comparison phyloseq_abundance_factor.xml @ 0:3856a1590a11 draft default tip

"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
author qfabrepo
date Mon, 14 Sep 2020 08:02:08 +0000
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1 <tool id="phyloseq_abundance" name="Phyloseq Abundance plot" version="1.22.3.3" hidden="false">
2 <description>Phyloseq Abundance Plot with the factors of choice</description>
3 <requirements>
4 <requirement type="package" version="3.4.1">r-base</requirement>
5 <requirement type="package" version="1.22.3">bioconductor-phyloseq</requirement>
6 <requirement type="package" version="1.20.0">r-getopt</requirement>
7 <requirement type="package" version="9.18">ghostscript</requirement>
8 </requirements>
9 <version_command><![CDATA[
10 echo $(R --version | grep version | grep -v GNU)", phyloseq version" $(R --vanilla --slave -e "library(phyloseq); cat(sessionInfo()\$otherPkgs\$phyloseq\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
11 ]]></version_command>
12 <command detect_errors="exit_code"><![CDATA[
13 Rscript '${__tool_directory__}/phyloseq_abundance_factor.r'
14 #if str($factor.type) == "one":
15 --biomfile=$biom_input
16 --metafile=$metadata_input
17 --xcolumn="${xaxis_column}"
18 --lcolumn="${legend_column}"
19 --factor1="${factor.factor_column1}"
20 --outdir="$htmlfile.files_path"
21 --htmlfile='$htmlfile'
22 #else if str($factor.type) == "two":
23 --biomfile='$biom_input'
24 --metafile='$metadata_input'
25 --xcolumn="${xaxis_column}"
26 --lcolumn="${legend_column}"
27 --factor1="${factor.factor_column1}"
28 --factor2="${factor.factor_column2}"
29 --outdir="$htmlfile.files_path"
30 --htmlfile='$htmlfile'
31 #end if
32 ]]> </command>
33
34
35 <inputs>
36
37 <param format="biom1" name="biom_input" type="data" label="BIOM file"/>
38 <param format="tabular" name="metadata_input" type="data" label="Metadata file"/>
39 <param name="xaxis_column" type="data_column" data_ref="metadata_input" use_header_names="TRUE" label="Column used for X-axis"/>
40 <param name="legend_column" type="data_column" data_ref="metadata_input" use_header_names="TRUE" label="Column used as legend"/>
41 <conditional name="factor">
42 <param name="type" type="select" label="Is this one factor or two factor">
43 <option value="one">1</option>
44 <option value="two">2</option>
45 </param>
46 <when value="one">
47 <param name="factor_column1" type="data_column" data_ref="metadata_input" use_header_names="TRUE" label="Column used as factor 1"/>
48 </when>
49 <when value="two">
50 <param name="factor_column1" type="data_column" data_ref="metadata_input" use_header_names="TRUE" label="Column used as factor 1"/>
51 <param name="factor_column2" type="data_column" data_ref="metadata_input" use_header_names="TRUE" label="Column used as factor 2"/>
52 </when>
53 </conditional>
54
55 </inputs>
56
57 <outputs>
58 <data format="html" name="htmlfile" label="${tool.name}.html"/>
59 </outputs>
60
61 <tests>
62 <test>
63 <param name="biom_input" value="test.biom" ftype="biom1" />
64 <param name="metadata_input" value="metadata.txt"/>
65 <param name="xaxis_column" value="5" />
66 <param name="legend_column" value="3" />
67 <param name="type" value="1" />
68 <param name="factor_column1" value="4"/>
69 <output name="htmlfile" ftype="html" file="abundace_factor.html" />
70 </test>
71 </tests>
72
73 <help>
74 **What it does**
75 Creates an abundance barplot using an R package called phyloseq_.
76
77 .. _phyloseq: https://joey711.github.io/phyloseq/plot_bar-examples.html
78
79 -----
80
81 **Input**
82
83
84 - **BIOM file** - this is a BIOM_ file format
85 - **Metadata file** - this is a metadata file of the experiment design
86 - **Column used for X-axis** - The horizontal x-axis display on the barplot.
87 - **Column used as legend** - select a group from the metadata to fill color to represent the group it belongs to.
88 - **Is this one factor or two factor** - This is the facet_grid feature of phyloseq's plot_bar to allow plotting with two factors (e.g, facet_grid=~protein + allergy)
89 - **Column used as factor 1** - select the first factor for facet_grid feature from the metadata file
90
91 .. _BIOM: http://biom-format.org/
92
93 -----
94
95 =========
96 Resources
97 =========
98
99 **Wrapper Authors**
100
101 QFAB Bioinformatics (support@qfab.org)
102
103 </help>
104 <citations>
105 <citation type="doi">10.18129/B9.bioc.phyloseq</citation>
106 <citation type="doi">doi:10.1186/2047-217X-1-7</citation>
107 </citations>
108 </tool>