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comparison ramclustr.xml @ 4:050cfef6ba65 draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
author recetox
date Thu, 15 Jun 2023 14:01:48 +0000
parents 2ec9253a647e
children 2410de08b55a
comparison
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3:2ec9253a647e 4:050cfef6ba65
1 <tool id="ramclustr" name="RAMClustR" version="@TOOL_VERSION@+galaxy2"> 1 <tool id="ramclustr" name="RAMClustR" version="@TOOL_VERSION@+galaxy0" profile="21.09">
2 <description>A feature clustering algorithm for non-targeted mass spectrometric metabolomics data.</description> 2 <description>A feature clustering algorithm for non-targeted mass spectrometric metabolomics data.</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="creator"/> 6 <expand macro="creator"/>
7 7
8 <requirements> 8 <requirements>
9 <requirement type="package" version="@TOOL_VERSION@">r-ramclustr</requirement> 9 <requirement type="package" version="@TOOL_VERSION@">r-ramclustr</requirement>
10 <requirement type="package" version="3.14.0">bioconductor-xcms</requirement> 10 <requirement type="package" version="3.20.0">bioconductor-xcms</requirement>
11 <requirement type="package" version="9.0.0">r-arrow</requirement>
11 </requirements> 12 </requirements>
12 13
13 <command detect_errors="aggressive"><![CDATA[ 14 <command detect_errors="exit_code"><![CDATA[
14 Rscript 15 Rscript
15 -e 'source("${__tool_directory__}/ramclustr_wrapper.R")' 16 -e 'source("${__tool_directory__}/ramclustr_wrapper.R")'
16 -e 'source("${ramclustr_method}")' 17 -e 'source("${ramclustr_method}")'
17 ]]> 18 ]]>
18 </command> 19 </command>
19 <configfiles> 20 <configfiles>
20 <configfile name="ramclustr_method"> 21 <configfile name="ramclustr_method">
22 #if $filetype.type_choice == "xcms":
23 obj = load("$filetype.xcms.input_xcms")
24 ramclustObj = RAMClustR::rc.get.xcms.data(
25 xcmsObj = xdata,
26 #if $extras.ExpDes:
27 ExpDes = load_experiment_definition("${$extras.ExpDes}"),
28 #end if
29 mzdec = $msp_output_details.mzdec,
30 ensure.no.na = $extras.replace_zeros
31 )
32 #else if $filetype.type_choice == "csv":
33 ramclustObj = RAMClustR::rc.get.csv.data(
34 csv = "$filetype.ms_csv.ms",
35 #if $filetype.ms_csv.idmsms:
36 idmsms = "$filetype.ms_csv.idmsms",
37 #end if
38 #if $filetype.ms_csv.csv_phenoData:
39 phenoData = "$filetype.ms_csv.csv_phenoData",
40 #end if
41 #if $extras.ExpDes:
42 ExpDes = load_experiment_definition("${$extras.ExpDes}"),
43 #end if
44 st = $filetype.required.st,
45 ensure.no.na = $extras.replace_zeros
46 )
47 #else if $filetype.type_choice == "recetox-aplcms":
48 ramclustObj = read_ramclustr_aplcms(
49 ms1_featuredefinitions = "$filetype.ms_dataframe.ms1_featureDefinitions",
50 ms1_featurevalues = "$filetype.ms_dataframe.ms1_featureValues",
51 #if $filetype.ms_dataframe.df_phenoData:
52 df_phenodata = "$filetype.ms_dataframe.df_phenoData",
53 phenodata_ext = "${filetype.ms_dataframe.df_phenoData.ext}",
54 #end if
55 #if $extras.ExpDes:
56 exp_des = "${$extras.ExpDes}",
57 #end if
58 st = $filetype.required.st,
59 ensure_no_na = $extras.replace_zeros
60 )
61 #end if
62
63 #if $extras.replace_zeros == "TRUE":
64 ramclustObj = RAMClustR::rc.feature.replace.na(ramclustObj = ramclustObj)
65 #end if
66
67 #if $normalisation.normalisation_method.normalize != "none":
68 ramclustObj = apply_normalisation(
69 ramclustr_obj = ramclustObj,
70 #if $normalisation.normalisation_method.normalize == "batch.qc":
71 metadata_file = "${$normalisation.normalisation_method.batch_order_qc}",
72 qc_inj_range = $normalisation.normalisation_method.qc_inj_range,
73 #end if
74 #if $normalisation.normalisation_method.normalize == "qc":
75 metadata_file = "${$normalisation.normalisation_method.batch_order_qc}",
76 p_cut = $normalisation.normalisation_method.p_cut,
77 rsq_cut = $normalisation.normalisation_method.rsq_cut,
78 p_adjust = $normalisation.normalisation_method.p_adjust,
79 #end if
80 normalize_method = "$normalisation.normalisation_method.normalize"
81 )
82 #end if
83
84 ramclustObj = RAMClustR::rc.ramclustr(
85 ramclustObj = ramclustObj,
86 st = $filetype.required.st,
87 sr = $filetype.required.sr,
88 maxt = $filetype.required.maxt,
89 deepSplit = $clustering.deepSplit,
90 blocksize = $performance.blocksize,
91 mult = $performance.mult,
92 hmax = $clustering.hmax,
93 minModuleSize = $clustering.minModuleSize,
94 linkage = "$clustering.linkage",
95 cor.method = "$filetype.required.cor_method",
96 rt.only.low.n = $extras.rt_only_low_n,
97 fftempdir = NULL,
98 )
99
21 store_output( 100 store_output(
22 #if $filetype.type_choice == "xcms": 101 ramclustr_obj = ramclustObj,
23 ramclustr_xcms( 102 output_merge_msp = $msp_output_details.merge_msp,
24 input_xcms = "$filetype.xcms.input_xcms", 103 output_spec_abundance = "$spec_abundance",
25 use_pheno = $filetype.xcms.usePheno, 104 #if $msp_output_details.merge_msp:
105 msp_file = "$mass_spectra_merged"
26 #else: 106 #else:
27 ramclustr_csv( 107 msp_file = NULL
28 ms = "$filetype.ms_csv.ms", 108 #end if
29 idmsms = "$filetype.ms_csv.idmsms", 109 )
30 #end if
31 sr = $filetype.required.sr,
32 #if $filetype.type_choice == "xcms":
33 #if $filetype.required.st
34 st = $filetype.required.st,
35 #end if
36 #else:
37 st = $filetype.required.st,
38 #end if
39 cor_method = "$filetype.required.cor_method",
40 maxt = $filetype.required.maxt,
41 linkage = "$clustering.linkage",
42 min_module_size = $clustering.minModuleSize,
43 hmax = $clustering.hmax,
44 deep_split = "$clustering.deepSplit",
45 normalize = "$normalisation.normalisation_method.normalize",
46 #if "$normalisation.normalisation_method.normalize" == "batch.qc":
47 metadata_file = "$normalisation.normalisation_method.batch_order_qc",
48 qc_inj_range = $normalisation.normalisation_method.qc_inj_range,
49 #end if
50 block_size = $performance.blocksize,
51 mult = $performance.mult,
52 mzdec = $msp_output_details.mzdec,
53 rt_only_low_n = $extras.rt_only_low_n,
54 replace_zeros = $extras.replace_zeros,
55 #if $extras.ExpDes:
56 exp_design = "${$extras.ExpDes}"
57 #end if
58 ),
59 $msp_output_details.merge_msp,
60 "$spec_abundance",
61 #if $msp_output_details.merge_msp:
62 "$mass_spectra_merged"
63 #else:
64 NULL
65 #end if
66 )
67 </configfile> 110 </configfile>
68 </configfiles> 111 </configfiles>
69 <inputs> 112 <inputs>
70 <conditional name="filetype"> 113 <conditional name="filetype">
71 <param name="type_choice" type="select" label="Choose input format:"> 114 <param name="type_choice" type="select" label="Choose input format:">
72 <option value="xcms" selected="true">XCMS</option> 115 <option value="xcms" selected="true">XCMS</option>
73 <option value="csv">CSV</option> 116 <option value="csv">CSV</option>
117 <option value="recetox-aplcms">RECETOX-APLCMS</option>
74 </param> 118 </param>
75 <when value="xcms"> 119 <when value="xcms">
76 <expand macro="parameters_xcms" /> 120 <expand macro="parameters_xcms" />
77 <section name="required" title="General parameters" expanded="true"> 121 <section name="required" title="General parameters" expanded="true">
78 <param label="Sigma t" name="st" type="float" optional="true" help="Retention time similarity (optional). 122 <param label="Sigma t" name="st" type="float" optional="true" help="Retention time similarity (optional).
86 <param label="Sigma t" name="st" type="float" value="1" help="Retention time similarity. 130 <param label="Sigma t" name="st" type="float" value="1" help="Retention time similarity.
87 A recommended starting point is half the value of your average chromatographic peak width at half max (seconds))."/> 131 A recommended starting point is half the value of your average chromatographic peak width at half max (seconds))."/>
88 <expand macro="parameters_required" /> 132 <expand macro="parameters_required" />
89 </section> 133 </section>
90 </when> 134 </when>
135 <when value="recetox-aplcms">
136 <expand macro="parameters_recetox_aplcms" />
137 <section name="required" title="General parameters" expanded="true">
138 <param label="Sigma t" name="st" type="float" value="1" help="Retention time similarity.
139 A recommended starting point is half the value of your average chromatographic peak width at half max (seconds))."/>
140 <expand macro="parameters_required" />
141 </section>
142 </when>
91 </conditional> 143 </conditional>
92 <expand macro="main_parameters" /> 144 <expand macro="main_parameters" />
93 </inputs> 145 </inputs>
94 146
95 <outputs> 147 <outputs>
106 </section> 158 </section>
107 <section name="required"> 159 <section name="required">
108 <param name="maxt" value="259.8"/> 160 <param name="maxt" value="259.8"/>
109 </section> 161 </section>
110 </section> 162 </section>
163 <section name="msp_output_details">
164 <param name="mzdec" value="4"/>
165 </section>
111 <section name="extras"> 166 <section name="extras">
112 <param name="ExpDes" value="lc-ramclustr-define-experiment.csv" ftype="csv"/> 167 <param name="ExpDes" value="lc-ramclustr-define-experiment.csv" ftype="csv"/>
113 </section> 168 </section>
114 <output name="mass_spectra_merged" file="test1_fill_xcms_1.msp" ftype="msp"/> 169 <output name="mass_spectra_merged" file="test1_fill_xcms_1.msp" ftype="msp"/>
115 <output name="spec_abundance" file="test1_spec_abundance_xcms_1.csv" ftype="csv" compare="sim_size" delta="100"/> 170 <output name="spec_abundance" file="test1_spec_abundance_xcms_1.csv" ftype="csv" compare="sim_size" delta="100"/>
122 </section> 177 </section>
123 <section name="required"> 178 <section name="required">
124 <param name="maxt" value="78.4"/> 179 <param name="maxt" value="78.4"/>
125 </section> 180 </section>
126 </section> 181 </section>
182 <section name="msp_output_details">
183 <param name="mzdec" value="4"/>
184 </section>
127 <section name="normalisation"> 185 <section name="normalisation">
128 <section name="normalisation_method"> 186 <section name="normalisation_method">
129 <param name="batch_order_qc" value="test2_sample_metadata_xcms_2.csv" ftype="csv" /> 187 <param name="batch_order_qc" value="test2_sample_metadata_xcms_2.csv" ftype="csv" />
130 </section> 188 </section>
131 </section> 189 </section>
132 <output name="mass_spectra_merged" file="test2_fill_xcms_2.msp" ftype="msp" compare="diff" lines_diff="20"/> 190 <output name="mass_spectra_merged" file="test2_fill_xcms_2.msp" ftype="msp" compare="sim_size" delta="100"/>
133 <output name="spec_abundance" file="test2_spec_abundance_xcms_2.csv" ftype="csv" compare="sim_size" delta="100"/> 191 <output name="spec_abundance" file="test2_spec_abundance_xcms_2.csv" ftype="csv" compare="sim_size" delta="100"/>
134 </test> 192 </test>
135 <test><!-- TEST 3 --> 193 <test><!-- TEST 3 -->
136 <section name="filetype"> 194 <section name="filetype">
137 <param name="type_choice" value="csv"/> 195 <param name="type_choice" value="csv"/>
156 <section name="ms_csv"> 214 <section name="ms_csv">
157 <param name="ms" value="test3_csv_test-input_1_2.csv" ftype="csv"/> 215 <param name="ms" value="test3_csv_test-input_1_2.csv" ftype="csv"/>
158 </section> 216 </section>
159 </section> 217 </section>
160 <output name="mass_spectra_merged" file="test4_spectra_csv_2.msp" ftype="msp" lines_diff="10"/> 218 <output name="mass_spectra_merged" file="test4_spectra_csv_2.msp" ftype="msp" lines_diff="10"/>
219 </test>
220 <test><!-- TEST 5 -->
221 <section name="filetype">
222 <param name="type_choice" value="recetox-aplcms"/>
223 <section name="ms_dataframe">
224 <param name="ms1_featureDefinitions" value="test5_df_featureDefinitions_input.parquet" ftype="parquet"/>
225 <param name="ms1_featureValues" value="test5_df_featureValues_input.parquet" ftype="parquet"/>
226 </section>
227 </section>
228 <output name="mass_spectra_merged" file="test5_spectra.msp" ftype="msp" lines_diff="10"/>
161 </test> 229 </test>
162 </tests> 230 </tests>
163 231
164 <help> 232 <help>
165 <![CDATA[ 233 <![CDATA[