Mercurial > repos > iuc > tracegroomer

annotate macros.xml @ 2:5147f08d67c9 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 26f0c7344995bfa302db821e77ae717636a4f4b2
author iuc
date Tue, 03 Sep 2024 19:23:14 +0000
parents ea6ea4029c47
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
1 <macros>
1
ea6ea4029c47 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32
iuc
parents: 0
diff changeset
2 <token name="@TOOL_VERSION@">0.1.4</token>
2
5147f08d67c9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 26f0c7344995bfa302db821e77ae717636a4f4b2
iuc
parents: 1
diff changeset
3 <token name="@VERSION_SUFFIX@">1</token>
0
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
4 <xml name="requirements">
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
5 <requirements>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
6 <requirement type="package" version="@TOOL_VERSION@">tracegroomer</requirement>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
7 </requirements>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
8 </xml>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
9 <xml name="input_datasets">
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
10 <param name="labeled_metabo_file" type="data" optional="false" format="tabular,xlsx" label="Labeled metabolomics file"/>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
11 <param name="sample_metadata_path" type="data" format="tabular" label="sample metadata file" help="The metadata, a unique file with the description of the samples in your measures files. This is compulsory, see section Metadata File Information."/>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
12 <param name="amount_material" type="data" optional="true" format="interval" label="amount material" help="Absolute path to the file having the amount of material by sample, for the normalization. This file must be a tab delimited file with exactly 2 columns with a header: the first column contains the original names of the samples, and the second column the numbers (tissue weight, number of cells, volume, etc)"/>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
13 <param name="remove_these_metabolites" type="data" optional="true" format="interval" label="remove metabolites using this file" help="Absolute path to the tab delimited file with columns: compartment, metabolite. This file lists the metabolites to be completely excluded, compartment specific. Defining such exclusion list requires deep knowledge of the data by the user (measurements coherence/quality, etc)"/>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
14 <conditional name="type_of_file">
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
15 <param name="type_of_file_selector" type="select" label="Choose which type of input file is used" help="One of the following: IsoCor_out_tsv|rule_tsv|VIBMEC_xlsx|generic_xlsx">
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
16 <option value="IsoCor_out_tsv" selected="true">isocor output file</option>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
17 <option value="VIBMEC_xlsx">VIBMEC xlsx file</option>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
18 <option value="generic_xlsx">generic xlsx file</option>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
19 <option value="rule_tsv">rule tsv file</option>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
20 </param>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
21 <when value="IsoCor_out_tsv">
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
22 </when>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
23 <when value="generic_xlsx">
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
24 <param name="sheetname" type="text" value="isotopologuesCorrValues" optional="false" label="name of the sheet containing the isotopologues corrected values" >
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
25 <sanitizer invalid_char="">
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
26 <valid initial="string.ascii_letters,string.digits">
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
27 <add value="_" />
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
28 </valid>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
29 </sanitizer>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
30 </param>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
31 </when>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
32 <when value="VIBMEC_xlsx">
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
33 <param name="raw_abundance_sheet_name" type="text" value="rawAbundances" optional="false" label="name of the sheet containing the raw abundances values" >
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
34 <sanitizer invalid_char="">
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
35 <valid initial="string.ascii_letters,string.digits">
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
36 <add value="_" />
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
37 </valid>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
38 </sanitizer>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
39 </param>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
40 <param name="frac_contribution_sheet_name" type="text" value="FracContribution_C" optional="false" label="name of the sheet containing the mean enrichment values" >
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
41 <sanitizer invalid_char="">
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
42 <valid initial="string.ascii_letters,string.digits">
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
43 <add value="_" />
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
44 </valid>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
45 </sanitizer>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
46 </param>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
47 <param name="corrected_isotopologues_sheet_name" type="text" value="CorrectedIsotopologues" optional="false" label="name of the sheet containing the isotopologues corrected values" >
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
48 <sanitizer invalid_char="">
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
49 <valid initial="string.ascii_letters,string.digits">
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
50 <add value="_" />
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
51 </valid>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
52 </sanitizer>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
53 </param>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
54 </when>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
55 <when value="rule_tsv">
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
56 <param name="variable_metadata_path" type="data" format="tabular" label="variable metadata file" help="The metadata, a unique file with the description of the samples in your measures files. This is compulsory, see section Metadata File Information."/>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
57 <section name="columns_variable_metadata_description" title="variable metadata file columns description" expanded="false">
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
58 <param name="identifier" type="text" value="ID" optional="false" label="identifier of your metabolite in variable metadata file" >
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
59 <sanitizer invalid_char="">
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
60 <valid initial="string.ascii_letters,string.digits">
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
61 <add value="_" />
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
62 </valid>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
63 </sanitizer>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
64 </param>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
65 <param name="compound" type="text" value="metabolite_name" optional="false" label="name of your metabolite in variable metadata file (formula is also accepted)" >
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
66 <sanitizer invalid_char="">
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
67 <valid initial="string.ascii_letters,string.digits">
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
68 <add value="_" />
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
69 </valid>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
70 </sanitizer>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
71 </param>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
72 <param name="isotopologue_number" value="isotope_numeric" type="text" optional="false" label="isotopologue number in variable metadata file" >
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
73 <sanitizer invalid_char="">
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
74 <valid initial="string.ascii_letters,string.digits">
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
75 <add value="_" />
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
76 </valid>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
77 </sanitizer>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
78 </param>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
79 </section>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
80 </when>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
81 </conditional>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
82 </xml>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
83 <xml name="advanced_options">
2
5147f08d67c9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 26f0c7344995bfa302db821e77ae717636a4f4b2
iuc
parents: 1
diff changeset
84 <section name="advanced_options" title="Advanced options" expanded="false" help="Default values explained in our Wiki page (link at the end of the Help section)">
5147f08d67c9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 26f0c7344995bfa302db821e77ae717636a4f4b2
iuc
parents: 1
diff changeset
85 <param name="div_isotopologues_by_amount_material" type="boolean" truevalue="--div_isotopologues_by_amount_material" checked="true" falsevalue="--no-div_isotopologues_by_amount_material" label="isotopologues division by amount material" help="Apply normalization by the amount of material at the level of isotopologue absolute values. Immediately after this, and before any other computation, tracegroomer re-computes all derived (thus normalized) metrics"/>
5147f08d67c9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 26f0c7344995bfa302db821e77ae717636a4f4b2
iuc
parents: 1
diff changeset
86 <param name="alternative_div_amount_material" type="boolean" truevalue="--alternative_div_amount_material" checked="true" falsevalue="--no-alternative_div_amount_material" label="alternative division of values by amount material" help="In the normalisation by the amount of material, not only the division of the given absolute values by these amounts is performed, but also the product of the resulting quotients 'q' and the averaged amount of material 'a' (q x a) so abundance units are preserved"/>
5147f08d67c9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 26f0c7344995bfa302db821e77ae717636a4f4b2
iuc
parents: 1
diff changeset
87 <param name="isotopologues_preview" type="boolean" truevalue="--isotopologues_preview" checked="false" falsevalue="--no-isotopologues_preview" label="Plot isotopologues" help="Generate simple plots that give a general overview of the isotopologue proportions given by the user. Performs a scatter plot of the individual isotopologue proportions for all metabolites, as well as a plot of the sums of isotopologue proportions (the sum must be equal to 1 for each metabolite and sample)"/>
5147f08d67c9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 26f0c7344995bfa302db821e77ae717636a4f4b2
iuc
parents: 1
diff changeset
88 <param name="fractions_stomp_values" type="boolean" truevalue="--fractions_stomp_values" checked="true" falsevalue="--no-fractions_stomp_values" label="Stomp fractional contributions" help="Stomps fractional contributions (synonym: mean enrichment), and isotopologue proportions, to max 1.0 and min 0.0"/>
5147f08d67c9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 26f0c7344995bfa302db821e77ae717636a4f4b2
iuc
parents: 1
diff changeset
89 <param name="subtract_blankavg" type="boolean" truevalue="--subtract_blankavg" checked="true" falsevalue="--no-subtract_blankavg" label="Subtract blanks avg (VIB input only)" help="from samples' abundances, subtracts the average of the blanks for all metabolites across all samples. Note that the Internal Standards are not subjected to this operation, as recommended by VIB platform"/>
5147f08d67c9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 26f0c7344995bfa302db821e77ae717636a4f4b2
iuc
parents: 1
diff changeset
90 <param name="under_detection_limit_set_nan" type="boolean" truevalue="--under_detection_limit_set_nan" checked="true" falsevalue="--no-under_detection_limit_set_nan" label="Limit Of Detection (VIB input only)" help="The Limit Of Detection, LOD, corresponds to the averaged blanks abundance values, multiplied by three times the blanks standard deviation. By default, any value that is strictly inferior to its corresponding LOD, is converted into NaN"/>
0
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
91 <param name="use_internal_standard" type="text" optional="true" help="The name of the internal standard, which is a compound or metabolite that has been stated as reference signal. By providing this name, the normalization by the internal standard is automatically performed" label="internal standard" />
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
92 <param name="isosprop_min_admitted" type="float" min="-1.0" max="1.0" value="-0.5" label="isotopologues cutoff" help="Metabolites whose isotopologue proportions are less or equal to this cutoff, are removed"/>
2
5147f08d67c9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 26f0c7344995bfa302db821e77ae717636a4f4b2
iuc
parents: 1
diff changeset
93 <param name="output_files_extension" type="select" value="tsv" display="radio" label="output files extension" help="Note that tab delimited files are always produced, for any chosen extension">
5147f08d67c9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 26f0c7344995bfa302db821e77ae717636a4f4b2
iuc
parents: 1
diff changeset
94 <option value="tsv">tsv</option>
5147f08d67c9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 26f0c7344995bfa302db821e77ae717636a4f4b2
iuc
parents: 1
diff changeset
95 <option value="csv">csv</option>
5147f08d67c9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 26f0c7344995bfa302db821e77ae717636a4f4b2
iuc
parents: 1
diff changeset
96 </param>
0
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
97 </section>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
98 </xml>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
99 <xml name="citations">
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
100 <citations>
2
5147f08d67c9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 26f0c7344995bfa302db821e77ae717636a4f4b2
iuc
parents: 1
diff changeset
101 <citation type="doi">10.1093/bioinformatics/btae282</citation>
0
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
102 <citation type="bibtex">
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
103 @software{Galvis_Rodriguez_DIMet,
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
104 author = {Galvis Rodriguez, Johanna and Guyon, Joris and Dartigues, Benjamin and Specque, Florian and Daubon, Thomas and Karkar, Slim and Nikolski, Macha},
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
105 license = {MIT},
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
106 title = {{DIMet}},
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
107 url = {https://github.com/cbib/DIMet}
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
108 }
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
109 </citation>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
110 </citations>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
111
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
112 </xml>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
iuc
parents:
diff changeset
113 </macros>