Mercurial > repos > recetox > ramclustr
comparison ramclustr.xml @ 9:d70dd1d6ac4d draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 8775353ea1dddf10877441e158c7271a401d036e
author | recetox |
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date | Wed, 17 Apr 2024 07:51:23 +0000 |
parents | c043e1fd79d1 |
children | 2d94da58904b |
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8:c043e1fd79d1 | 9:d70dd1d6ac4d |
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1 <tool id="ramclustr" name="RAMClustR" version="@TOOL_VERSION@+galaxy4" profile="21.09"> | 1 <tool id="ramclustr" name="RAMClustR" version="@TOOL_VERSION@+galaxy5" 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='annotation'/> | 6 <expand macro='annotation'/> |
70 | 70 |
71 #if $extras.replace_zeros == "TRUE": | 71 #if $extras.replace_zeros == "TRUE": |
72 ramclustObj = RAMClustR::rc.feature.replace.na(ramclustObj = ramclustObj) | 72 ramclustObj = RAMClustR::rc.feature.replace.na(ramclustObj = ramclustObj) |
73 #end if | 73 #end if |
74 | 74 |
75 #if $filtering.feature_filter_blanks.filter_blanks == "TRUE": | |
76 ramclustObj = RAMClustR::rc.feature.filter.blanks( | |
77 ramclustObj = ramclustObj, | |
78 qc.tag = "${filtering.feature_filter_blanks.qc_tag}", | |
79 blank.tag = "${filtering.feature_filter_blanks.blank_tag}", | |
80 sn = $filtering.feature_filter_blanks.sn, | |
81 remove.blanks = $filtering.feature_filter_blanks.remove_blanks | |
82 ) | |
83 #end if | |
84 | |
75 #if $normalisation.normalisation_method.normalize != "none": | 85 #if $normalisation.normalisation_method.normalize != "none": |
76 ramclustObj = apply_normalisation( | 86 ramclustObj = apply_normalisation( |
77 ramclustr_obj = ramclustObj, | 87 ramclustr_obj = ramclustObj, |
78 #if $normalisation.normalisation_method.normalize == "batch.qc": | 88 #if $normalisation.normalisation_method.normalize == "batch.qc": |
79 metadata_file = "${$normalisation.normalisation_method.batch_order_qc}", | 89 metadata_file = "${$normalisation.normalisation_method.batch_order_qc}", |
84 p_cut = $normalisation.normalisation_method.p_cut, | 94 p_cut = $normalisation.normalisation_method.p_cut, |
85 rsq_cut = $normalisation.normalisation_method.rsq_cut, | 95 rsq_cut = $normalisation.normalisation_method.rsq_cut, |
86 p_adjust = $normalisation.normalisation_method.p_adjust, | 96 p_adjust = $normalisation.normalisation_method.p_adjust, |
87 #end if | 97 #end if |
88 normalize_method = "$normalisation.normalisation_method.normalize" | 98 normalize_method = "$normalisation.normalisation_method.normalize" |
99 ) | |
100 #end if | |
101 | |
102 #if $filtering.feature_filter_cv.filter_cv == "TRUE": | |
103 ramclustObj = RAMClustR::rc.feature.filter.cv( | |
104 ramclustObj = ramclustObj, | |
105 qc.tag = "${filtering.feature_filter_cv.qc_tag}", | |
106 max.cv = $filtering.feature_filter_cv.max_cv | |
89 ) | 107 ) |
90 #end if | 108 #end if |
91 | 109 |
92 ramclustObj = RAMClustR::rc.ramclustr( | 110 ramclustObj = RAMClustR::rc.ramclustr( |
93 ramclustObj = ramclustObj, | 111 ramclustObj = ramclustObj, |
102 linkage = "$clustering.linkage", | 120 linkage = "$clustering.linkage", |
103 cor.method = "$filetype.required.cor_method", | 121 cor.method = "$filetype.required.cor_method", |
104 rt.only.low.n = $extras.rt_only_low_n, | 122 rt.only.low.n = $extras.rt_only_low_n, |
105 fftempdir = NULL, | 123 fftempdir = NULL, |
106 ) | 124 ) |
125 | |
126 #if $extras.quality_control == "TRUE": | |
127 ramclustObj = RAMClustR::rc.qc(ramclustObj = ramclustObj) | |
128 #end if | |
107 | 129 |
108 store_output( | 130 store_output( |
109 ramclustr_obj = ramclustObj, | 131 ramclustr_obj = ramclustObj, |
110 output_merge_msp = $msp_output_details.merge_msp, | 132 output_merge_msp = $msp_output_details.merge_msp, |
111 output_spec_abundance = "$spec_abundance", | 133 output_spec_abundance = "$spec_abundance", |
233 <param name="ms1_featureValues" value="test5_df_featureValues_input.parquet" ftype="parquet"/> | 255 <param name="ms1_featureValues" value="test5_df_featureValues_input.parquet" ftype="parquet"/> |
234 </section> | 256 </section> |
235 </section> | 257 </section> |
236 <output name="mass_spectra_merged" file="test5_spectra.msp" ftype="msp" lines_diff="10"/> | 258 <output name="mass_spectra_merged" file="test5_spectra.msp" ftype="msp" lines_diff="10"/> |
237 </test> | 259 </test> |
260 <test expect_num_outputs="3"><!-- TEST 6 --> | |
261 <section name="filetype"> | |
262 <param name="type_choice" value="xcms"/> | |
263 <section name="xcms"> | |
264 <param name="input_xcms" value="test6.fillpeaks" ftype="rdata.xcms.fillpeaks"/> | |
265 </section> | |
266 </section> | |
267 <section name="msp_output_details"> | |
268 <param name="mzdec" value="4"/> | |
269 </section> | |
270 <section name="extras"> | |
271 <param name="quality_control" value="TRUE"/> | |
272 </section> | |
273 <section name="filtering"> | |
274 <section name="feature_filter_blanks"> | |
275 <param name="filter_blanks" value="TRUE"/> | |
276 <param name="blank_tag" value="Blanc"/> | |
277 </section> | |
278 <section name="feature_filter_cv"> | |
279 <param name="filter_cv" value="TRUE"/> | |
280 </section> | |
281 </section> | |
282 <output name="mass_spectra_merged" file="test6_out.msp" ftype="msp"/> | |
283 <output name="spec_abundance"> | |
284 <assert_contents> | |
285 <has_size value="309" delta="10"/> | |
286 </assert_contents> | |
287 </output> | |
288 <output name="pdf_plot"> | |
289 <assert_contents> | |
290 <has_size value="6842" delta="100"/> | |
291 </assert_contents> | |
292 </output> | |
293 </test> | |
238 </tests> | 294 </tests> |
239 | 295 |
240 <help> | 296 <help> |
241 <![CDATA[ | 297 <![CDATA[ |
242 @HELP@ | 298 @HELP@ |