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comparison export2graphlan.xml @ 0:ed1becc01910 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
author iuc
date Sat, 04 Mar 2017 11:44:38 -0500
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children b16989c1e3a7
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-1:000000000000 0:ed1becc01910
1 <tool id="export2graphlan" name="Export to GraPhlAn" version="0.19">
2 <description></description>
3 <requirements>
4 <requirement type="package" version="0.19">export2graphlan</requirement>
5 </requirements>
6 <stdio>
7 </stdio>
8 <version_command>
9 <![CDATA[
10 export2graphlan.py -v
11 ]]>
12 </version_command>
13 <command>
14 <![CDATA[
15 export2graphlan.py
16 --lefse_input '$lefse_input'
17 #if $input_lefse_output.input_lefse_output_test == "true"
18 --lefse_output '$input_lefse_output.lefse_output'
19 #end if
20 -t '$tree'
21 -a '$annotation'
22 #if $annotations
23 --annotations '$annotations'
24 #end if
25 #if $external_annotations
26 --external_annotations '$external_annotations'
27 #end if
28 #if $background_levels
29 --background_levels '$background_levels'
30 #end if
31 #if $background_clades
32 --background_clades '$background_clades'
33 #end if
34 #if $background_colors
35 --background_colors '$background_colors'
36 #end if
37 #if $title
38 --title '$title'
39 #end if
40
41 --title_font_size '$title_font_size'
42 --def_clade_size '$def_clade_size'
43 --min_clade_size '$min_clade_size'
44 --max_clade_size '$max_clade_size'
45 --def_font_size '$def_font_size'
46 --min_font_size '$min_font_size'
47 --max_font_size '$max_font_size'
48 --annotation_legend_font_size '$annotation_legend_font_size'
49 --abundance_threshold '$abundance_threshold'
50
51 #if $most_abundant
52 --most_abundant '$most_abundant'
53 #end if
54 #if $least_biomarkers
55 --least_biomarkers '$least_biomarkers'
56 #end if
57
58 --fname_row '$fname_row'
59 --sname_row '$sname_row'
60
61 #if $metadata_rows
62 --metadata_rows '$metadata_rows'
63 #end if
64 #if $skip_rows
65 --skip_rows '$skip_rows'
66 #end if
67 #if $sperc
68 --sperc '$sperc'
69 #end if
70 #if $fperc
71 --fperc '$fperc'
72 #end if
73 #if $stop
74 --stop '$stop'
75 #end if
76 #if $ftop
77 --ftop '$ftop'
78 #end if
79 ]]>
80 </command>
81 <inputs>
82 <param argument="--lefse_input" type="data" format="tabular,txt,tsv" label="Input file" help="Identical to LEfSe input file"/>
83 <conditional name="input_lefse_output">
84 <param name="input_lefse_output_test" type="select" label="Use a LEfSe output file as input?" help="">
85 <option value="true">Yes</option>
86 <option value="false" selected="true">No</option>
87 </param>
88 <when value="true">
89 <param argument="--lefse_output" type="data" format="tabular" label="Input file corresponding to LEfSe output file"/>
90 </when>
91 <when value="false"/>
92 </conditional>
93 <param argument="--annotations" type="text" label="List which levels should be annotated in the tree" help="The levels must be in comma-separated form" optional="True"/>
94 <param argument="--external_annotations" type="text" label="List which levels should use the external legend for the annotation" help="The levels must be in comma-separated form" optional="True"/>
95 <param argument="--background_levels" type="text" label="List which levels should be highlight with a shaded background" help="The levels must be in comma-separated form" optional="True"/>
96 <param argument="--background_clades" type="text" label="List of the clades that should be highlight with a shaded background" help="The clades must be in comma-separated form" optional="True"/>
97 <param argument="--background_colors" type="text" label="List of color to use for the shaded background" 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" optional="True"/>
98 <param argument="--title" type="text" label="Title of the GraPhlAn plot" optional="True"/>
99 <param argument="--title_font_size" type="integer" value="15" label="Title font size"/>
100 <param argument="--def_clade_size" type="integer" value="10" label="Default size for clades that are not found as biomarkers"/>
101 <param argument="--min_clade_size" type="integer" value="20" label="Minimum value of clades that are biomarkers"/>
102 <param argument="--max_clade_size" type="integer" value="200" label="Maximum value of clades that are biomarkers"/>
103 <param argument="--def_font_size" type="integer" value="10" label="Default font size"/>
104 <param argument="--min_font_size" type="integer" value="8" label="Minimum font size"/>
105 <param argument="--max_font_size" type="integer" value="12" label="Maximum font size"/>
106 <param argument="--annotation_legend_font_size" type="integer" value="10" label="Font size for the annotation legend"/>
107 <param argument="--abundance_threshold" type="float" value="20.0" label="Minimun abundance value for a clade to be annotated"/>
108 <param argument="--most_abundant" type="integer" label="Number of clades to highlight" optional="True"/>
109 <param argument="--least_biomarkers" type="integer" label="Minimum number of biomarkers to extract" help=" The taxonomy is parsed, and the level is choosen in order to have at least the specified number of biomarkers" optional="True"/>
110 <param argument="--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"/>
111 <param argument="--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"/>
112 <param argument="--metadata_rows" type="integer" label="Row number to use as metadata" optional="True"/>
113 <param argument="--skip_rows" type="text" label="Row number to skip from the input file" help="The row numbers are indexed to 0 and comma separated" optional="True"/>
114 <param argument="--sperc" type="float" label="Percentile of sample value distribution for sample selection" optional="True"/>
115 <param argument="--fperc" type="float" label="Percentile of feature value distribution for sample selection" optional="True"/>
116 <param argument="--stop" type="integer" label="Number of top samples to select" help="The order is based on percentile specified by --sperc" optional="True"/>
117 <param argument="--ftop" type="integer" label="Number of top features to select" help="The order is based on percentile specified by --fperc" optional="True"/>
118 </inputs>
119 <outputs>
120 <data format="txt" name="tree" label="${tool.name} on ${on_string}: Tree" />
121 <data format="txt" name="annotation" label="${tool.name} on ${on_string}: Annotation" />
122 </outputs>
123 <tests>
124 <test>
125 <param name="lefse_input" value="input_profile.tabular"/>
126 <param name="input_lefse_output_test" value="no" />
127 <param name="annotations" value=""/>
128 <param name="external_annotations" value=""/>
129 <param name="background_levels" value=""/>
130 <param name="background_clades" value=""/>
131 <param name="background_colors" value=""/>
132 <param name="title" value=""/>
133 <param name="title_font_size" value="15"/>
134 <param name="def_clade_size" value="10"/>
135 <param name="min_clade_size" value="20"/>
136 <param name="max_clade_size" value="200"/>
137 <param name="def_font_size" value="10"/>
138 <param name="min_font_size" value="8"/>
139 <param name="max_font_size" value="12"/>
140 <param name="annotation_legend_font_size" value="10"/>
141 <param name="abundance_threshold" value="20.0"/>
142 <param name="most_abundant" value=""/>
143 <param name="least_biomarkers" value=""/>
144 <param name="fname_row" value="0"/>
145 <param name="sname_row" value="0" />
146 <param name="metadata_rows" value=""/>
147 <param name="skip_rows" value=""/>
148 <param name="sperc" value=""/>
149 <param name="fperc" value=""/>
150 <param name="stop" value=""/>
151 <param name="ftop" value=""/>
152 <output name="annotation" file="annotation_output.txt"/>
153 <output name="tree" file="tree_output.txt"/>
154 </test>
155 </tests>
156 <help><![CDATA[
157
158 **What it does**
159
160 export2graphlan is a conversion software tool to produce both annotation and tree file for GraPhlAn. It can convert MetaPhlAn, LEfSe, and/or HUMAnN output to GraPhlAn input format
161
162 In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important.
163
164 For more information, check the `user manual <https://bitbucket.org/CibioCM/export2graphlan/overview/>`_.
165
166 ]]></help>
167 <citations>
168 </citations>
169 </tool>