Mercurial > repos > iuc > export2graphlan
comparison export2graphlan.xml @ 1:b16989c1e3a7 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
author | iuc |
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date | Wed, 07 Aug 2019 14:49:12 -0400 |
parents | ed1becc01910 |
children | 635c90a27692 |
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0:ed1becc01910 | 1:b16989c1e3a7 |
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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[ |