Mercurial > repos > recetox > ramclustr_csv

comparison ramclustr_csv.xml @ 0:43b60b28ccf7 draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
author recetox
date Mon, 07 Dec 2020 22:14:48 +0000
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-1:000000000000 0:43b60b28ccf7
1 <tool id="ramclustr_csv" name="RAMClustR (CSV)" version="@TOOL_VERSION@+galaxy0">
2 <macros>
3 <import>ramclustr_macros.xml</import>
4 </macros>
5
6 <requirements>
7 <container type="docker">recetox/ramclustr:1.1.0-recetox0</container>
8 </requirements>
9
10 <inputs>
11 <expand macro="parameters_csv" />
12 <expand macro="parameters_required" />
13 <expand macro="parameters_optional" />
14 </inputs>
15
16 <command detect_errors="aggressive"><![CDATA[
17 Rscript
18 -e 'source("${__tool_directory__}/ramclustr_wrapper.R")'
19 -e 'x <- ramclustr_csv(
20 ms="$ms_csv.ms",
21 idmsms="$ms_csv.idmsms",
22 feature_delimiter="$ms_csv.feature_delimiter",
23 sample_name_column = $ms_csv.sample_name_column,
24 retention_time_column= $ms_csv.retention_time_column,
25 sr = $required.sr,
26 deep_split = $required.deepSplit,
27 block_size = $required.blocksize,
28 mult = $required.mult,
29 hmax = $required.hmax,
30 collapse = $required.collapse,
31 use_pheno = $required.usePheno,
32 qc_inj_range = $required.qc_inj_range,
33 normalize = "$required.normalize",
34 min_module_size = $required.minModuleSize,
35 linkage = "$required.linkage",
36 mzdec = $required.mzdec,
37 cor_method = "$required.cor_method",
38 rt_only_low_n = $required.rt_only_low_n,
39 replace_zeros = $required.replace_zeros,
40 #if $optional.st
41 st = $optional.st,
42 #end if
43 #if $optional.maxt
44 maxt = $optional.maxt,
45 #end if
46 #if $optional.fftempdir
47 fftempdir = $optional.fftempdir,
48 #end if
49 )'
50 -e 'store_output(x, "$result", "$method_metadata", $required.merge_msp, "$spec_abundance")'
51
52 ]]>
53 </command>
54
55 <outputs>
56 <data label="${tool.name} on ${on_string}" name="result" format="RData" />
57 <data label="Spec Abundance of ${on_string}" name="spec_abundance" format="csv" />
58 <data label="Metadata for ${tool.name} on ${on_string}" name="method_metadata" format="txt"/>
59 <expand macro="output_msp"/>
60 </outputs>
61
62 <help>
63 Documentation
64 For documentation on the tool see https://github.com/cbroeckl/RAMClustR/blob/master/vignettes/RAMClustR.Rmd
65
66 Upstream Tools
67 +-------+------------------------+--------+------------+
68 | Name | Output File | Format | Parameter |
69 +=======+========================+========+============+
70 | ??? | Feature Table with MS1 | csv | ms |
71 +-------+------------------------+--------+------------+
72 | ??? | Feature Table with MS2 | csv | idmsms |
73 +-------+------------------------+--------+------------+
74
75 The tool takes a **csv** table as input which has to fulfill the following requirements
76
77 (1) no more than one sample (or file) name column and one feature name row;
78 (2) feature names that contain the mass and retention times, separated by a constant delimiter; and
79 (3) features in columns and samples in rows.
80
81 Downstream Tools
82 +---------+--------------+----------------------+
83 | Name | Output File | Format |
84 +=========+==============+======================+
85 | matchMS | Mass Spectra | collection (tgz/msp) |
86 +---------+--------------+----------------------+
87
88 @GENERAL_HELP@
89 </help>
90
91 <expand macro="citations" />
92 </tool>