Mercurial > repos > qfabrepo > metadegalaxy_phyloseq_richness
comparison phyloseq_richness.xml @ 0:0ab4501d805b draft
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
author | qfabrepo |
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date | Mon, 14 Sep 2020 07:38:57 +0000 |
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children | e0225f3e8ef6 |
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1 <tool id="phyloseq_richness" name="Phyloseq Richness" version="1.22.3.2" hidden="false"> | |
2 <description>Phyloseq Richness Plot</description> | |
3 <requirements> | |
4 <requirement type="package" version="1.22.3">bioconductor-phyloseq</requirement> | |
5 <requirement type="package" version="1.20.0">r-getopt</requirement> | |
6 <requirement type="package" version="9.18">ghostscript</requirement> | |
7 </requirements> | |
8 <version_command><![CDATA[ | |
9 echo $(R --version | grep version | grep -v GNU)", phyloseq version" $(R --vanilla --slave -e "library(phyloseq); cat(sessionInfo()\$otherPkgs\$phyloseq\$Version)" 2> /dev/null | grep -v -i "WARNING: ") | |
10 ]]></version_command> | |
11 <command detect_errors="exit_code"><![CDATA[ | |
12 Rscript '${__tool_directory__}/phyloseq_richness.r' | |
13 --biomfile='$biom_input' | |
14 --metafile='$metadata_input' | |
15 --xcolumn="${xaxis_column}" | |
16 --lcolumn="${legend_column}" | |
17 --outdir="$htmlfile.files_path" | |
18 --htmlfile='$htmlfile' | |
19 ]]></command> | |
20 | |
21 <inputs> | |
22 <param format="biom1" name="biom_input" type="data" label="BIOM file"/> | |
23 <param format="tabular" name="metadata_input" type="data" label="Metadata file"/> | |
24 <param name="xaxis_column" type="data_column" data_ref="metadata_input" use_header_names="TRUE" label="Column used for X-axis"/> | |
25 <param name="legend_column" type="data_column" data_ref="metadata_input" use_header_names="TRUE" label="Column used as legend"/> | |
26 </inputs> | |
27 | |
28 <outputs> | |
29 <data format="html" name="htmlfile" label="${tool.name}.html"/> | |
30 </outputs> | |
31 | |
32 <tests> | |
33 <test> | |
34 <param name="biom_input" value="test.biom" ftype="biom1" /> | |
35 <param name="metadata_input" value="metadata.txt" /> | |
36 <param name="xaxis_column" value="5" /> | |
37 <param name="legend_column" value="4" /> | |
38 <output name="htmlfile" ftype="html" file="biom_out.html" /> | |
39 </test> | |
40 </tests> | |
41 | |
42 | |
43 <help> | |
44 **What it does** | |
45 Creates an alpha biodivesrsity abundance plot using an R package called phyloseq_. | |
46 | |
47 .. _phyloseq: https://joey711.github.io/phyloseq/plot_richness-examples.html | |
48 | |
49 ----- | |
50 | |
51 **Input** | |
52 | |
53 | |
54 - **BIOM file** - this is a BIOM_ file format | |
55 - **Metadata file** - this is a metadata file of the experiment design | |
56 - **Column used for X-axis** - The horizontal x-axis display on the barplot. | |
57 - **Column used as legend** - select a group from the metadata to fill color to represent the group it belongs to. | |
58 | |
59 .. _BIOM: http://biom-format.org/ | |
60 | |
61 ----- | |
62 | |
63 ========= | |
64 Resources | |
65 ========= | |
66 | |
67 **Wrapper Authors** | |
68 | |
69 QFAB Bioinformatics (support@qfab.org) | |
70 | |
71 </help> | |
72 <citations> | |
73 <citation type="doi">10.18129/B9.bioc.phyloseq</citation> | |
74 <citation type="doi">doi:10.1186/2047-217X-1-7</citation> | |
75 </citations> | |
76 ----- | |
77 | |
78 </help> | |
79 </tool> |