Mercurial > repos > artbio > ez_histograms

annotate ez_histograms.xml @ 1:fbedb212982d draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 5e25392164eca5585239b62c82b7f6ba326cda6e
author artbio
date Thu, 08 Feb 2024 02:15:11 +0000
parents bdf40b0924cb
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
1 <tool id="ez_histograms" name="ez_histograms" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
2 <macros>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
3 <token name="@TOOL_VERSION@">3.4.4</token>
1
fbedb212982d planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 5e25392164eca5585239b62c82b7f6ba326cda6e
artbio
parents: 0
diff changeset
4 <token name="@VERSION_SUFFIX@">1</token>
0
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
5 <token name="@PROFILE@">23.0</token>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
6 </macros>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
7 <requirements>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
8 <requirement type="package" version="3.4.4">r-ggplot2</requirement>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
9 <requirement type="package" version="1.4.4">r-reshape2</requirement>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
10 <requirement type="package" version="1.1.4">r-dplyr</requirement>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
11 <requirement type="package" version="1.3.0">r-scales</requirement>
1
fbedb212982d planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 5e25392164eca5585239b62c82b7f6ba326cda6e
artbio
parents: 0
diff changeset
12 <requirement type="package" version="2.4.1">r-psych</requirement>
0
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
13 <requirement type="package" version="1.7.4">r-optparse</requirement>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
14 </requirements>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
15
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
16 <stdio>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
17 <exit_code range="1:" level="fatal" />
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
18 </stdio>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
19
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
20 <command detect_errors="exit_code"><![CDATA[
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
21 Rscript $__tool_directory__/ez_histograms.R
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
22 --file '$file'
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
23 --profile '$plot_options.plot_options_selector'
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
24 --xscale '$plot_options.xscale'
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
25 #if str($plot_options.plot_options_selector) == "count":
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
26 --yscale '$plot_options.yscale'
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
27 #end if
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
28 --pdf '$pdf'
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
29 --summary '$summary'
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
30 ]]></command>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
31
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
32 <inputs>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
33 <param name="file" type="data" format="tabular" label="Input tabular dataset"
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
34 help="Only numeric columns will be plotted"/>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
35 <conditional name="plot_options">
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
36 <param name="plot_options_selector" type="select" label="Set plot types">
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
37 <option value="count" selected="true">Count Histograms</option>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
38 <option value="density">Density Plots</option>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
39 </param>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
40 <when value="density">
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
41 <param name="xscale" type="select" label="Set x-axis scale">
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
42 <option value="cartesian" selected="true">Cartesian</option>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
43 <option value="log2">log2</option>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
44 <option value="log10">log10</option>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
45 </param>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
46 </when>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
47 <when value="count">
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
48 <param name="xscale" type="select" label="Set x-axis scale">
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
49 <option value="cartesian" selected="true">Cartesian</option>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
50 <option value="log2">log2</option>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
51 <option value="log10">log10</option>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
52 </param>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
53 <param name="yscale" type="select" label="Set y-axis scale">
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
54 <option value="cartesian" selected="true">Cartesian</option>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
55 <option value="log2">log2</option>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
56 <option value="log10">log10</option>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
57 </param>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
58 </when>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
59 </conditional>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
60 </inputs>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
61 <outputs>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
62 <data name="pdf" format="pdf" label="${tool.name} plots from ${on_string}"/>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
63 <data name="summary" format="tabular" label="Statistics Summary from ${on_string}"/>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
64 </outputs>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
65 <tests>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
66 <test expect_num_outputs="2">
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
67 <param name="file" value="classic.tsv"/>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
68 <param name="plot_options_selector" value="count"/>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
69 <param name="xscale" value="cartesian"/>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
70 <param name="yscale" value="cartesian"/>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
71 <output name="pdf" file="classic.pdf"/>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
72 <output name="summary" file="summary_1.tsv"/>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
73 </test>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
74 <test expect_num_outputs="2">
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
75 <param name="file" value="counts.tsv"/>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
76 <param name="plot_options_selector" value="count"/>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
77 <param name="xscale" value="log2"/>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
78 <param name="yscale" value="cartesian"/>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
79 <output name="pdf" file="count.pdf"/>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
80 <output name="summary" file="summary_2.tsv"/>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
81 </test>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
82 <test expect_num_outputs="2">
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
83 <param name="file" value="headless.tsv"/>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
84 <param name="plot_options_selector" value="count"/>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
85 <param name="xscale" value="log10"/>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
86 <param name="yscale" value="log2"/>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
87 <output name="pdf" file="headless.pdf"/>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
88 <output name="summary" file="summary_3.tsv"/>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
89 </test>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
90 <test expect_num_outputs="2">
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
91 <param name="file" value="large.tsv"/>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
92 <param name="plot_options_selector" value="density"/>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
93 <param name="xscale" value="log2"/>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
94 <output name="pdf" file="large.pdf"/>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
95 <output name="summary" file="summary_4.tsv"/>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
96 </test>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
97 <test expect_num_outputs="2">
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
98 <param name="file" value="rowheadless.tsv"/>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
99 <param name="plot_options_selector" value="density"/>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
100 <param name="xscale" value="cartesian"/>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
101 <output name="pdf" file="rowheadless.pdf"/>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
102 <output name="summary" file="summary_5.tsv"/>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
103 </test>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
104 <test expect_num_outputs="2">
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
105 <param name="file" value="single_headed_col.tsv"/>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
106 <param name="plot_options_selector" value="density"/>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
107 <param name="xscale" value="log10"/>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
108 <output name="pdf" file="single_headed_col.pdf"/>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
109 <output name="summary" file="summary_6.tsv"/>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
110 </test>
1
fbedb212982d planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 5e25392164eca5585239b62c82b7f6ba326cda6e
artbio
parents: 0
diff changeset
111 <test expect_num_outputs="2">
fbedb212982d planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 5e25392164eca5585239b62c82b7f6ba326cda6e
artbio
parents: 0
diff changeset
112 <param name="file" value="misleading_ids.tsv"/>
fbedb212982d planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 5e25392164eca5585239b62c82b7f6ba326cda6e
artbio
parents: 0
diff changeset
113 <param name="plot_options_selector" value="density"/>
fbedb212982d planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 5e25392164eca5585239b62c82b7f6ba326cda6e
artbio
parents: 0
diff changeset
114 <param name="xscale" value="cartesian"/>
fbedb212982d planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 5e25392164eca5585239b62c82b7f6ba326cda6e
artbio
parents: 0
diff changeset
115 <output name="pdf" file="misleading_ids.pdf"/>
fbedb212982d planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 5e25392164eca5585239b62c82b7f6ba326cda6e
artbio
parents: 0
diff changeset
116 <output name="summary" file="summary_7.tsv"/>
fbedb212982d planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 5e25392164eca5585239b62c82b7f6ba326cda6e
artbio
parents: 0
diff changeset
117 </test>
0
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
118 </tests>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
119 <help><![CDATA[
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
120 **What it does**
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
121
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
122 The tool generates faceted histograms or density plots using the ggplot2 functions
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
123 geom_histogram() or geom_density(), respectively.
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
124
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
125 **Inputs**
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
126
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
127 Any regular tabular data, provided that the number of columns (tabulations) is unchanged
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
128 for any row.
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
129
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
130 Except for the first one, any column will be considered as one variable with n_rows
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
131 observations. However, non-numeric columns will be filtered and will not be considered
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
132 variables.
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
133
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
134 If the first column is not numeric, it will be taken as row names (ie observation identifiers),
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
135 otherwise, it will be considered as the first numerical variable of the table.
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
136
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
137 If the first row is not numerical, it will be considered as a header, ie as describing the
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
138 variable names.
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
139
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
140 If you provide a table without header, variable names will be assigned to each column
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
141 following the R default rule: (V1), V2, ..., Vn
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
142
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
143 **Parameters**
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
144
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
145 For Count Histograms, both x- and y-axis can have linear (cartesian), log2 or log10 scales.
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
146
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
147 For Density Plots, only x-axis can be customized with linear (cartesian), log2, or log10
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
148 scales
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
149
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
150 **Outputs**
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
151
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
152 The ez_histograms Galaxy tool returns
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
153
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
154 - A pdf file with plots faceted on three columns
1
fbedb212982d planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 5e25392164eca5585239b62c82b7f6ba326cda6e
artbio
parents: 0
diff changeset
155 - A tsv file with statistics summary of the variables generated by the R package psych
0
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
156
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
157 ]]></help>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
158 <citations>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
159 <citation type="bibtex">
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
160 @BOOK{Wickham2016-ic,
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
161 title = "Ggplot2: Elegant graphics for data analysis",
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
162 author = "Wickham, Hadley",
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
163 publisher = "Springer International Publishing",
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
164 series = "Use R!",
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
165 edition = 2,
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
166 month = jun,
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
167 year = 2016,
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
168 address = "Cham, Switzerland",
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
169 language = "en",
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
170 isbn = "9783319242774"
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
171 } </citation>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
172 </citations>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
parents:
diff changeset
173 </tool>