Mercurial > repos > iuc > export2graphlan

comparison export2graphlan.xml @ 1:fd7e308fdd11 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/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
author iuc
date Wed, 07 Aug 2019 14:48:52 -0400
parents 20f96e852e24
children
comparison
equal deleted inserted replaced
0:20f96e852e24 1:fd7e308fdd11
1 <tool id="export2graphlan" name="Export to GraPhlAn" version="0.19"> 1 <tool id="export2graphlan" name="Export to GraPhlAn" version="@VERSION@+@GALAXY_VERSION@">
2 <description></description> 2 <macros>
3 <token name="@VERSION@">0.20</token>
4 <token name="@GALAXY_VERSION@">galaxy0</token>
5 </macros>
3 <requirements> 6 <requirements>
4 <requirement type="package" version="0.19">export2graphlan</requirement> 7 <requirement type="package" version="@VERSION@">export2graphlan</requirement>
5 </requirements> 8 </requirements>
6 <stdio>
7 </stdio>
8 <version_command> 9 <version_command>
9 <![CDATA[ 10 <![CDATA[
10 export2graphlan.py -v 11 export2graphlan.py -h | grep "ver."
11 ]]> 12 ]]>
12 </version_command> 13 </version_command>
13 <command> 14 <command detect_errors="exit_code">
14 <![CDATA[ 15 <![CDATA[
15 export2graphlan.py 16 export2graphlan.py
16 --lefse_input '$lefse_input' 17 --lefse_input '$lefse_input'
17 #if $input_lefse_output.input_lefse_output_test == "true" 18 #if $input_lefse_output.input_lefse_output_test == "true"
18 --lefse_output '$input_lefse_output.lefse_output' 19 --lefse_output '$input_lefse_output.lefse_output'
19 #end if 20 #end if
20 -t '$tree' 21 -t '$tree'
21 -a '$annotation' 22 -a '$annotation'
22 #if $annotations 23 #if str($annotations) != ''
23 --annotations '$annotations' 24 --annotations $annotations
24 #end if 25 #end if
25 #if $external_annotations 26 #if str($external_annotations) != ''
26 --external_annotations '$external_annotations' 27 --external_annotations $external_annotations
27 #end if 28 #end if
28 #if $background_levels 29 #if str($background_levels) != ''
29 --background_levels '$background_levels' 30 --background_levels $background_levels
30 #end if 31 #end if
31 #if $background_clades 32 #if str($background_clades) != ''
32 --background_clades '$background_clades' 33 --background_clades '$background_clades'
33 #end if 34 #end if
34 #if $background_colors 35 #if str($background_colors) != ''
35 --background_colors '$background_colors' 36 --background_colors '$background_colors'
36 #end if 37 #end if
37 #if $title 38 #if str($title) != ''
38 --title '$title' 39 --title '$title'
39 #end if 40 #end if
40 41 #if str($title_font_size) != ''
41 --title_font_size '$title_font_size' 42 --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 43 #end if
54 #if $least_biomarkers 44 #if str($def_clade_size) != ''
55 --least_biomarkers '$least_biomarkers' 45 --def_clade_size $def_clade_size
56 #end if 46 #end if
57 47 #if str($min_clade_size) != ''
58 --fname_row '$fname_row' 48 --min_clade_size $min_clade_size
59 --sname_row '$sname_row'
60
61 #if $metadata_rows
62 --metadata_rows '$metadata_rows'
63 #end if 49 #end if
64 #if $skip_rows 50 #if str($max_clade_size) != ''
65 --skip_rows '$skip_rows' 51 --max_clade_size $max_clade_size
66 #end if 52 #end if
67 #if $sperc 53 #if str($def_font_size) != ''
68 --sperc '$sperc' 54 --def_font_size $def_font_size
69 #end if 55 #end if
70 #if $fperc 56 #if str($min_font_size) != ''
71 --fperc '$fperc' 57 --min_font_size $min_font_size
72 #end if 58 #end if
73 #if $stop 59 #if str($max_font_size) != ''
74 --stop '$stop' 60 --max_font_size $max_font_size
75 #end if 61 #end if
76 #if $ftop 62 #if str($annotation_legend_font_size) != ''
77 --ftop '$ftop' 63 --annotation_legend_font_size $annotation_legend_font_size
64 #end if
65 #if str($abundance_threshold) != ''
66 --abundance_threshold $abundance_threshold
67 #end if
68 #if str($most_abundant) != ''
69 --most_abundant $most_abundant
70 #end if
71 #if str($least_biomarkers) != ''
72 --least_biomarkers $least_biomarkers
73 #end if
74 #if str($title_font_size) != ''
75 --fname_row $fname_row
76 #end if
77 #if str($title_font_size) != ''
78 --sname_row $sname_row
79 #end if
80 #if str($metadata_rows) != ''
81 --metadata_rows $metadata_rows
82 #end if
83 #if str($skip_rows) != ''
84 --skip_rows $skip_rows
85 #end if
86 #if str($sperc) != ''
87 --sperc $sperc
88 #end if
89 #if str($fperc) != ''
90 --fperc $fperc
91 #end if
92 #if str($stop) != ''
93 --stop $stop
94 #end if
95 #if str($ftop) != ''
96 --ftop $ftop
78 #end if 97 #end if
79 ]]> 98 ]]>
80 </command> 99 </command>
81 <inputs> 100 <inputs>
82 <param argument="--lefse_input" type="data" format="tabular,txt,tsv" label="Input file" help="Identical to LEfSe input file"/> 101 <param argument="--lefse_input" type="data" format="tabular,txt,tsv" label="Input file" help="Identical to LEfSe input file"/>
88 <when value="true"> 107 <when value="true">
89 <param argument="--lefse_output" type="data" format="tabular" label="Input file corresponding to LEfSe output file"/> 108 <param argument="--lefse_output" type="data" format="tabular" label="Input file corresponding to LEfSe output file"/>
90 </when> 109 </when>
91 <when value="false"/> 110 <when value="false"/>
92 </conditional> 111 </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"/> 112 <param argument="--annotations" type="text" optional="True" label="List which levels should be annotated in the tree" help="The levels must be in comma-separated form"/>
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"/> 113 <param argument="--external_annotations" type="text" optional="True" label="List which levels should use the external legend for the annotation" help="The levels must be in comma-separated form"/>
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"/> 114 <param argument="--background_levels" type="text" optional="True" label="List which levels should be highlight with a shaded background" help="The levels must be in comma-separated form"/>
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"/> 115 <param argument="--background_clades" type="text" optional="True" label="List of the clades that should be highlight with a shaded background" help="The clades must be in comma-separated form"/>
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"/> 116 <param argument="--background_colors" type="text" optional="True" 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"/>
98 <param argument="--title" type="text" label="Title of the GraPhlAn plot" optional="True"/> 117 <param argument="--title" type="text" optional="True" label="Title of the GraPhlAn plot" />
99 <param argument="--title_font_size" type="integer" value="15" label="Title font size"/> 118 <param argument="--title_font_size" type="integer" optional="True" 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"/> 119 <param argument="--def_clade_size" type="integer" optional="True" 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"/> 120 <param argument="--min_clade_size" type="integer" optional="True" 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"/> 121 <param argument="--max_clade_size" type="integer" optional="True" label="Maximum value of clades that are biomarkers"/>
103 <param argument="--def_font_size" type="integer" value="10" label="Default font size"/> 122 <param argument="--def_font_size" type="integer" optional="True" label="Default font size"/>
104 <param argument="--min_font_size" type="integer" value="8" label="Minimum font size"/> 123 <param argument="--min_font_size" type="integer" optional="True" label="Minimum font size"/>
105 <param argument="--max_font_size" type="integer" value="12" label="Maximum font size"/> 124 <param argument="--max_font_size" type="integer" optional="True" label="Maximum font size"/>
106 <param argument="--annotation_legend_font_size" type="integer" value="10" label="Font size for the annotation legend"/> 125 <param argument="--annotation_legend_font_size" type="integer" optional="True" 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"/> 126 <param argument="--abundance_threshold" type="float" optional="True" 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"/> 127 <param argument="--most_abundant" type="integer" optional="True" label="Number of clades to highlight"/>
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"/> 128 <param argument="--least_biomarkers" type="integer" optional="True" 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"/>
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"/> 129 <param argument="--fname_row" type="integer" optional="True" 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"/> 130 <param argument="--sname_row" type="integer" optional="True" 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"/> 131 <param argument="--metadata_rows" type="integer" optional="True" label="Row number to use as metadata"/>
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"/> 132 <param argument="--skip_rows" type="text" optional="True" label="Row number to skip from the input file" help="The row numbers are indexed to 0 and comma separated"/>
114 <param argument="--sperc" type="float" label="Percentile of sample value distribution for sample selection" optional="True"/> 133 <param argument="--sperc" type="float" optional="True" label="Percentile of sample value distribution for sample selection"/>
115 <param argument="--fperc" type="float" label="Percentile of feature value distribution for sample selection" optional="True"/> 134 <param argument="--fperc" type="float" optional="True" label="Percentile of feature value distribution for sample selection"/>
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"/> 135 <param argument="--stop" type="integer" optional="True" label="Number of top samples to select" help="The order is based on percentile specified by --sperc"/>
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"/> 136 <param argument="--ftop" type="integer" optional="True" label="Number of top features to select" help="The order is based on percentile specified by --fperc"/>
118 </inputs> 137 </inputs>
119 <outputs> 138 <outputs>
120 <data format="txt" name="tree" label="${tool.name} on ${on_string}: Tree" /> 139 <data format="txt" name="tree" label="${tool.name} on ${on_string}: Tree" />
121 <data format="txt" name="annotation" label="${tool.name} on ${on_string}: Annotation" /> 140 <data format="txt" name="annotation" label="${tool.name} on ${on_string}: Annotation" />
122 </outputs> 141 </outputs>
137 <param name="def_font_size" value="10"/> 156 <param name="def_font_size" value="10"/>
138 <param name="min_font_size" value="8"/> 157 <param name="min_font_size" value="8"/>
139 <param name="max_font_size" value="12"/> 158 <param name="max_font_size" value="12"/>
140 <param name="annotation_legend_font_size" value="10"/> 159 <param name="annotation_legend_font_size" value="10"/>
141 <param name="abundance_threshold" value="20.0"/> 160 <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"/> 161 <param name="fname_row" value="0"/>
145 <param name="sname_row" value="0" /> 162 <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"/> 163 <output name="annotation" file="annotation_output.txt"/>
153 <output name="tree" file="tree_output.txt"/> 164 <output name="tree" file="tree_output.txt"/>
154 </test> 165 </test>
155 </tests> 166 </tests>
156 <help><![CDATA[ 167 <help><![CDATA[