Mercurial > repos > recetox > bioconductor_scp

annotate macros.xml @ 0:cd2f3a280463 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/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
author recetox
date Wed, 22 Jan 2025 07:44:00 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
1 <macros>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
2 <token name="@TOOL_VERSION@">1.16.0</token>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
3 <xml name="creator">
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
4 <creator>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
5 <person
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
6 givenName="Kristina"
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
7 familyName="Gomoryova"
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
8 url="https://github.com/KristinaGomoryova"
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
9 identifier="0000-0003-4407-3917" />
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
10 <person
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
11 givenName="Helge"
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
12 familyName="Hecht"
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
13 url="https://github.com/hechth"
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
14 identifier="0000-0001-6744-996X" />
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
15 <organization
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
16 url="https://www.recetox.muni.cz/"
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
17 email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
18 name="RECETOX MUNI" />
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
19 </creator>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
20 </xml>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
21
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
22 <xml name="aggregation_options">
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
23 <option value="matrixStats::colMedians" selected="true">Aggregate using the median of each sample (colMedians)</option>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
24 <option value="MsCoreUtils::medianPolish">Fit an additive model (two way decomposition) using Tukey's median polish procedure (medianPolish)</option>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
25 <option value="BiocGenerics::colMeans">Aggregate using the mean of each sample (colMeans)</option>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
26 <option value="BiocGenerics::colSums">Aggregate using the sum of each sample (colSums)</option>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
27 <option value="MsCoreUtils::robustSummary">Calculate a robust aggregation using MASS::rlm() (robustSummary)</option>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
28 </xml>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
29
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
30 <xml name="normalization_options">
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
31 <option value="center.mean" selected="true">Center sample intensities by subtracting the respective column means (center.mean)</option>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
32 <option value="sum">Divide each feature's intensity by the sum of the feature (sum)</option>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
33 <option value="max">Divide each feature's intensity by the maximum of the feature (max)</option>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
34 <option value="center.median">Center sample intensities by subtracting the respective column medians (center.median)</option>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
35 <option value="div.mean">Divide by the column means (div.mean)</option>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
36 <option value="div.median">Divide by the column medians (div.median)</option>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
37 <option value="diff.median">Center all samples so that they all match the grand median by subtracting the respective columns medians differences to the grand median (diff.median)</option>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
38 <option value="quantiles">Quantile normalization (quantiles)</option>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
39 <option value="vsn">Variance-stabilizing normalization (vsn)</option>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
40 </xml>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
41
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
42 <xml name="scp_param">
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
43 <param name="input_data" type="data" format="tabular" label="Input evidence table" help= "Input file is the evidence.txt table from MaxQuant"/>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
44 <param name="input_annotations" type="data" format="tabular" label="Sample annotations table" help= "A data table specifying metadata; sample annotations."/>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
45 <param name="runcol" type="data_column" data_ref="input_data" use_header_names="true" label="Which column specifies the run identifier and batch name?" help="Column to specify both the run identifier and batch name, has to be present in both tables."/>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
46 <param name="remove_empty_columns" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Remove empty columns?" help="Whether the empty columns should be removed."/>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
47 <param name="generate_QC_plots" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Generate QC plots?" help="Whether to generate quality-control plots (distribution of the average SCR, distribution of median CV and median intensities)."/>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
48
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
49 <section name="filtering_data" title="Data Filtering" expanded="true">
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
50 <param name="filter_reverse" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Filter reverse sequences?" help="Whether to filter the proteins labelled as 'reverse'."/>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
51 <param name="filter_contaminants" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Filter potential contaminants?" help="Whether to filter the proteins labelled as 'potential contaminant'."/>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
52 <param name="PIF_threshold" type="float" value="0.8" min="0" max="1" label="Parental ion fraction (PIF) threshold" help="The threshold for parental ion fraction (PIF)."/>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
53 <param name="minimum_features" type="integer" value="150" min="1" label="Minimum number of PSMs per assay required" help="What is the minimum number of peptide-to-spectrum matches per assay to keep the assay?"/>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
54 <param name="count_cell_carrier" type="integer" value="200" min="0" label="Number of cells in the carrier channel" help="What is the number of cells in the carrier channel?"/>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
55 <param name="single_cells" type="select" label="Single-cell channels present in the experiment" multiple="true" optional="false" min="1" help="What are the single-cell channels present in the experiment? At least one channel must be selected!">
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
56 <options from_dataset="input_annotations">
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
57 <column name="name" index="3"/>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
58 <column name="value" index="3"/>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
59 <filter type="unique_value" name="unique" column="3"/>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
60 </options>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
61 </param>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
62 <param name="SCR_threshold" type="float" value="0.1" min="0" max="1" label="Mean SCR threshold" help="Mean sample-to-carrier (SCR) threshold. 0.1 corresponds to 10%."/>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
63 <param name="qvalue_level" type="select" display="radio" label="Filter based on PSM, peptide or protein-level q-values?" help="Whether to perform the q-value computation and filtration on the PSM, peptide or protein level.">
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
64 <option value="PSM">PSM</option>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
65 <option value="Modified.sequence">peptide</option>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
66 <option value="Leading.razor.protein" selected="true">protein</option>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
67 </param>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
68 <param name="qvalue_threshold" type="float" value="0.01" min="0" max="1" label="q-value threshold" help="Q-value threshold."/>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
69 <param name="divide_reference" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Compute relative reporter ion intensities?" help="Whether to compute the relative reporter ion intensities by dividing the single-cell intensities by the reference channel. Specific for SCOPE2 data."/>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
70 </section>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
71
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
72 <section name="peptide_aggregation" title="Aggregation to peptides" expanded="true">
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
73 <param name="aggregation_peptides" type="select" label="Which function to use for the aggregation?" help="How to aggregate PSMs to peptides?">
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
74 <expand macro="aggregation_options"/>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
75 </param>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
76 <param name="column_aggregation_peptides" type="data_column" data_ref="input_data" use_header_names="true" label="Which column should be used for the PSM to peptide aggregation?" help="Which column should be used for the PSM to peptide aggregation. Modified.sequence is recommended."/>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
77 </section>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
78
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
79 <section name="peptide_filtering" title="Peptide filtering" expanded="true">
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
80 <param name="samples_to_keep" type="select" min="1" optional="false" label="Which samples to keep?" multiple="true" help="Which samples to keep? We recommend filtering out Carrier and Unused channels at this step.">
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
81 <options from_dataset="input_annotations">
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
82 <column name="name" index="3"/>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
83 <column name="value" index="3"/>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
84 <filter type="unique_value" name="unique" column="3"/>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
85 </options>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
86 </param>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
87 <conditional name="filter_median_intensity">
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
88 <param type="select" name="cut_median_intensity" label="Filter based on median relative intensity?" help="Whether to filter based on median intensity.">
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
89 <option value="no" selected="true">no</option>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
90 <option value="yes">yes</option>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
91 </param>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
92 <when value="yes">
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
93 <param label="Median intensity threshold" name="median_intensity_threshold" type="float" min="0" value="0.4" help="Threshold for relative median intensity filtering."/>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
94 </when>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
95 <when value="no"/>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
96 </conditional>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
97 <conditional name="filter_median_CV">
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
98 <param type="select" name="cut_median_CV" label="Filter based on median CV?" help="Whether to filter based on median CV.">
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
99 <option value="yes" selected="true">yes</option>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
100 <option value="no">no</option>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
101 </param>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
102 <when value="yes">
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
103 <param label="How many peptides per protein are required to compute CV?" name="minimum_peptides_CV" type="integer" value="5" min="1" help="Minimum number of peptides per protein required for the CV computation."/>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
104 <param label="Median CV threshold" name="median_CV_threshold" type="float" value="0.65" min="0" max="1" help="Threshold for median CV filtering."/>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
105 </when>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
106 <when value="no"/>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
107 </conditional>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
108 <param name="remove_blank" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Remove blank sample?" help="Whether to remove the blank sample. If it has been already removed, set to 'false'."/>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
109 </section>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
110
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
111 <section name="peptide_processing" title="Processing peptide data" expanded="true">
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
112 <conditional name="normalization_method">
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
113 <param type="select" label="How to perform normalization?" name = "choose_normalization" display="radio" help="How to normalize peptide intensities?">
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
114 <option value="simple">Normalize columns or normalize rows (one only).</option>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
115 <option value="advanced" selected="true">Firstly normalize columns, then rows.</option>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
116 </param>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
117 <when value="simple">
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
118 <param label="Normalization method" name="normalize_simple_method" type="select" help="Which normalization method to choose?">
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
119 <expand macro="normalization_options"/>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
120 </param>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
121 </when>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
122 <when value="advanced">
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
123 <param label="Normalization method columns" name="normalize_columns" type="select" display="radio" help="Which normalization method to choose for columns?">
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
124 <option value="matrixStats::colMeans2">colMeans</option>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
125 <option value="matrixStats::colMedians" selected="true">colMedians</option>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
126 </param>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
127 <param label="Normalization method rows" name="normalize_rows" type="select" display="radio" help="Which normalization method to choose for rows?">
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
128 <option value="matrixStats::rowMeans2" selected="true">rowMeans</option>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
129 <option value="matrixStats::rowMedians">rowMedians</option>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
130 </param>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
131 </when>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
132 </conditional>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
133 <param label="Log transformation base" name="base" type="select" display="radio" help="Which base to use for the log transformation?">
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
134 <option value="2" selected="true">2</option>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
135 <option value="10">10</option>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
136 </param>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
137 <conditional name="remove_missing_peptides">
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
138 <param type="select" name="remove_peptides" label="Remove peptides with high missing rate?" help="Whether to remove the peptides with the high missing rate.">
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
139 <option value="yes" selected="true">yes</option>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
140 <option value="no">no</option>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
141 </param>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
142 <when value="yes">
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
143 <param label="% of NA values filtering threshold" name="pNA_peptides" type="float" value="99" min="0" max="100" help="If peptide has this % of missing values, it will be removed."/>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
144 </when>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
145 <when value="no"/>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
146 </conditional>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
147 </section>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
148
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
149 <section name="protein_aggregation" title="Aggregation to proteins" expanded="true">
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
150 <param name = "aggregation_proteins" type="select" label="Which function to use for the aggregation?" help="How to aggregate peptides to proteins?">
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
151 <expand macro="aggregation_options"/>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
152 </param>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
153 <param name="column_aggregation_proteins" type="data_column" data_ref="input_data" use_header_names="true" label="Which column should be used for the peptide to protein aggregation?" help="Which column should be used for the peptide to protein aggregation. Leading.razor.protein is recommended."/>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
154 </section>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
155
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
156 <section name="protein_processing" title="Processing protein data" expanded="true">
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
157 <conditional name="normalization_method_protein">
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
158 <param type="select" label="How to perform normalization?" name="choose_normalization_protein" display="radio" help="How to normalize protein intensities?">
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
159 <option value="simple_prot">Normalize columns or normalize rows (one only).</option>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
160 <option value="advanced_prot" selected="true">Firstly normalize columns, then rows.</option>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
161 </param>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
162 <when value="simple_prot">
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
163 <param label="Normalization method" name="normalize_simple_method_prot" type="select" help="Which normalization method to choose?">
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
164 <expand macro="normalization_options"/>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
165 </param>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
166 </when>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
167 <when value="advanced_prot">
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
168 <param label="Normalization method columns" name="normalize_columns_prot" display="radio" type="select" help="Which normalization method to choose for columns?">
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
169 <option value="matrixStats::colMeans2">colMeans</option>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
170 <option value="matrixStats::colMedians" selected="true">colMedians</option>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
171 </param>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
172 <param label="Normalization method rows" name="normalize_rows_prot" display="radio" type="select" help="Which normalization method to choose for rows?">
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
173 <option value="matrixStats::rowMeans2" selected="true">rowMeans</option>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
174 <option value="matrixStats::rowMedians">rowMedians</option>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
175 </param>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
176 </when>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
177 </conditional>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
178 <param label="Which k to use for the kNN imputation?" name="impute_k" type="integer" value="3" min="1" help="Number of k-nearest neighbours to consider for kNN imputation."/>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
179 </section>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
180
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
181 <section name="batch_correction" title="Batch correction" expanded="true">
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
182 <conditional name="select_batch_correction">
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
183 <param type="select" label="Which batch correction method to use?" name="batch_correction_method" display="radio" help="Which method to use for correcting the batch effect?">
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
184 <option value="combat" selected="true">ComBat()</option>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
185 <option value="removebatcheffect">removeBatchEffect()</option>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
186 </param>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
187 <when value="combat">
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
188 <param name="batch_col" type="data_column" data_ref="input_annotations" use_header_names="true" label="Which column is the technical variable to be corrected?" help="Column to specify both the run identifier and batch name, has to be present in both tables."/>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
189 </when>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
190 <when value="removebatcheffect">
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
191 <param name="preserve_col" type="data_column" data_ref="input_annotations" use_header_names="true" label="Which column is the variable to be preserved?" help="Which column is the variable to be preserved."/>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
192 <param name="batch_col" type="data_column" data_ref="input_annotations" use_header_names="true" label="Which column is the technical variable to be corrected?" help="Column to specify both the run identifier and batch name, has to be present in both tables."/>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
193 </when>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
194 </conditional>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
195 </section>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
196
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
197 <section name="dimensionality_reduction" title="Dimensionality reduction" expanded="true">
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
198 <conditional name="PCA_computation">
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
199 <param type="select" label="Run principal component analysis (PCA)?" name="run_PCA" display="radio" help="Run the PCA on imputed batch-corrected protein intensities?">
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
200 <option value="yes" selected="true">yes</option>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
201 <option value="no">no</option>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
202 </param>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
203 <when value="yes">
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
204 <param label="Number of components" name="ncomponents_PCA" type="integer" value="5" min="2" help="Number of components in the PCA analysis."/>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
205 <param name="pca_coloring" type="data_column" data_ref="input_annotations" use_header_names="true" label="What column to color the PCA according to?" help="Based on which column from the sampleAnnotation file should be the PCA colored."/>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
206 <conditional name="UMAP_computation">
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
207 <param type="select" label="Run UMAP on PCA data?" name="run_UMAP" display="radio" help="Run the UMAP on PCA-reduced data?">
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
208 <option value="yes" selected="true">yes</option>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
209 <option value="no">no</option>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
210 </param>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
211 <when value="yes">
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
212 <param label="Number of components" name="ncomponents_UMAP" type="integer" value="2" min="2" help="Number of components in the UMAP analysis."/>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
213 </when>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
214 <when value="no"/>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
215 </conditional>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
216 </when>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
217 <when value="no"/>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
218 </conditional>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
219 </section>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
220
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
221 <section name="data_export" title="Export data" expanded="true">
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
222 <param name="export_tables" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Export intermediate results" help="Whether only the final result table (log2 transformed, normalized, imputed, batch-corrected data) should be exported or all intermediate results."/>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
223 <param name="export_RData" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Export scp object as .rds" help="Whether to export the scp object as rds file format."/>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
224 <param name="export_R_script" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Export the R script to reproduce the analysis"
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
225 help="Check this box to export the script executed in the Galaxy tool as an R file to be able to reproduce the same processing offline. Not that in this case, the file paths need to be altered and all the dependencies have to be managed manually."/>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
226 </section>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
227 </xml>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
228
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
229 <xml name="citations">
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
230 <citations>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
231 <citation type="doi">10.1002/cpz1.658</citation>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
232 <citation type="doi">10.1080/14789450.2021.1988571</citation>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
233 <citation type="doi">10.1021/acs.jproteome.3c00227</citation>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
234 <citation type="doi">10.1007/978-1-0716-3934-4_14</citation>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
235 <citation type="doi">10.1101/2023.12.14.571792</citation>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
236 </citations>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
237 </xml>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
238
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
recetox
parents:
diff changeset
239 </macros>