Mercurial > repos > galaxyp > maxquant_phosphopeptide_intensity

comparison maxquant_phosphopeptide_intensity.xml @ 0:b09ed1684301 draft default tip

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15"
author galaxyp
date Thu, 04 Nov 2021 18:35:10 +0000
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1 <tool id="maxquant_phosphopeptide_intensity" name="MaxQuant Phosphopeptide Intensity" version="0.1.0" python_template_version="3.5">
2 <description>for each sample</description>
3 <requirements>
4 <requirement type="package" version="1.14.2">r-data.table</requirement>
5 <requirement type="package" version="1.7.1">r-optparse</requirement>
6 <requirement type="package" version="1.4.0">r-stringr</requirement>
7 </requirements>
8 <command detect_errors="exit_code"><![CDATA[
9 Rscript '$__tool_directory__/MaxQuantProcessingScript.R'
10 -i '$phospho_sites'
11 --enriched $enriched
12 --phosphoCol $phosphoCol
13 --numSamples $numSamples
14 --startCol $startCol
15 --intervalCol $intervalCol
16 --localProbCutoff $localProbCutoff
17 --collapse_func $collapse_func
18 -o phosphopeptide_intensities.tsv
19 && head phosphopeptide_intensities.tsv
20
21 ]]></command>
22 <inputs>
23 <param name="phospho_sites" type="data" format="tabular" label="MaxQuant Phospho (STY)Sites.txt"/>
24 <param name="phosphoCol" type="data_column" numerical="false" data_ref="phospho_sites" label="Column: Number of Phospho (STY)" />
25 <param name="numSamples" type="integer" value="1" min="1" label="Number of samples or runs"/>
26 <param name="startCol" type="data_column" numerical="false" data_ref="phospho_sites" label="Column: Intensity of the first sample" />
27 <param name="intervalCol" type="integer" value="1" min="1" label="Interval between the intensity column of samples" help="eg, 1 if subsequent column; 2 if every other column"/>
28 <param name="enriched" type="select" label="Phospho enrichemnt type">
29 <option value="ST">ST</option>
30 <option value="Y">Y</option>
31 </param>
32 <param name="collapse_func" type="select" label="Intensity merge function">
33 <option value="sum">sum</option>
34 <option value="averge">averge</option>
35 </param>
36 <param name="localProbCutoff" type="float" value="0.75" min="0" max="1.0" label="Localization Probability Cutoff"/>
37 </inputs>
38 <outputs>
39 <data name="output" format="tabular" from_work_dir="phosphopeptide_intensities.tsv"/>
40 </outputs>
41 <tests>
42 <test>
43 <param name="phospho_sites" ftype="tabular" value="Phospho (ST)Sites_NancyDu.txt"/>
44 <param name="phosphoCol" value="37"/>
45 <param name="numSamples" value="6"/>
46 <param name="startCol" value="58"/>
47 <param name="intervalCol" value="1"/>
48 <param name="enriched" value="ST"/>
49 <param name="collapse_func" value="sum"/>
50 <param name="localProbCutoff" value="0.75"/>
51 <output name="output">
52 <assert_contents>
53 <has_text text="Phosphopeptide" />
54 <has_text text="AAAAAAAGDpSDpSWDADAFSVEDPVRK" />
55 <has_text text="997800000" />
56 </assert_contents>
57 </output>
58 </test>
59 </tests>
60 <help><![CDATA[
61 TODO: Fill in help.
62 ]]></help>
63 </tool>