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comparison ramclustr.xml @ 0:36104baf75da draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
author recetox
date Tue, 22 Mar 2022 16:09:16 +0000
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children 9a0d83c1b4b3
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-1:000000000000 0:36104baf75da
1 <tool id="ramclustr" name="RAMClustR" version="@TOOL_VERSION@+galaxy2">
2 <macros>
3 <import>macros.xml</import>
4 </macros>
5 <expand macro="creator"/>
6
7 <requirements>
8 <requirement type="package" version="@TOOL_VERSION@">r-ramclustr</requirement>
9 <requirement type="package" version="3.14.0">bioconductor-xcms</requirement>
10 </requirements>
11
12 <command detect_errors="aggressive"><![CDATA[
13 Rscript
14 -e 'source("${__tool_directory__}/ramclustr_wrapper.R")'
15 -e 'source("${ramclustr_method}")'
16 ]]>
17 </command>
18 <configfiles>
19 <configfile name="ramclustr_method">
20 store_output(
21 #if $filetype.type_choice == "xcms":
22 ramclustr_xcms(
23 input_xcms = "$filetype.xcms.input_xcms",
24 use_pheno = $filetype.xcms.usePheno,
25 #else:
26 ramclustr_csv(
27 ms = "$filetype.ms_csv.ms",
28 idmsms = "$filetype.ms_csv.idmsms",
29 #end if
30 sr = $filetype.required.sr,
31 #if $filetype.type_choice == "xcms":
32 #if $filetype.required.st
33 st = $filetype.required.st,
34 #end if
35 #else:
36 st = $filetype.required.st,
37 #end if
38 cor_method = "$filetype.required.cor_method",
39 maxt = $filetype.required.maxt,
40 linkage = "$clustering.linkage",
41 min_module_size = $clustering.minModuleSize,
42 hmax = $clustering.hmax,
43 deep_split = "$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,
48 #end if
49 block_size = $performance.blocksize,
50 mult = $performance.mult,
51 mzdec = $msp_output_details.mzdec,
52 rt_only_low_n = $extras.rt_only_low_n,
53 replace_zeros = $extras.replace_zeros,
54 #if $extras.ExpDes:
55 exp_design = "${$extras.ExpDes}"
56 #end if
57 ),
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 )
66 </configfile>
67 </configfiles>
68 <inputs>
69 <conditional name="filetype">
70 <param name="type_choice" type="select" label="Choose input format:">
71 <option value="xcms" selected="true">XCMS</option>
72 <option value="csv">CSV</option>
73 </param>
74 <when value="xcms">
75 <expand macro="parameters_xcms" />
76 <section name="required" title="General parameters" expanded="true">
77 <param label="Sigma t" name="st" type="float" optional="true" help="Retention time similarity (optional).
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>
82 <when value="csv">
83 <expand macro="parameters_csv" />
84 <section name="required" title="General parameters" expanded="true">
85 <param label="Sigma t" name="st" type="float" value="1" help="Retention time similarity.
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>
89 </when>
90 </conditional>
91 <expand macro="main_parameters" />
92 </inputs>
93
94 <outputs>
95 <data label="Spec Abundance of ${on_string}" name="spec_abundance" format="csv" />
96 <expand macro="output_msp"/>
97 </outputs>
98
99 <tests>
100 <test><!-- TEST 1 -->
101 <section name="filetype">
102 <param name="type_choice" value="xcms"/>
103 <section name="xcms">
104 <param name="input_xcms" value="test1_xcmsObj_1.rdata.xcms.fillpeaks" ftype="rdata.xcms.fillpeaks"/>
105 </section>
106 <section name="required">
107 <param name="maxt" value="259.8"/>
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"/>
114 <output name="spec_abundance" file="test1_spec_abundance_xcms_1.csv" ftype="csv" compare="sim_size" delta="100"/>
115 </test>
116 <test><!-- TEST 2 -->
117 <section name="filetype">
118 <param name="type_choice" value="xcms"/>
119 <section name="xcms">
120 <param name="input_xcms" value="test2_xcmsObj_2.rdata.xcms.fillpeaks" ftype="rdata.xcms.fillpeaks"/>
121 </section>
122 <section name="required">
123 <param name="maxt" value="78.4"/>
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"/>
132 <output name="spec_abundance" file="test2_spec_abundance_xcms_2.csv" ftype="csv" compare="sim_size" delta="100"/>
133 </test>
134 <test><!-- TEST 3 -->
135 <section name="filetype">
136 <param name="type_choice" value="csv"/>
137 <section name="ms_csv">
138 <param name="ms" value="test3_csv_test-input_1_2.csv" ftype="csv"/>
139 </section>
140 <section name="required">
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"/>
150 <output name="spec_abundance" file="test3_spec_abundance_csv_1.csv" ftype="csv"/>
151 </test>
152 <test><!-- TEST 4 -->
153 <section name="filetype">
154 <param name="type_choice" value="csv"/>
155 <section name="ms_csv">
156 <param name="ms" value="test3_csv_test-input_1_2.csv" ftype="csv"/>
157 </section>
158 </section>
159 <output name="mass_spectra_merged" file="test4_spectra_csv_2.msp" ftype="msp" lines_diff="10"/>
160 </test>
161 </tests>
162
163 <help>
164 <![CDATA[
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>`_
171 ]]>
172 </help>
173
174 <expand macro="citations" />
175 </tool>