called pseudospectra. This pseudospectra contains peaks, with have a high correlation between each other. So far three different kind of information are available. Correlation of intensities across samples (need more than 3 samples), EIC correlation between peaks inside a sample and additional the informationen about recognized isotope cluster can be included. After calculation of all these informations, they are combined as edge value into a graph object. A following graph clustering algorithm separate the peaks (nodes in the graph) into the pseudospectra.
161
162 ---------------------------------------------------
163
164 --------------
165 Changelog/News
166 --------------
167
168 .. _News: https://bioconductor.org/packages/release/bioc/news/CAMERA/NEWS
169
170 @HELP_CAMERA_SUITE@
171
172 ]]> </help>
173
174 <expand macro="citation"/>
175 <expand macro="creator"/>
176 </tool>