Mercurial > repos > qfabrepo > metadegalaxy_phyloseq_abundance_factor
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 |
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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> |