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comparison humann2_barplot.xml @ 0:efd98a5e8255 draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
author iuc
date Tue, 01 Aug 2017 07:57:29 -0400
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-1:000000000000 0:efd98a5e8255
1 <tool id="humann2_barplot" name="Barplot" version="@WRAPPER_VERSION@.0">
2 <description>stratified HUMAnN2 features</description>
3 <macros>
4 <import>humann2_macros.xml</import>
5 </macros>
6 <expand macro="requirements">
7 <requirement type="package" version="2.0.2">matplotlib</requirement>
8 <requirement type="package" version="1.13.1">numpy</requirement>
9 <requirement type="package" version="0.19.1">scipy</requirement>
10 </expand>
11 <expand macro="version"/>
12 <command detect_errors="exit_code"><![CDATA[
13 humann2_barplot
14 --input '$input'
15 --focal-feature '$focal_feature'
16 #if str($top_strata) != ''
17 --top-strata '$top_strata'
18 #end if
19 --sort $sort
20 --last-metadatum '$last_metadatum'
21 --focal-metadatum '$focal_metadatum'
22 #if str($colormap) != ''
23 --colormap '$'colormap'
24 #end if
25 #if str($meta_colormap) != ''
26 --meta-colormap '$meta_colormap'
27 #end if
28 $exclude_unclassified
29 --scaling '$scaling'
30 $as_genera
31 $grid
32 $remove_zeroes
33 --width '$width'
34 --dimensions '$height' '$width'
35 #if str($ylims) != ''
36 --ylims '$ylims'
37 #end if
38 #if $format == 'png'
39 --output 'output.png'
40 #elif $format == 'pdf'
41 --output 'output.pdf'
42 #elif $format == 'svg'
43 --output 'output.svg'
44 #end if
45 ]]></command>
46 <inputs>
47 <param argument="--input" type="data" format="tsv,tabular" label="HUMAnN2 table with optional metadata"/>
48 <param name="focal_feature" argument="--focal-feature" type="text" value="" label="Feature ID of interest (give ID not full name)">
49 <validator type="empty_field" />
50 </param>
51 <param name="top_strata" argument="--top-strata" type="integer" value="" optional="true" label="Number of top stratifications to highlight" help="top = highest grand means"/>
52 <param argument="--sort" type="select" label="Sample sorting methods">
53 <option value="none">Default</option>
54 <option value="sum">Sum of stratified values</option>
55 <option value="dominant">Value of the most dominant stratification</option>
56 <option value="similarity">Bray-Curtis agreement of relative stratifications</option>
57 <option value="usimilarity">Bray-Curtis agreement of raw stratifications</option>
58 <option value="metadata">Given metadata label</option>
59 </param>
60 <param name="focal_metadatum" argument="--focal-metadatum" type="text" value="" label="Metadatum to highlight / group by">
61 <validator type="empty_field" />
62 </param>
63 <param name="last_metadatum" argument="--last-metadatum" type="text" value="" label="End of metadata rows">
64 <validator type="empty_field" />
65 </param>
66 <param argument="--colormap" type="text" value="" optional="true" label="Color space for stratifications"/>
67 <param name="meta_colormap" argument="--meta-colormap" type="text" value="" optional="true" label="Color space for metadata levels"/>
68 <param name="exclude_unclassified" argument="--exclude-unclassified" type="boolean" truevalue="--exclude-unclassified" falsevalue="" checked="false" label="Do not include the 'unclassified' stratum?"/>
69 <param argument="--scaling" type="select" label="Scaling options for total bar heights" help="Strata are always proportional to height">
70 <option value="none">Default</option>
71 <option value="pseudolog">Total bar heights log-scaled (strata are NOT log scaled)</option>
72 <option value="normalize">Bars all have height=1 (highlighting relative attribution)</option>
73 </param>
74 <param name="as_genera" argument="--as-genera" type="boolean" truevalue="--as-genera" falsevalue="" checked="false" label="Collapse species to genera?"/>
75 <param argument="--grid" type="boolean" truevalue="--grid" falsevalue="" checked="false" label="Add y-axis grid?"/>
76 <param name="remove_zeroes" argument="--remove-zeroes" type="boolean" truevalue="--remove-zeroes" falsevalue="" checked="false" label="Do not plot samples with zero sum for this feature?"/>
77 <param argument="--width" type="integer" value="5" label="Relative width of the plot vs. legend"/>
78 <param name="height" argument="--dimensions" type="text" value="8" label="Image height in inches"/>
79 <param name="width" argument="--dimensions" type="text" value="4" label="Image width in inches"/>
80 <param argument="--ylims" type="text" value="" optional="true" label="Limits of y-axis (2 floats separated with a space)"/>
81 <param name="format" type="select" label="Format for the output">
82 <option value="pdf">PDF</option>
83 <option value="png">PNG</option>
84 <option value="svg">SVG</option>
85 </param>
86 </inputs>
87 <outputs>
88 <data format="png" name="barplot_png" from_work_dir="output.png" label="${tool.name} on ${on_string}">
89 <filter>format == 'png'</filter>
90 </data>
91 <data format="pdf" name="barplot_pdf" from_work_dir="output.pdf" label="${tool.name} on ${on_string}">
92 <filter>format == 'pdf'</filter>
93 </data>
94 <data format="svg" name="barplot_svg" from_work_dir="output.svg" label="${tool.name} on ${on_string}">
95 <filter>format == 'svg'</filter>
96 </data>
97 </outputs>
98 <tests>
99 <test>
100 <param name="input" value="hmp_pathabund.txt"/>
101 <param name="focal_feature" value="ANAGLYCOLYSIS-PWY"/>
102 <param name="sort" value="none"/>
103 <param name="last_metadatum" value="STSite"/>
104 <param name="focal_metadatum" value="STSite"/>
105 <param name="exclude_unclassified" value=""/>
106 <param name="scaling" value="none"/>
107 <param name="as_genera" value=""/>
108 <param name="grid" value=""/>
109 <param name="remove_zeroes" value=""/>
110 <param name="width" value="5"/>
111 <param name="height" value="8"/>
112 <param name="width" value="4"/>
113 <param name="format" value="png"/>
114 <output name="barplot_png" file="barplot1.png" ftype="png" compare="sim_size"/>
115 </test>
116 <test>
117 <param name="input" value="hmp_pathabund.txt"/>
118 <param name="focal_feature" value="ANAGLYCOLYSIS-PWY"/>
119 <param name="sort" value="sum"/>
120 <param name="last_metadatum" value="STSite"/>
121 <param name="focal_metadatum" value="STSite"/>
122 <param name="exclude_unclassified" value=""/>
123 <param name="scaling" value="none"/>
124 <param name="as_genera" value=""/>
125 <param name="grid" value=""/>
126 <param name="remove_zeroes" value=""/>
127 <param name="width" value="5"/>
128 <param name="height" value="8"/>
129 <param name="width" value="4"/>
130 <param name="format" value="pdf"/>
131 <output name="barplot_pdf" file="barplot2.pdf" ftype="pdf" compare="sim_size"/>
132 </test>
133 <test>
134 <param name="input" value="hmp_pathabund.txt"/>
135 <param name="focal_feature" value="ANAGLYCOLYSIS-PWY"/>
136 <param name="sort" value="metadata"/>
137 <param name="last_metadatum" value="STSite"/>
138 <param name="focal_metadatum" value="STSite"/>
139 <param name="exclude_unclassified" value="--exclude-unclassified"/>
140 <param name="scaling" value="none"/>
141 <param name="as_genera" value="--as-genera"/>
142 <param name="grid" value="--grid"/>
143 <param name="remove_zeroes" value="--remove-zeroes"/>
144 <param name="width" value="5"/>
145 <param name="height" value="8"/>
146 <param name="width" value="4"/>
147 <param name="format" value="svg"/>
148 <output name="barplot_svg" file="barplot3.svg" ftype="svg" compare="sim_size"/>
149 </test>
150 <test>
151 <param name="input" value="hmp_pathabund.txt"/>
152 <param name="focal_feature" value="ANAGLYCOLYSIS-PWY"/>
153 <param name="top_strata" value="12"/>
154 <param name="sort" value="sum"/>
155 <param name="last_metadatum" value="STSite"/>
156 <param name="focal_metadatum" value="STSite"/>
157 <param name="exclude_unclassified" value=""/>
158 <param name="scaling" value="normalize"/>
159 <param name="as_genera" value=""/>
160 <param name="grid" value=""/>
161 <param name="remove_zeroes" value=""/>
162 <param name="width" value="5"/>
163 <param name="height" value="8"/>
164 <param name="width" value="4"/>
165 <param name="format" value="png"/>
166 <output name="barplot_png" file="barplot4.png" ftype="png" compare="sim_size"/>
167 </test>
168 </tests>
169 <help><![CDATA[
170 @HELP_HEADER@
171
172 humann2_barplot produces plots of stratified HUMAnN2 features and includes many options for sorting and scaling data
173
174 Here is an example of a HUMAnN2 barplot for a pathway (denitrification) that was preferentially enriched in Human Microbiome Project oral samples relative to other body sites. This figure uses many options from humann2_barplot, including regrouping by genus, pseudolog scaling, and sorting samples by similarity and metadata:
175
176 .. image:: $PATH_TO_IMAGES/731303924-page_DENITRIFICATION-PWY.png
177 :width: 800
178 ]]></help>
179 <expand macro="citations"/>
180 </tool>