Mercurial > repos > iuc > phyloseq_plot_bar
annotate phyloseq_plot_bar.xml @ 3:d0fa6a43c838 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 26f87cc62468c9c329b33246af4f14e2659856f9
author | iuc |
---|---|
date | Fri, 10 Jan 2025 14:58:52 +0000 |
parents | ad81e112f4d9 |
children | 94563110275d |
rev | line source |
---|---|
0
ad81e112f4d9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
iuc
parents:
diff
changeset
|
1 <tool id="phyloseq_plot_bar" name="Phyloseq: Bar Chart" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
ad81e112f4d9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
iuc
parents:
diff
changeset
|
2 <description>Generate bar charts from a phyloseq object</description> |
ad81e112f4d9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
iuc
parents:
diff
changeset
|
3 <macros> |
ad81e112f4d9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
iuc
parents:
diff
changeset
|
4 <import>macros.xml</import> |
ad81e112f4d9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
iuc
parents:
diff
changeset
|
5 </macros> |
ad81e112f4d9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
iuc
parents:
diff
changeset
|
6 <expand macro="bio_tools"/> |
ad81e112f4d9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
iuc
parents:
diff
changeset
|
7 <expand macro="requirements"/> |
ad81e112f4d9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
iuc
parents:
diff
changeset
|
8 <command detect_errors="exit_code"><![CDATA[ |
ad81e112f4d9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
iuc
parents:
diff
changeset
|
9 Rscript '${__tool_directory__}/phyloseq_plot_bar.R' |
ad81e112f4d9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
iuc
parents:
diff
changeset
|
10 --input '$input' |
ad81e112f4d9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
iuc
parents:
diff
changeset
|
11 --x '$x' |
ad81e112f4d9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
iuc
parents:
diff
changeset
|
12 --fill '$fill' |
ad81e112f4d9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
iuc
parents:
diff
changeset
|
13 --facet '${facet}' |
ad81e112f4d9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
iuc
parents:
diff
changeset
|
14 --output '$output' |
3
d0fa6a43c838
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 26f87cc62468c9c329b33246af4f14e2659856f9
iuc
parents:
0
diff
changeset
|
15 --topX '${topX}' |
d0fa6a43c838
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 26f87cc62468c9c329b33246af4f14e2659856f9
iuc
parents:
0
diff
changeset
|
16 --keepOthers '${keepOthers}' |
d0fa6a43c838
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 26f87cc62468c9c329b33246af4f14e2659856f9
iuc
parents:
0
diff
changeset
|
17 --keepNonAssigned '${keepNonAssigned}' |
d0fa6a43c838
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 26f87cc62468c9c329b33246af4f14e2659856f9
iuc
parents:
0
diff
changeset
|
18 --normalize '${normalize}' |
d0fa6a43c838
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 26f87cc62468c9c329b33246af4f14e2659856f9
iuc
parents:
0
diff
changeset
|
19 --width '${width}' |
d0fa6a43c838
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 26f87cc62468c9c329b33246af4f14e2659856f9
iuc
parents:
0
diff
changeset
|
20 --height '${height}' |
d0fa6a43c838
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 26f87cc62468c9c329b33246af4f14e2659856f9
iuc
parents:
0
diff
changeset
|
21 --device '${device}' |
0
ad81e112f4d9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
iuc
parents:
diff
changeset
|
22 ]]></command> |
ad81e112f4d9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
iuc
parents:
diff
changeset
|
23 <inputs> |
ad81e112f4d9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
iuc
parents:
diff
changeset
|
24 <expand macro="phyloseq_input"/> |
3
d0fa6a43c838
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 26f87cc62468c9c329b33246af4f14e2659856f9
iuc
parents:
0
diff
changeset
|
25 <param name="x" type="text" optional="true" label="X-axis variable" help="Variable for the x-axis (e.g., Sample, Phylum). If not specified, the Samples are taken." /> |
d0fa6a43c838
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 26f87cc62468c9c329b33246af4f14e2659856f9
iuc
parents:
0
diff
changeset
|
26 <param name="fill" type="text" label="Fill variable" help="Variable to color the bars (e.g., Genus, Order)." /> |
d0fa6a43c838
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 26f87cc62468c9c329b33246af4f14e2659856f9
iuc
parents:
0
diff
changeset
|
27 <param name="facet" type="text" optional="true" label="Facet by variable" help="Variable to facet the chart by (e.g., SampleType)." /> |
d0fa6a43c838
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 26f87cc62468c9c329b33246af4f14e2659856f9
iuc
parents:
0
diff
changeset
|
28 <param name="topX" value="10" type="integer" optional="true" label="Top X" help="Only show the ranks with the top X abundance." /> |
d0fa6a43c838
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 26f87cc62468c9c329b33246af4f14e2659856f9
iuc
parents:
0
diff
changeset
|
29 <param name="keepOthers" type="boolean" label="Keep 'Others'" help="Keep OTUs which are not in top X as 'Others'." /> |
d0fa6a43c838
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 26f87cc62468c9c329b33246af4f14e2659856f9
iuc
parents:
0
diff
changeset
|
30 <param name="keepNonAssigned" type="boolean" label="Keep Non Assigned" help="Keep OTUs that are not assigned at this rank and label as 'Not Assigned'." /> |
d0fa6a43c838
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 26f87cc62468c9c329b33246af4f14e2659856f9
iuc
parents:
0
diff
changeset
|
31 <param name="normalize" type="boolean" label="Normalize" help="Normalize abundances to sum to 100%. Normalization is performed before Top X selection." /> |
d0fa6a43c838
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 26f87cc62468c9c329b33246af4f14e2659856f9
iuc
parents:
0
diff
changeset
|
32 <param name="width" type="float" value="10" optional="true" label="Plot Width" help="Width of the output plot in inches." /> |
d0fa6a43c838
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 26f87cc62468c9c329b33246af4f14e2659856f9
iuc
parents:
0
diff
changeset
|
33 <param name="height" type="float" value="8" optional="true" label="Plot Height" help="Height of the output plot in inches." /> |
d0fa6a43c838
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 26f87cc62468c9c329b33246af4f14e2659856f9
iuc
parents:
0
diff
changeset
|
34 <param name="device" type="select" value="pdf" label="Output Device" help="Device to use for the output file. Options include pdf, png, and others."> |
d0fa6a43c838
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 26f87cc62468c9c329b33246af4f14e2659856f9
iuc
parents:
0
diff
changeset
|
35 <option value="pdf">PDF</option> |
d0fa6a43c838
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 26f87cc62468c9c329b33246af4f14e2659856f9
iuc
parents:
0
diff
changeset
|
36 <option value="png">PNG</option> |
d0fa6a43c838
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 26f87cc62468c9c329b33246af4f14e2659856f9
iuc
parents:
0
diff
changeset
|
37 <option value="jpeg">JPEG</option> |
d0fa6a43c838
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 26f87cc62468c9c329b33246af4f14e2659856f9
iuc
parents:
0
diff
changeset
|
38 <option value="tiff">TIFF</option> |
d0fa6a43c838
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 26f87cc62468c9c329b33246af4f14e2659856f9
iuc
parents:
0
diff
changeset
|
39 </param> |
0
ad81e112f4d9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
iuc
parents:
diff
changeset
|
40 </inputs> |
ad81e112f4d9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
iuc
parents:
diff
changeset
|
41 <outputs> |
ad81e112f4d9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
iuc
parents:
diff
changeset
|
42 <data name="output" format="pdf" label="Bar Chart (PDF)" /> |
ad81e112f4d9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
iuc
parents:
diff
changeset
|
43 </outputs> |
3
d0fa6a43c838
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 26f87cc62468c9c329b33246af4f14e2659856f9
iuc
parents:
0
diff
changeset
|
44 <tests> |
d0fa6a43c838
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 26f87cc62468c9c329b33246af4f14e2659856f9
iuc
parents:
0
diff
changeset
|
45 <!-- Test 1: Basic functionality with x and fill variables --> |
0
ad81e112f4d9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
iuc
parents:
diff
changeset
|
46 <test> |
3
d0fa6a43c838
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 26f87cc62468c9c329b33246af4f14e2659856f9
iuc
parents:
0
diff
changeset
|
47 <param name="input" value="output.phyloseq" ftype="phyloseq"/> |
d0fa6a43c838
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 26f87cc62468c9c329b33246af4f14e2659856f9
iuc
parents:
0
diff
changeset
|
48 <param name="x" value="Property"/> |
d0fa6a43c838
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 26f87cc62468c9c329b33246af4f14e2659856f9
iuc
parents:
0
diff
changeset
|
49 <param name="fill" value="Phylum"/> |
d0fa6a43c838
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 26f87cc62468c9c329b33246af4f14e2659856f9
iuc
parents:
0
diff
changeset
|
50 <param name="device" value="pdf"/> |
d0fa6a43c838
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 26f87cc62468c9c329b33246af4f14e2659856f9
iuc
parents:
0
diff
changeset
|
51 <output name="output" ftype="pdf"> |
d0fa6a43c838
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 26f87cc62468c9c329b33246af4f14e2659856f9
iuc
parents:
0
diff
changeset
|
52 <assert_contents> |
d0fa6a43c838
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 26f87cc62468c9c329b33246af4f14e2659856f9
iuc
parents:
0
diff
changeset
|
53 <has_text text="%PDF"/> |
d0fa6a43c838
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 26f87cc62468c9c329b33246af4f14e2659856f9
iuc
parents:
0
diff
changeset
|
54 <has_text text="%%EOF"/> |
d0fa6a43c838
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 26f87cc62468c9c329b33246af4f14e2659856f9
iuc
parents:
0
diff
changeset
|
55 </assert_contents> |
d0fa6a43c838
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 26f87cc62468c9c329b33246af4f14e2659856f9
iuc
parents:
0
diff
changeset
|
56 </output> |
0
ad81e112f4d9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
iuc
parents:
diff
changeset
|
57 </test> |
3
d0fa6a43c838
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 26f87cc62468c9c329b33246af4f14e2659856f9
iuc
parents:
0
diff
changeset
|
58 |
d0fa6a43c838
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 26f87cc62468c9c329b33246af4f14e2659856f9
iuc
parents:
0
diff
changeset
|
59 <!-- Test 2: TopX filtering and normalization --> |
0
ad81e112f4d9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
iuc
parents:
diff
changeset
|
60 <test> |
3
d0fa6a43c838
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 26f87cc62468c9c329b33246af4f14e2659856f9
iuc
parents:
0
diff
changeset
|
61 <param name="input" value="output.phyloseq" ftype="phyloseq"/> |
d0fa6a43c838
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 26f87cc62468c9c329b33246af4f14e2659856f9
iuc
parents:
0
diff
changeset
|
62 <param name="x" value="Property"/> |
d0fa6a43c838
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 26f87cc62468c9c329b33246af4f14e2659856f9
iuc
parents:
0
diff
changeset
|
63 <param name="fill" value="Genus"/> |
d0fa6a43c838
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 26f87cc62468c9c329b33246af4f14e2659856f9
iuc
parents:
0
diff
changeset
|
64 <param name="facet" value="SampleType"/> |
d0fa6a43c838
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 26f87cc62468c9c329b33246af4f14e2659856f9
iuc
parents:
0
diff
changeset
|
65 <param name="topX" value="10"/> |
d0fa6a43c838
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 26f87cc62468c9c329b33246af4f14e2659856f9
iuc
parents:
0
diff
changeset
|
66 <param name="normalize" value="true"/> |
d0fa6a43c838
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 26f87cc62468c9c329b33246af4f14e2659856f9
iuc
parents:
0
diff
changeset
|
67 <output name="output" ftype="pdf"> |
d0fa6a43c838
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 26f87cc62468c9c329b33246af4f14e2659856f9
iuc
parents:
0
diff
changeset
|
68 <assert_contents> |
d0fa6a43c838
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 26f87cc62468c9c329b33246af4f14e2659856f9
iuc
parents:
0
diff
changeset
|
69 <has_text text="%PDF"/> |
d0fa6a43c838
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 26f87cc62468c9c329b33246af4f14e2659856f9
iuc
parents:
0
diff
changeset
|
70 <has_text text="%%EOF"/> |
d0fa6a43c838
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 26f87cc62468c9c329b33246af4f14e2659856f9
iuc
parents:
0
diff
changeset
|
71 </assert_contents> |
d0fa6a43c838
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 26f87cc62468c9c329b33246af4f14e2659856f9
iuc
parents:
0
diff
changeset
|
72 </output> |
0
ad81e112f4d9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
iuc
parents:
diff
changeset
|
73 </test> |
3
d0fa6a43c838
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 26f87cc62468c9c329b33246af4f14e2659856f9
iuc
parents:
0
diff
changeset
|
74 </tests> |
0
ad81e112f4d9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
iuc
parents:
diff
changeset
|
75 |
ad81e112f4d9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
iuc
parents:
diff
changeset
|
76 <help> |
ad81e112f4d9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
iuc
parents:
diff
changeset
|
77 **Description** |
ad81e112f4d9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
iuc
parents:
diff
changeset
|
78 |
ad81e112f4d9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
iuc
parents:
diff
changeset
|
79 This tool generates bar charts from a phyloseq object using the `plot_bar` function. |
ad81e112f4d9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
iuc
parents:
diff
changeset
|
80 |
ad81e112f4d9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
iuc
parents:
diff
changeset
|
81 **Inputs** |
ad81e112f4d9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
iuc
parents:
diff
changeset
|
82 |
ad81e112f4d9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
iuc
parents:
diff
changeset
|
83 - **Input**: A phyloseq object in RDS format. |
ad81e112f4d9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
iuc
parents:
diff
changeset
|
84 - **X-axis variable**: The variable to use for the x-axis (e.g., Sample, Phylum). |
ad81e112f4d9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
iuc
parents:
diff
changeset
|
85 - **Fill variable**: (Optional) The variable to use for the bar fill colors (e.g., Genus, Order). |
ad81e112f4d9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
iuc
parents:
diff
changeset
|
86 - **Facet by variable**: (Optional) A variable to facet the bar chart (e.g., SampleType). |
3
d0fa6a43c838
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 26f87cc62468c9c329b33246af4f14e2659856f9
iuc
parents:
0
diff
changeset
|
87 - **Width and Height**: Dimensions of the plot in inches (default: 10x8). |
d0fa6a43c838
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 26f87cc62468c9c329b33246af4f14e2659856f9
iuc
parents:
0
diff
changeset
|
88 - **Device**: Output format (e.g., pdf, png, jpeg, tiff). |
0
ad81e112f4d9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
iuc
parents:
diff
changeset
|
89 |
ad81e112f4d9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
iuc
parents:
diff
changeset
|
90 **Outputs** |
ad81e112f4d9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
iuc
parents:
diff
changeset
|
91 |
3
d0fa6a43c838
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 26f87cc62468c9c329b33246af4f14e2659856f9
iuc
parents:
0
diff
changeset
|
92 - A file containing the bar chart in the specified format. |
0
ad81e112f4d9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
iuc
parents:
diff
changeset
|
93 |
ad81e112f4d9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
iuc
parents:
diff
changeset
|
94 **Usage Notes** |
ad81e112f4d9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
iuc
parents:
diff
changeset
|
95 |
ad81e112f4d9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
iuc
parents:
diff
changeset
|
96 Ensure that the input file is a valid phyloseq object in RDS format. |
ad81e112f4d9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
iuc
parents:
diff
changeset
|
97 </help> |
ad81e112f4d9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
iuc
parents:
diff
changeset
|
98 <expand macro="citations"/> |
ad81e112f4d9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
iuc
parents:
diff
changeset
|
99 </tool> |