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comparison export2graphlan.xml @ 0:f3a11239c704 draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
author bebatut
date Mon, 01 Feb 2016 07:45:45 -0500
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children f7e87cc38f57
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1 <tool id="export2graphlan" name="Export to GraPhlAn" version="0.1.0">
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="1.0">export2graphlan</requirement>
10 </requirements>
11
12 <stdio>
13 </stdio>
14
15 <version_command>
16 <![CDATA[
17 python \${EXPORT2GRAPHLAN_DIR}/export2graphlan.py -v
18 ]]>
19 </version_command>
20
21 <command>
22 <![CDATA[
23 python \${EXPORT2GRAPHLAN_DIR}/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" label="Input file"
106 help="Identical to LEfSe input file (--lefse_input)"/>
107
108 <param name="lefse_output" type="data" format="tabular" label="Input file
109 corresponding to LEfSe output file (Optional)" help="(--lefse_output)"
110 optional="True"/>
111
112 <param name="annotations" type="text" label="List which levels should be
113 annotated in the tree (Optional)" help="The levels must be in
114 comma-separated form (--annotations)" optional="True"/>
115
116 <param name="external_annotations" type="text" label="List which levels
117 should use the external legend for the annotation (Optional)"
118 help="The levels must be in comma-separated form (--external_annotations)"
119 optional="True"/>
120
121 <param name="background_levels" type="text" label="List which levels should
122 be highlight with a shaded background (Optional)"
123 help="The levels must be in comma-separated form (--background_levels)"
124 optional="True"/>
125
126 <param name="background_clades" type="text" label="List of the clades that
127 should be highlight with a shaded background (Optional)"
128 help="The clades must be in comma-separated form (--background_clades)"
129 optional="True"/>
130
131 <param name="background_colors" type="text" label="List of color to use
132 for the shaded background (Optional)"
133 help="Colors can be either in RGB or HSV (using a semi-colon to
134 separate values, surrounded with ()). The different colors must be
135 in comma-separated form (--background_colors)"
136 optional="True"/>
137
138 <param name="title" type="text" label="Title of the GraPhlAn plot (Optional)"
139 help="(--title)" optional="True"/>
140
141 <param name="title_font_size" type="integer" value="15" label="Title
142 font size" help="(--title_font_size)"/>
143
144 <param name="def_clade_size" type="integer" value="10" label="Default
145 size for clades that are not found as biomarkers"
146 help="(--def_clade_size)"/>
147
148 <param name="min_clade_size" type="integer" value="20" label="Minimum
149 value of clades that are biomarkers" help="(--min_clade_size)"/>
150
151 <param name="max_clade_size" type="integer" value="200" label="Maximum
152 value of clades that are biomarkers" help="(--max_clade_size)"/>
153
154 <param name="def_font_size" type="integer" value="10" label="Default
155 font size" help="(--def_font_size)"/>
156
157 <param name="min_font_size" type="integer" value="8" label="Minimum
158 font size" help="(--min_font_size)"/>
159
160 <param name="max_font_size" type="integer" value="12" label="Maximum
161 font size" help="(--max_font_size)"/>
162
163 <param name="annotation_legend_font_size" type="integer" value="10"
164 label="Font size for the annotation legend"
165 help="(--annotation_legend_font_size)"/>
166
167 <param name="abundance_threshold" type="float" value="20.0"
168 label="Minimun abundance value for a clade to be annotated"
169 help="(--abundance_threshold)"/>
170
171 <param name="most_abundant" type="integer" label="Number of clades to
172 highlight (Optional)" help="(--most_abundant)" optional="True"/>
173
174 <param name="least_biomarkers" type="integer" label="Minimum number of
175 biomarkers to extract (Optional)" help=" The taxonomy is parsed, and
176 the level is choosen in order to have at least the specified number
177 of biomarkers(--least_biomarkers)" optional="True"/>
178
179 <param name="fname_row" type="integer" value="0" label="Row number
180 containing the names of the features" help="-1 specifies that no
181 names are present in the matrix (--fname_row)"/>
182
183 <param name="sname_row" type="integer" value="0" label="Row number
184 containing the names of the samples" help="-1 specifies that no
185 names are present in the matrix (--sname_row)"/>
186
187 <param name="metadata_rows" type="integer" label="Row number
188 to use as metadata (Optional)" help="(--metadata_rows)" optional="True"/>
189
190 <param name="skip_rows" type="text" label="Row number to skip
191 from the input file" help="The row numbers ar indexed to 0 and comma
192 separated (--skip_rows)" optional="True"/>
193
194 <param name="sperc" type="float" label="Percentile of sample value
195 distribution for sample selection (Optional)" help="(--sperc)"
196 optional="True"/>
197
198 <param name="fperc" type="float" label="Percentile of feature value
199 distribution for sample selection (Optional)" help="(--fperc)"
200 optional="True"/>
201
202 <param name="stop" type="integer" label="Number of top samples to select
203 (Optional)" help="The order is based on percentile specified by --sperc
204 (--stop)" optional="True"/>
205
206 <param name="ftop" type="integer" label="Number of top features to select
207 (Optional)" help="The order is based on percentile specified by --fperc
208 (--ftop)" optional="True"/>
209 </inputs>
210
211 <outputs>
212 <data format="txt" name="tree"
213 label="${tool.name} on ${on_string}: Tree" />
214 <data format="txt" name="annotation"
215 label="${tool.name} on ${on_string}: Annotation" />
216
217 </outputs>
218
219 <tests>
220 <test>
221 </test>
222 </tests>
223
224 <help><![CDATA[
225
226 **What it does**
227
228 export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn. In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important. For more information, check the
229 `user manual <https://bitbucket.org/CibioCM/export2graphlan/overview/>`_.
230
231 ]]></help>
232
233 <citations>
234 </citations>
235 </tool>