Mercurial > repos > iuc > metagenomeseq_normalization
comparison metagenomeseq_normalization.xml @ 0:d16f7cc26516 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metagenomeseq commit c7e28b83e8636a5d11010bea9997a449be1d48e0
author | iuc |
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date | Wed, 12 Apr 2017 17:19:48 -0400 |
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1 <tool id="metagenomeseq_normalizaton" name="metagenomeSeq Normalization" version="1.16.0-0.0.1"> | |
2 <description>Cumulative sum scaling</description> | |
3 <requirements> | |
4 <requirement type="package" version="1.16.0">bioconductor-metagenomeseq</requirement> | |
5 <requirement type="package" version="1.2.0">bioconductor-biomformat</requirement> | |
6 </requirements> | |
7 <version_command><![CDATA[Rscript -e 'suppressMessages(library("metagenomeSeq"));cat(toString(packageVersion("metagenomeSeq")))']]></version_command> | |
8 <command detect_errors="exit_code"><![CDATA[ | |
9 #if "output_r_script" in str( $include_outputs ).split( "," ): | |
10 cp '${metagenomeseq_normalization_script}' '${output_r_script}' && | |
11 #end if | |
12 Rscript '${metagenomeseq_normalization_script}' | |
13 ]]> | |
14 </command> | |
15 <configfiles> | |
16 <configfile name="metagenomeseq_normalization_script"><![CDATA[#!/usr/bin/env RScript | |
17 #set $include_files = str( $include_outputs ).split( "," ) | |
18 library(metagenomeSeq) | |
19 library(biomformat) | |
20 | |
21 #if $input_abundance_file.is_of_type( 'biom1' ): | |
22 inputMRe = biom2MRexperiment( biomformat::read_biom( "${input_abundance_file}" ) ) | |
23 #else: | |
24 ##inputMRe = newMRexperiment( counts, phenoData = NULL, featureData = NULL, libSize = NULL, normFactors = NULL) | |
25 #raise "Not yet implemented" | |
26 #end if | |
27 | |
28 #if str( $percentile_type.percentile_type_selector ) == 'cumNormStat': | |
29 p = cumNormStat( inputMRe, qFlag = ${percentile_type.qFlag}, rel = ${percentile_type.rel} ) | |
30 #elif str( $percentile_type.percentile_type_selector ) == 'cumNormStatFast': | |
31 p = cumNormStatFast( inputMRe, rel = ${percentile_type.rel} ) | |
32 #else: | |
33 p = ${percentile_type.raw_value} | |
34 #end if | |
35 | |
36 inputMRe = cumNorm(inputMRe, p = p ) | |
37 | |
38 #if "output_tabular" in $include_files: | |
39 mat = MRcounts(inputMRe, norm = TRUE, log = ${log2}, sl = ${sl}) | |
40 exportMat(mat, file = "${output_tabular_dataset}") | |
41 #end if | |
42 | |
43 #if "output_biom" in $include_files: | |
44 biomformat::write_biom( MRexperiment2biom(inputMRe, id = NULL, norm = TRUE, log = ${log2}, sl = ${sl}, qiimeVersion = TRUE), "${output_biom_dataset}" ) | |
45 #end if | |
46 | |
47 #if "output_stats" in $include_files: | |
48 exportStats(inputMRe, p = p, file = "${output_stats}") | |
49 #end if | |
50 ]]> | |
51 </configfile> | |
52 </configfiles> | |
53 <inputs> | |
54 <param name="input_abundance_file" type="data" format="biom1" label="Input Matrix" help="BIOM format"/> | |
55 | |
56 <conditional name="percentile_type"> | |
57 <param name="percentile_type_selector" type="select" label="Percentile for which to scale data"> | |
58 <option value="cumNormStat" selected="True">cumNormStat</option> | |
59 <option value="cumNormStatFast" selected="False">cumNormStatFast</option> | |
60 <option value="raw" selected="False">Raw</option> | |
61 </param> | |
62 <when value="cumNormStat"> | |
63 <param name="qFlag" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="qFlag" help="Flag to either calculate the proper percentile using R's step-wise quantile function or approximate function."/> | |
64 <param name="rel" type="float" value="0.1" label="rel" help="Cutoff for the relative difference from one median difference from the reference to the next"/> | |
65 </when> | |
66 <when value="cumNormStatFast"> | |
67 <param name="rel" type="float" value="0.1" label="rel" help="Cutoff for the relative difference from one median difference from the reference to the next"/> | |
68 </when> | |
69 <when value="raw"> | |
70 <param name="raw_value" type="float" value=".80" label="Percentile" help="Manual Percentile"/> | |
71 </when> | |
72 </conditional> | |
73 | |
74 <param name="log2" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="Log2 transform scaling" help=""/> | |
75 <param name="sl" type="integer" value="1000" label="The value to scale by." help="(default=1000)"/> | |
76 | |
77 <param name="include_outputs" type="select" multiple="True" label="Datasets to create"> | |
78 <option value="output_tabular" selected="True">Normalized Tabular Matrix</option> | |
79 <!-- <option value="output_biom" selected="True">Normalized BIOM</option> --> | |
80 <option value="output_stats" selected="True">Simple Statistics</option> | |
81 <option value="output_r_script" selected="False">R script</option> | |
82 </param> | |
83 </inputs> | |
84 <outputs> | |
85 <!-- <data format="biom1" name="output_biom_dataset" label="${tool.name} on ${on_string} (BIOM1)"> | |
86 <filter>"output_biom" in include_outputs</filter> | |
87 </data> --> | |
88 <data format="tabular" name="output_tabular_dataset" label="${tool.name} on ${on_string} (Tabular)"> | |
89 <filter>"output_tabular" in include_outputs</filter> | |
90 </data> | |
91 <data format="tabular" name="output_stats" label="${tool.name} on ${on_string} (Simple Statistics)"> | |
92 <filter>"output_stats" in include_outputs</filter> | |
93 </data> | |
94 <data format="txt" name="output_r_script" label="${tool.name} on ${on_string} (Rscript)"> | |
95 <filter>"output_r_script" in include_outputs</filter> | |
96 </data> | |
97 </outputs> | |
98 <tests> | |
99 <test> | |
100 <param name="input_abundance_file" value="input_1.biom1" ftype="biom1"/> | |
101 <conditional name="percentile_type"> | |
102 <param name="percentile_type_selector" value="cumNormStat"/> | |
103 <param name="qFlag" value="TRUE"/> | |
104 <param name="rel" value=".1"/> | |
105 </conditional> | |
106 <param name="log2" value="FALSE"/> | |
107 <param name="sl" value="1000"/> | |
108 <output name="output_tabular_dataset"> | |
109 <assert_contents> | |
110 <has_text_matching expression="SAMPLE_2" /> | |
111 </assert_contents> | |
112 </output> | |
113 </test> | |
114 </tests> | |
115 <help><![CDATA[ | |
116 metagenomeSeq Cumulative sum scaling | |
117 ==================================== | |
118 | |
119 Info | |
120 ---- | |
121 | |
122 :: | |
123 | |
124 Cumulative sum scaling based upon percentile selection. You can manually specificy the percentile or calculate it using cumNormStat or cumNormStatFast. | |
125 | |
126 Inputs | |
127 ------ | |
128 | |
129 :: | |
130 | |
131 Requires a BIOM formatted file for input. | |
132 | |
133 Outputs | |
134 ------- | |
135 | |
136 :: | |
137 | |
138 Creates a normalized and scaled output abundance matrix in Tabular format. Additionally can create simple statistics and the RScript. | |
139 | |
140 ]]></help> | |
141 <citations> | |
142 <citation type="doi">10.1038/nmeth.2658</citation> | |
143 </citations> | |
144 </tool> |