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comparison ramclustr.xml @ 5:10ded21d47c0 draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
author recetox
date Fri, 11 Feb 2022 14:14:38 +0000
parents 69e0da4703b5
children 8d6f7543a56a
comparison
equal deleted inserted replaced
4:69e0da4703b5 5:10ded21d47c0
18 <configfiles> 18 <configfiles>
19 <configfile name="ramclustr_method"> 19 <configfile name="ramclustr_method">
20 store_output( 20 store_output(
21 #if $filetype.type_choice == "xcms": 21 #if $filetype.type_choice == "xcms":
22 ramclustr_xcms( 22 ramclustr_xcms(
23 input_xcms = "$filetype.input_xcms", 23 input_xcms = "$filetype.xcms.input_xcms",
24 use_pheno = $filetype.xcms.usePheno,
24 #else: 25 #else:
25 ramclustr_csv( 26 ramclustr_csv(
26 ms="$filetype.ms_csv.ms", 27 ms = "$filetype.ms_csv.ms",
27 idmsms="$filetype.ms_csv.idmsms", 28 idmsms = "$filetype.ms_csv.idmsms",
28 feature_delimiter="$filetype.ms_csv.feature_delimiter",
29 sample_name_column = $filetype.ms_csv.sample_name_column,
30 retention_time_column= $filetype.ms_csv.retention_time_column,
31 #end if 29 #end if
32 sr = $filetype.required.sr, 30 sr = $filetype.required.sr,
33 deep_split = $filetype.required.deepSplit, 31 #if $filetype.type_choice == "xcms":
34 block_size = $filetype.required.blocksize, 32 #if $filetype.required.st
35 mult = $filetype.required.mult, 33 st = $filetype.required.st,
36 hmax = $filetype.required.hmax, 34 #end if
37 collapse = $filetype.required.collapse, 35 #else:
38 use_pheno = $filetype.required.usePheno, 36 st = $filetype.required.st,
39 qc_inj_range = $filetype.required.qc_inj_range, 37 #end if
40 normalize = "$filetype.required.normalize",
41 min_module_size = $filetype.required.minModuleSize,
42 linkage = "$filetype.required.linkage",
43 mzdec = $filetype.required.mzdec,
44 cor_method = "$filetype.required.cor_method", 38 cor_method = "$filetype.required.cor_method",
45 rt_only_low_n = $filetype.required.rt_only_low_n, 39 maxt = $filetype.required.maxt,
46 replace_zeros = $filetype.required.replace_zeros, 40 linkage = "$clustering.linkage",
47 #if $filetype.type_choice == "xcms": 41 min_module_size = $clustering.minModuleSize,
48 #if $filetype.optional.st 42 hmax = $clustering.hmax,
49 st = $filetype.optional.st, 43 deep_split = "$clustering.deepSplit",
44 normalize = "$normalisation.normalisation_method.normalize",
45 #if "$normalisation.normalisation_method.normalize" == "batch.qc":
46 metadata_file = "$normalisation.normalisation_method.batch_order_qc",
47 qc_inj_range = $normalisation.normalisation_method.qc_inj_range,
50 #end if 48 #end if
51 #else: 49 block_size = $performance.blocksize,
52 st = $filetype.ms_csv.st, 50 mult = $performance.mult,
53 #end if 51 mzdec = $msp_output_details.mzdec,
54 #if $filetype.optional.maxt 52 rt_only_low_n = $extras.rt_only_low_n,
55 maxt = $filetype.optional.maxt, 53 replace_zeros = $extras.replace_zeros,
56 #end if 54 #if $extras.ExpDes:
57 #if $filetype.optional.fftempdir 55 exp_design = "${$extras.ExpDes}"
58 fftempdir = $filetype.optional.fftempdir,
59 #end if
60 #if $filetype.metadata.batch_order_qc
61 metadata_file = "${filetype.metadata.batch_order_qc}",
62 #end if
63 #if $filetype.metadata.ExpDes
64 exp_design = "${filetype.metadata.ExpDes}"
65 #end if 56 #end if
66 ), 57 ),
67 "$result", "$method_metadata", $filetype.required.merge_msp, "$spec_abundance") 58 $msp_output_details.merge_msp,
59 "$spec_abundance",
60 #if $msp_output_details.merge_msp:
61 "$mass_spectra_merged"
62 #else:
63 NULL
64 #end if
65 )
68 </configfile> 66 </configfile>
69 </configfiles> 67 </configfiles>
70 <inputs> 68 <inputs>
71 <conditional name="filetype"> 69 <conditional name="filetype">
72 <param name="type_choice" type="select" label="Choose input format:"> 70 <param name="type_choice" type="select" label="Choose input format:">
73 <option value="xcms" selected="true">XCMS</option> 71 <option value="xcms" selected="true">XCMS</option>
74 <option value="csv">CSV</option> 72 <option value="csv">CSV</option>
75 </param> 73 </param>
76 <when value="xcms"> 74 <when value="xcms">
77 <param name="input_xcms" label="input_xcms" type="data" format="rdata.xcms.fillpeaks" help="Grouped feature data for clustering by ramclustR" /> 75 <expand macro="parameters_xcms" />
78 <expand macro="parameters_required" /> 76 <section name="required" title="General parameters" expanded="true">
79 <expand macro="parameters_optional_xcms" /> 77 <param label="Sigma t" name="st" type="float" optional="true" help="Retention time similarity (optional).
80 <expand macro="parameters_optional_metadata" /> 78 A recommended starting point is half the value of your average chromatographic peak width at half max (seconds))."/>
79 <expand macro="parameters_required" />
80 </section>
81 </when> 81 </when>
82 <when value="csv"> 82 <when value="csv">
83 <expand macro="parameters_csv" /> 83 <expand macro="parameters_csv" />
84 <expand macro="parameters_required" /> 84 <section name="required" title="General parameters" expanded="true">
85 <expand macro="parameters_optional_csv" /> 85 <param label="Sigma t" name="st" type="float" value="1" help="Retention time similarity.
86 <expand macro="parameters_optional_metadata" /> 86 A recommended starting point is half the value of your average chromatographic peak width at half max (seconds))."/>
87 <expand macro="parameters_required" />
88 </section>
87 </when> 89 </when>
88 </conditional> 90 </conditional>
91 <expand macro="main_parameters" />
89 </inputs> 92 </inputs>
90 93
91 <outputs> 94 <outputs>
92 <data label="${tool.name} on ${on_string}" name="result" format="RData" />
93 <data label="Spec Abundance of ${on_string}" name="spec_abundance" format="csv" /> 95 <data label="Spec Abundance of ${on_string}" name="spec_abundance" format="csv" />
94 <data label="Metadata for ${tool.name} on ${on_string}" name="method_metadata" format="txt"/>
95 <expand macro="output_msp"/> 96 <expand macro="output_msp"/>
96 </outputs> 97 </outputs>
97 98
98 <tests> 99 <tests>
99 <test><!-- TEST 1 --> 100 <test><!-- TEST 1 -->
100 <param name="type_choice" value="xcms"/> 101 <section name="filetype">
101 <param name="input_xcms" value="test1_xcmsObj_1.rdata.xcms.fillpeaks" ftype="rdata.xcms.fillpeaks"/> 102 <param name="type_choice" value="xcms"/>
102 <param name="ExpDes" value="lc-ramclustr-define-experiment.csv" ftype="csv"/> 103 <section name="xcms">
103 <output name="result" file="test1_ramclustObj_xcms_1.rdata" ftype="RData" compare="sim_size" delta="200"/> 104 <param name="input_xcms" value="test1_xcmsObj_1.rdata.xcms.fillpeaks" ftype="rdata.xcms.fillpeaks"/>
104 <output_collection name="mass_spectra" type="list"> 105 </section>
105 <element name="experiment_lc" file="test1_fill_xcms_1.msp" ftype="msp"/> 106 <section name="required">
106 </output_collection> 107 <param name="maxt" value="259.8"/>
107 <output name="method_metadata" file="test1_metadata_xcms_1.txt" ftype="txt"/> 108 </section>
109 </section>
110 <section name="extras">
111 <param name="ExpDes" value="lc-ramclustr-define-experiment.csv" ftype="csv"/>
112 </section>
113 <output name="mass_spectra_merged" file="test1_fill_xcms_1.msp" ftype="msp"/>
108 <output name="spec_abundance" file="test1_spec_abundance_xcms_1.csv" ftype="csv" compare="sim_size" delta="100"/> 114 <output name="spec_abundance" file="test1_spec_abundance_xcms_1.csv" ftype="csv" compare="sim_size" delta="100"/>
109 </test> 115 </test>
110 <test><!-- TEST 2 --> 116 <test><!-- TEST 2 -->
111 <param name="type_choice" value="xcms"/> 117 <section name="filetype">
112 <param name="input_xcms" value="test2_xcmsObj_2.rdata.xcms.fillpeaks" ftype="rdata.xcms.fillpeaks"/> 118 <param name="type_choice" value="xcms"/>
113 <param name="batch_order_qc" value="test2_sample_metadata_xcms_2.csv" ftype="csv" /> 119 <section name="xcms">
114 <output name="result" file="test2_ramclustObj_xcms_2.rdata" ftype="RData" compare="sim_size" delta="200"/> 120 <param name="input_xcms" value="test2_xcmsObj_2.rdata.xcms.fillpeaks" ftype="rdata.xcms.fillpeaks"/>
115 <output_collection name="mass_spectra" type="list"> 121 </section>
116 <element name="fill" file="test2_fill_xcms_2.msp" ftype="msp" compare="diff" lines_diff="10"/> 122 <section name="required">
117 </output_collection> 123 <param name="maxt" value="78.4"/>
118 <output name="method_metadata" file="test2_metadata_xcms_2.txt" ftype="txt"/> 124 </section>
125 </section>
126 <section name="normalisation">
127 <section name="normalisation_method">
128 <param name="batch_order_qc" value="test2_sample_metadata_xcms_2.csv" ftype="csv" />
129 </section>
130 </section>
131 <output name="mass_spectra_merged" file="test2_fill_xcms_2.msp" ftype="msp" compare="diff" lines_diff="10"/>
119 <output name="spec_abundance" file="test2_spec_abundance_xcms_2.csv" ftype="csv" compare="sim_size" delta="100"/> 132 <output name="spec_abundance" file="test2_spec_abundance_xcms_2.csv" ftype="csv" compare="sim_size" delta="100"/>
120 </test> 133 </test>
121 <test><!-- TEST 3 --> 134 <test><!-- TEST 3 -->
122 <param name="type_choice" value="csv"/> 135 <section name="filetype">
123 <param name="ms" value="test3_csv_test-input_1_2.csv" ftype="csv"/> 136 <param name="type_choice" value="csv"/>
124 <param name="st" value="5.0"/> 137 <section name="ms_csv">
125 <param name="blocksize" value="1000"/> 138 <param name="ms" value="test3_csv_test-input_1_2.csv" ftype="csv"/>
126 <param name="mult" value="1"/> 139 </section>
127 <param name="maxt" value="1"/> 140 <section name="required">
128 <output name="result" file="test3_ramclustObj_csv_1.rdata" ftype="RData" compare="sim_size" delta="200"/> 141 <param name="st" value="5.0"/>
142 <param name="maxt" value="1"/>
143 </section>
144 </section>
145 <section name="performance">
146 <param name="blocksize" value="1000"/>
147 <param name="mult" value="1"/>
148 </section>
149 <output name="mass_spectra_merged" file="test3_spectra_csv_1.msp" ftype="msp"/>
129 <output name="spec_abundance" file="test3_spec_abundance_csv_1.csv" ftype="csv"/> 150 <output name="spec_abundance" file="test3_spec_abundance_csv_1.csv" ftype="csv"/>
130 <output name="method_metadata" file="test3_metadata_csv_1.txt" ftype="txt"/>
131 <output_collection name="mass_spectra" type="list">
132 <element name="fill" file="test3_spectra_csv_1.msp" ftype="msp"/>
133 </output_collection>
134 </test> 151 </test>
135 <test><!-- TEST 4 --> 152 <test><!-- TEST 4 -->
136 <param name="type_choice" value="csv"/> 153 <section name="filetype">
137 <param name="ms" value="test3_csv_test-input_1_2.csv" ftype="csv"/> 154 <param name="type_choice" value="csv"/>
138 <param name="batch_order_qc" value="test4_sample_metadata_csv_2.csv" ftype="csv" /> 155 <section name="ms_csv">
139 <output name="result" file="test4_ramclustObj_csv_2.rdata" ftype="RData" compare="sim_size" delta="200"/> 156 <param name="ms" value="test3_csv_test-input_1_2.csv" ftype="csv"/>
140 <output name="spec_abundance" file="test4_spec_abundance_csv_2.csv" ftype="csv"/> 157 </section>
141 <output name="method_metadata" file="test4_metadata_csv_2.txt" ftype="txt"/> 158 </section>
142 <output_collection name="mass_spectra" type="list"> 159 <output name="mass_spectra_merged" file="test4_spectra_csv_2.msp" ftype="msp" lines_diff="10"/>
143 <element name="fill" file="test4_spectra_csv_2.msp" ftype="msp" lines_diff="10"/>
144 </output_collection>
145 </test> 160 </test>
146 </tests> 161 </tests>
147 162
148 <help> 163 <help>
149 <![CDATA[ 164 <![CDATA[
150 @HELP@ 165 @HELP@
166
167 .. rubric:: **Footnotes**
168 .. [1] Correlation, Variance and Covariance - `stats::cor <https://www.rdocumentation.org/packages/stats/versions/3.6.2/topics/cor>`_
169 .. [2] Hierarchical Clustering - `stats::hclust <https://www.rdocumentation.org/packages/stats/versions/3.6.2/topics/hclust>`_
170 .. [3] Dynamic Dendrogram Pruning Based on Dendrogram Only - `dynamicTreeCut::cutreeDynamicTree <https://www.rdocumentation.org/packages/dynamicTreeCut/versions/1.63-1/topics/cutreeDynamicTree>`_
151 ]]> 171 ]]>
152 </help> 172 </help>
153 173
154 <expand macro="citations" /> 174 <expand macro="citations" />
155 </tool> 175 </tool>