Mercurial > repos > recetox > ramclustr_define_experiment

comparison macros.xml @ 2:25625114618e 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 14:02:02 +0000
parents 42c2a25ff197
children 049285068dad
comparison
equal deleted inserted replaced
1:2e012f4c062e 2:25625114618e
1 <macros> 1 <macros>
2 <token name="@TOOL_VERSION@">1.2.4</token> 2 <token name="@TOOL_VERSION@">1.3.0</token>
3 3
4 <xml name="creator"> 4 <xml name="creator">
5 <creator> 5 <creator>
6 <person 6 <person
7 givenName="Helge" 7 givenName="Helge"
21 <person 21 <person
22 givenName="Martin" 22 givenName="Martin"
23 familyName="Čech" 23 familyName="Čech"
24 url="https://github.com/martenson" 24 url="https://github.com/martenson"
25 identifier="0000-0002-9318-1781" /> 25 identifier="0000-0002-9318-1781" />
26 <person
27 givenName="Zargham"
28 familyName="Ahmad"
29 url="https://github.com/zargham-ahmad"
30 identifier="0000-0002-6096-224X" />
26 <organization 31 <organization
27 url="https://www.recetox.muni.cz/" 32 url="https://www.recetox.muni.cz/"
28 email="GalaxyToolsDevelopmentandDeployment@space.muni.cz" 33 email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
29 name="RECETOX MUNI"/> 34 name="RECETOX MUNI"/>
30 </creator> 35 </creator>
34 <section name="ms_csv" title="Input MS Data as CSV" expanded="true"> 39 <section name="ms_csv" title="Input MS Data as CSV" expanded="true">
35 <param label="Input CSV" name="ms" type="data" format="csv" 40 <param label="Input CSV" name="ms" type="data" format="csv"
36 help="Features as columns, rows as samples. Column header in format mz_rt."/> 41 help="Features as columns, rows as samples. Column header in format mz_rt."/>
37 <param label="idMSMS" name="idmsms" type="data" format="csv" optional="true" 42 <param label="idMSMS" name="idmsms" type="data" format="csv" optional="true"
38 help="Optional idMSMS / MSe csv data. Same dimension and names as in input CSV are required."/> 43 help="Optional idMSMS / MSe csv data. Same dimension and names as in input CSV are required."/>
44 <param label="phenoData" name="csv_phenoData" type="data" format="csv" optional="true"
45 help="Optional csv containing phenoData."/>
39 </section> 46 </section>
40 </xml> 47 </xml>
41 48
42 <xml name="parameters_xcms"> 49 <xml name="parameters_xcms">
43 <section name="xcms" title="Input MS Data as XCMS" expanded="true"> 50 <section name="xcms" title="Input MS Data as XCMS" expanded="true">
44 <param name="input_xcms" label="Input XCMS" type="data" format="rdata.xcms.fillpeaks" 51 <param name="input_xcms" label="Input XCMS" type="data" format="rdata.xcms.fillpeaks"
45 help="Grouped feature data for clustering." /> 52 help="Grouped feature data for clustering." />
46 <param label="Preserve phenotype" name="usePheno" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" 53 </section>
47 help="Transfer phenotype data from XCMS object to Spec abundance file."/> 54 </xml>
55
56 <xml name="parameters_recetox_aplcms">
57 <section name="ms_dataframe" title="Input MS Data as parquet (output from recetox-aplcms)" expanded="true">
58 <param label="Input MS1 featureDefinitions" name="ms1_featureDefinitions" type="data" format="parquet"
59 help="Metadata with columns: mz, rt, feature names containing MS data."/>
60 <param label="Input MS1 featureValues" name="ms1_featureValues" type="data" format="parquet"
61 help="data with rownames = sample names, colnames = feature names containing MS data."/>
62 <param label="phenoData" name="df_phenoData" type="data" format="tsv,csv" optional="true"
63 help="CSV/TSV file containing phenoData (optional)."/>
48 </section> 64 </section>
49 </xml> 65 </xml>
50 66
51 <xml name="parameters_required"> 67 <xml name="parameters_required">
52 <param label="Sigma r" name="sr" type="float" value="0.5" help="Correlational similarity between features."/> 68 <param label="Sigma r" name="sr" type="float" value="0.5" help="Correlational similarity between features."/>
53 <param label="Correlation method" name="cor_method" type="select" display="radio" 69 <param label="Correlation method" name="cor_method" type="select" display="radio"
54 help="Choose correlational method to be used - see [1] for details."> 70 help="Choose correlational method to be used - see [1] for details.">
55 <option value="pearson" selected="true">pearson</option> 71 <option value="pearson" selected="true">pearson</option>
56 <option value="everything">everything</option>
57 <option value="spearman">spearman</option> 72 <option value="spearman">spearman</option>
58 <option value="kendall">kendall</option> 73 <option value="kendall">kendall</option>
59 </param> 74 </param>
60 <param label="Maximum RT difference" name="maxt" value="60" type="float" 75 <param label="Maximum RT difference" name="maxt" value="60" type="float"
61 help="Maximum difference to calculate RT similarity - values beyond this are assigned zero similarity."/> 76 help="Maximum difference to calculate RT similarity - values beyond this are assigned zero similarity."/>
88 help="Choose method for normalization of feature intensities."> 103 help="Choose method for normalization of feature intensities.">
89 <option value="none" selected="true">none</option> 104 <option value="none" selected="true">none</option>
90 <option value="TIC">TIC</option> 105 <option value="TIC">TIC</option>
91 <option value="quantile">quantile</option> 106 <option value="quantile">quantile</option>
92 <option value="batch.qc">batch.qc</option> 107 <option value="batch.qc">batch.qc</option>
108 <option value="qc">qc</option>
93 </param> 109 </param>
94 <when value="batch.qc"> 110 <when value="batch.qc">
95 <param label="Metadata details" name="batch_order_qc" type="data" format="csv" optional="true" 111 <param label="Metadata details" name="batch_order_qc" type="data" format="csv"
96 help="CSV with sample names (or indices, currently not handled) on rows and columns with: 112 help="CSV with sample names (or indices, currently not handled) on rows and columns with:
97 batch number ('batch'), position in sequence ('order'), and whether it is a QC sample or not 113 batch number ('batch'), position in sequence ('order'), and whether it is a QC sample or not
98 ('qc' with true/false OR 'sampleType' with 'sample/qc/blank')."/> 114 ('qc' with true/false OR 'sampleType' with 'sample/qc/blank')."/>
99 <param label="QC injection range" name="qc_inj_range" type="integer" value="20" 115 <param label="QC injection range" name="qc_inj_range" type="integer" value="20"
100 help="How many injections around each injection are to be scanned for presence of QC samples? 116 help="How many injections around each injection are to be scanned for presence of QC samples?
103 between 7 and 21. Smaller values provide more local precision but make normalization sensitive 119 between 7 and 21. Smaller values provide more local precision but make normalization sensitive
104 to individual poor outliers (though these are first removed using the boxplot function outlier 120 to individual poor outliers (though these are first removed using the boxplot function outlier
105 detection), while wider values provide less local precision in normalization but better 121 detection), while wider values provide less local precision in normalization but better
106 stability to individual peak areas."/> 122 stability to individual peak areas."/>
107 </when> 123 </when>
124 <when value="qc">
125 <param label="Metadata details" name="batch_order_qc" type="data" format="csv" optional="true"
126 help="CSV with sample names (or indices, currently not handled) on rows and columns with:
127 batch number ('batch'), position in sequence ('order'), and whether it is a QC sample or not
128 ('qc' with true/false OR 'sampleType' with 'sample/qc/blank')."/>
129 <param label="p.cut" name="p_cut" type="float" value="0.05"
130 help="Numeric when run order correction is applied, only features showing a run order vs
131 signal with a linear p-value (after FDR correction) &lt; p.cut will be adjusted. also requires
132 r-squared &lt; rsq.cut."/>
133 <param label="rsq.cut" name="rsq_cut" type="float" value="0.1"
134 help="Numeric when run order correction is applied, only features showing a run order vs signal
135 with a linear r-squared &gt; rsq.cut will be adjusted. also requires p values &lt; p.cut."/>
136 <param label="p.adjust" name="p_adjust" type="text" value="none"
137 help="Which p-value adjustment should be used? one of ['holm', 'hochberg', 'hommel', 'bonferroni', 'BH',
138 'BY', 'fdr', 'none']"/>
139 </when>
140 <when value="none"/>
141 <when value="TIC"/>
142 <when value="quantile"/>
108 </conditional> 143 </conditional>
109 </section> 144 </section>
110 145
111 <section name="performance" title="Performance"> 146 <section name="performance" title="Performance">
112 <param label="Blocksize" name="blocksize" type="integer" value="2000" 147 <param label="Blocksize" name="blocksize" type="integer" value="2000"
141 help="Definition of experimental design in CSV format." /> 176 help="Definition of experimental design in CSV format." />
142 </section> 177 </section>
143 </xml> 178 </xml>
144 179
145 <xml name="output_msp"> 180 <xml name="output_msp">
146 <collection label="Mass spectra from ${tool.name} on ${on_string}" name="mass_spectra_collection" type="list"> 181 <collection label="Mass spectra from ${tool.name} on ${on_string} list" name="mass_spectra_collection" type="list">
147 <discover_datasets pattern="__name_and_ext__" directory="spectra" recurse="true" ext="msp"/> 182 <discover_datasets pattern="__name_and_ext__" directory="spectra" recurse="true" ext="msp"/>
148 <filter>not msp_output_details['merge_msp']</filter> 183 <filter>not msp_output_details['merge_msp']</filter>
149 </collection> 184 </collection>
150 <data label="Mass spectra from ${tool.name} on ${on_string}" name="mass_spectra_merged" format="msp"> 185 <data label="Mass spectra from ${tool.name} on ${on_string}" name="mass_spectra_merged" format="msp">
151 <filter>msp_output_details['merge_msp']</filter> 186 <filter>msp_output_details['merge_msp']</filter>