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comparison export2graphlan.xml @ 0:b344522045f3 draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit 1b95965e1a861ec37867be554e324eb5bc1ece82-dirty
author bebatut
date Wed, 20 Apr 2016 06:09:29 -0400
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-1:000000000000 0:b344522045f3
1 <tool id="export2graphlan" name="Export to GraPhlAn" version="0.19">
2
3 <description></description>
4
5 <requirements>
6 <requirement type="package" version="0.16">pandas</requirement>
7 <requirement type="package" version="0.16">scipy</requirement>
8 <requirement type="package" version="1.4">matplotlib</requirement>
9 <requirement type="package" version="0.19">export2graphlan</requirement>
10 </requirements>
11
12 <stdio>
13 </stdio>
14
15 <version_command>
16 <![CDATA[
17 export2graphlan.py -v
18 ]]>
19 </version_command>
20
21 <command>
22 <![CDATA[
23 export2graphlan.py
24 -i $lefse_input
25
26 #if $lefse_output
27 -o lefse_output
28 #end if
29
30 -t $tree
31 -a $annotation
32
33 #if $annotations
34 --annotations $annotations
35 #end if
36
37 #if $external_annotations
38 --external_annotations $external_annotations
39 #end if
40
41 #if $background_levels
42 --background_levels $background_levels
43 #end if
44
45 #if $background_clades
46 --background_clades "$background_clades"
47 #end if
48
49 #if $background_colors
50 --background_colors "$background_colors"
51 #end if
52
53 #if $title
54 --title "title"
55 #end if
56
57 --title_font_size $title_font_size
58 --def_clade_size $def_clade_size
59 --min_clade_size $min_clade_size
60 --max_clade_size $max_clade_size
61 --def_font_size $def_font_size
62 --min_font_size $min_font_size
63 --max_font_size $max_font_size
64 --annotation_legend_font_size $annotation_legend_font_size
65 --abundance_threshold $abundance_threshold
66
67 #if $most_abundant
68 --most_abundant $most_abundant
69 #end if
70
71 #if $least_biomarkers
72 --least_biomarkers $least_biomarkers
73 #end if
74
75 --fname_row $fname_row
76 --sname_row $sname_row
77
78 #if $metadata_rows
79 --metadata_rows $metadata_rows
80 #end if
81
82 #if $skip_rows
83 --skip_rows $skip_rows
84 #end if
85
86 #if $sperc
87 --sperc $sperc
88 #end if
89
90 #if $fperc
91 --fperc $fperc
92 #end if
93
94 #if $stop
95 --stop $stop
96 #end if
97
98 #if $ftop
99 --ftop $ftop
100 #end if
101 ]]>
102 </command>
103
104 <inputs>
105 <param name="lefse_input" type="data" format="tabular,txt,tsv" label="Input file" help="Identical to LEfSe input file (--lefse_input)"/>
106
107 <param name="lefse_output" type="data" format="tabular" label="Input file corresponding to LEfSe output file (Optional)" help="(--lefse_output)" optional="True"/>
108
109 <param name="annotations" type="text" label="List which levels should be annotated in the tree (Optional)" help="The levels must be in comma-separated form (--annotations)" optional="True"/>
110
111 <param name="external_annotations" type="text" label="List which levels should use the external legend for the annotation (Optional)" help="The levels must be in comma-separated form (--external_annotations)" optional="True"/>
112
113 <param name="background_levels" type="text" label="List which levels should be highlight with a shaded background (Optional)" help="The levels must be in comma-separated form (--background_levels)" optional="True"/>
114
115 <param name="background_clades" type="text" label="List of the clades that should be highlight with a shaded background (Optional)" help="The clades must be in comma-separated form (--background_clades)" optional="True"/>
116
117 <param name="background_colors" type="text" label="List of color to use for the shaded background (Optional)" help="Colors can be either in RGB or HSV (using a semi-colon to separate values, surrounded with ()). The different colors must be in comma-separated form (--background_colors)" optional="True"/>
118
119 <param name="title" type="text" label="Title of the GraPhlAn plot (Optional)" help="(--title)" optional="True"/>
120
121 <param name="title_font_size" type="integer" value="15" label="Title font size" help="(--title_font_size)"/>
122
123 <param name="def_clade_size" type="integer" value="10" label="Default size for clades that are not found as biomarkers" help="(--def_clade_size)"/>
124
125 <param name="min_clade_size" type="integer" value="20" label="Minimum value of clades that are biomarkers" help="(--min_clade_size)"/>
126
127 <param name="max_clade_size" type="integer" value="200" label="Maximum value of clades that are biomarkers" help="(--max_clade_size)"/>
128
129 <param name="def_font_size" type="integer" value="10" label="Default font size" help="(--def_font_size)"/>
130
131 <param name="min_font_size" type="integer" value="8" label="Minimum font size" help="(--min_font_size)"/>
132
133 <param name="max_font_size" type="integer" value="12" label="Maximum font size" help="(--max_font_size)"/>
134
135 <param name="annotation_legend_font_size" type="integer" value="10" label="Font size for the annotation legend" help="(--annotation_legend_font_size)"/>
136
137 <param name="abundance_threshold" type="float" value="20.0" label="Minimun abundance value for a clade to be annotated" help="(--abundance_threshold)"/>
138
139 <param name="most_abundant" type="integer" label="Number of clades to highlight (Optional)" help="(--most_abundant)" optional="True"/>
140
141 <param name="least_biomarkers" type="integer" label="Minimum number of biomarkers to extract (Optional)" help=" The taxonomy is parsed, and the level is choosen in order to have at least the specified number of biomarkers(--least_biomarkers)" optional="True"/>
142
143 <param name="fname_row" type="integer" value="0" label="Row number containing the names of the features" help="-1 specifies that no names are present in the matrix (--fname_row)"/>
144
145 <param name="sname_row" type="integer" value="0" label="Row number containing the names of the samples" help="-1 specifies that no names are present in the matrix (--sname_row)"/>
146
147 <param name="metadata_rows" type="integer" label="Row number to use as metadata (Optional)" help="(--metadata_rows)" optional="True"/>
148
149 <param name="skip_rows" type="text" label="Row number to skip from the input file" help="The row numbers ar indexed to 0 and comma separated (--skip_rows)" optional="True"/>
150
151 <param name="sperc" type="float" label="Percentile of sample value
152 distribution for sample selection (Optional)" help="(--sperc)"
153 optional="True"/>
154
155 <param name="fperc" type="float" label="Percentile of feature value distribution for sample selection (Optional)" help="(--fperc)" optional="True"/>
156
157 <param name="stop" type="integer" label="Number of top samples to select (Optional)" help="The order is based on percentile specified by --sperc (--stop)" optional="True"/>
158
159 <param name="ftop" type="integer" label="Number of top features to select (Optional)" help="The order is based on percentile specified by --fperc (--ftop)" optional="True"/>
160 </inputs>
161
162 <outputs>
163 <data format="txt" name="tree" label="${tool.name} on ${on_string}: Tree" />
164 <data format="txt" name="annotation" label="${tool.name} on ${on_string}: Annotation" />
165 </outputs>
166
167 <tests>
168 <test>
169 <param name="lefse_input" value="input_profile.tabular"/>
170 <param name="annotations" value=""/>
171 <param name="external_annotations" value=""/>
172 <param name="background_levels" value=""/>
173 <param name="background_clades" value=""/>
174 <param name="background_colors" value=""/>
175 <param name="title" value=""/>
176 <param name="title_font_size" value="15"/>
177 <param name="def_clade_size" value="10"/>
178 <param name="min_clade_size" value="20"/>
179 <param name="max_clade_size" value="200"/>
180 <param name="def_font_size" value="10"/>
181 <param name="min_font_size" value="8"/>
182 <param name="max_font_size" value="12"/>
183 <param name="annotation_legend_font_size" value="10"/>
184 <param name="abundance_threshold" value="20.0"/>
185 <param name="most_abundant" value=""/>
186 <param name="least_biomarkers" value=""/>
187 <param name="fname_row" value="0"/>
188 <param name="sname_row" value="0" />
189 <param name="metadata_rows" value=""/>
190 <param name="skip_rows" value=""/>
191 <param name="sperc" value=""/>
192 <param name="fperc" value=""/>
193 <param name="stop" value=""/>
194 <param name="ftop" value=""/>
195 <output name="annotation" file="annotation_output.txt"/>
196 <output name="tree" file="tree_output.txt"/>
197 </test>
198 </tests>
199
200 <help><![CDATA[
201
202 **What it does**
203
204 export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn. It can convert MetaPhlAn, LEfSe, and/or HUMAnN output to GraPhlAn input format
205
206 In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important.
207
208 For more information, check the
209 `user manual <https://bitbucket.org/CibioCM/export2graphlan/overview/>`_.
210
211 ]]></help>
212
213 <citations>
214 </citations>
215 </tool>