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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit 3472a70f35769aaeafa40e8fbce97aac2c4ea4f8-dirty
author bebatut
date Tue, 21 Jun 2016 08:04:10 -0400
parents 4a3676d020e7
children
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4:4a3676d020e7 5:f05bc567f1a5
17 export2graphlan.py -v 17 export2graphlan.py -v
18 ]]> 18 ]]>
19 </version_command> 19 </version_command>
20 20
21 <command> 21 <command>
22 <![CDATA[ 22 <![CDATA[
23 export2graphlan.py 23 export2graphlan.py
24 -i $lefse_input 24 -i $lefse_input
25 25
26 #if $lefse_output 26 #if $input_lefse_output.input_lefse_output_test == "true"
27 -o lefse_output 27 -o $input_lefse_output.lefse_output
28 #end if 28 #end if
29 29
30 -t $tree 30 -t $tree
31 -a $annotation 31 -a $annotation
32 32
47 #end if 47 #end if
48 48
49 #if $background_colors 49 #if $background_colors
50 --background_colors "$background_colors" 50 --background_colors "$background_colors"
51 #end if 51 #end if
52 52
53 #if $title 53 #if $title
54 --title "title" 54 --title "title"
55 #end if 55 #end if
56 56
57 --title_font_size $title_font_size 57 --title_font_size $title_font_size
58 --def_clade_size $def_clade_size 58 --def_clade_size $def_clade_size
59 --min_clade_size $min_clade_size 59 --min_clade_size $min_clade_size
60 --max_clade_size $max_clade_size 60 --max_clade_size $max_clade_size
61 --def_font_size $def_font_size 61 --def_font_size $def_font_size
62 --min_font_size $min_font_size 62 --min_font_size $min_font_size
63 --max_font_size $max_font_size 63 --max_font_size $max_font_size
76 --sname_row $sname_row 76 --sname_row $sname_row
77 77
78 #if $metadata_rows 78 #if $metadata_rows
79 --metadata_rows $metadata_rows 79 --metadata_rows $metadata_rows
80 #end if 80 #end if
81 81
82 #if $skip_rows 82 #if $skip_rows
83 --skip_rows $skip_rows 83 --skip_rows $skip_rows
84 #end if 84 #end if
85 85
86 #if $sperc 86 #if $sperc
87 --sperc $sperc 87 --sperc $sperc
102 </command> 102 </command>
103 103
104 <inputs> 104 <inputs>
105 <param name="lefse_input" type="data" format="tabular,txt,tsv" label="Input file" help="Identical to LEfSe input file (--lefse_input)"/> 105 <param name="lefse_input" type="data" format="tabular,txt,tsv" label="Input file" help="Identical to LEfSe input file (--lefse_input)"/>
106 106
107 <param name="lefse_output" type="data" format="tabular" label="Input file corresponding to LEfSe output file (Optional)" help="(--lefse_output)" optional="True"/> 107 <conditional name="input_lefse_output">
108 <param name="input_lefse_output_test" type="select" label="Use a LEfSe output file as input?" help="">
109 <option value="true">Yes</option>
110 <option value="false" selected="true">No</option>
111 </param>
112
113 <when value="true">
114 <param name="lefse_output" type="data" format="tabular" label="Input file corresponding to LEfSe output file" help="(--lefse_output)"/>
115 </when>
116 <when value="false"/>
117 </conditional>
108 118
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"/> 119 <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"/>
110 120
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"/> 121 <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"/>
112 122
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"/> 123 <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"/>
114 124
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"/> 125 <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"/>
116 126
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"/> 127 <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"/>
118 128
119 <param name="title" type="text" label="Title of the GraPhlAn plot (Optional)" help="(--title)" optional="True"/> 129 <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)"/> 130 <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)"/> 131 <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)"/> 132 <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)"/> 133 <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)"/> 134 <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)"/> 135 <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)"/> 136 <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)"/> 137 <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 <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"/> 139 <param name="most_abundant" type="integer" label="Number of clades to highlight (Optional)" help="(--most_abundant)" optional="True"/>
140 140
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"/> 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"/>
142 142
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)"/> 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)"/> 144 <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"/> 145 <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"/> 146 <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"/>
150 147 <param name="sperc" type="float" label="Percentile of sample value distribution for sample selection (Optional)" help="(--sperc)" optional="True"/>
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"/> 148 <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"/> 149 <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"/> 150 <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> 151 </inputs>
161 152
162 <outputs> 153 <outputs>
163 <data format="txt" name="tree" label="${tool.name} on ${on_string}: Tree" /> 154 <data format="txt" name="tree" label="${tool.name} on ${on_string}: Tree" />
165 </outputs> 156 </outputs>
166 157
167 <tests> 158 <tests>
168 <test> 159 <test>
169 <param name="lefse_input" value="input_profile.tabular"/> 160 <param name="lefse_input" value="input_profile.tabular"/>
161 <param name="input_lefse_output_test" value="no" />
170 <param name="annotations" value=""/> 162 <param name="annotations" value=""/>
171 <param name="external_annotations" value=""/> 163 <param name="external_annotations" value=""/>
172 <param name="background_levels" value=""/> 164 <param name="background_levels" value=""/>
173 <param name="background_clades" value=""/> 165 <param name="background_clades" value=""/>
174 <param name="background_colors" value=""/> 166 <param name="background_colors" value=""/>
196 <output name="tree" file="tree_output.txt"/> 188 <output name="tree" file="tree_output.txt"/>
197 </test> 189 </test>
198 </tests> 190 </tests>
199 191
200 <help><![CDATA[ 192 <help><![CDATA[
201
202 **What it does** 193 **What it does**
203 194
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 195 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
205 196
206 In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important. 197 In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important.
207 198
208 For more information, check the 199 For more information, check the `user manual <https://bitbucket.org/CibioCM/export2graphlan/overview/>`_.
209 `user manual <https://bitbucket.org/CibioCM/export2graphlan/overview/>`_.
210
211 ]]></help> 200 ]]></help>
212 201
213 <citations> 202 <citations>
214 </citations> 203 </citations>
215 </tool> 204 </tool>