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comparison export2graphlan.xml @ 1:f7e87cc38f57 draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit 11b919f18ba85a40ff0ff4df82aac9be6da188c5-dirty
author bebatut
date Thu, 31 Mar 2016 03:58:09 -0400
parents f3a11239c704
children 953621231a6c
comparison
equal deleted inserted replaced
0:f3a11239c704 1:f7e87cc38f57
12 <stdio> 12 <stdio>
13 </stdio> 13 </stdio>
14 14
15 <version_command> 15 <version_command>
16 <![CDATA[ 16 <![CDATA[
17 python \${EXPORT2GRAPHLAN_DIR}/export2graphlan.py -v 17 python export2graphlan.py -v
18 ]]> 18 ]]>
19 </version_command> 19 </version_command>
20 20
21 <command> 21 <command>
22 <![CDATA[ 22 <![CDATA[
23 python \${EXPORT2GRAPHLAN_DIR}/export2graphlan.py 23 python export2graphlan.py
24 -i $lefse_input 24 -i $lefse_input
25 25
26 #if $lefse_output 26 #if $lefse_output
27 -o lefse_output 27 -o lefse_output
28 #end if 28 #end if
100 #end if 100 #end if
101 ]]> 101 ]]>
102 </command> 102 </command>
103 103
104 <inputs> 104 <inputs>
105 <param name="lefse_input" type="data" format="tabular" label="Input file" 105 <param name="lefse_input" type="data" format="tabular,txt,tsv" label="Input file" help="Identical to LEfSe input file (--lefse_input)"/>
106 help="Identical to LEfSe input file (--lefse_input)"/>
107 106
108 <param name="lefse_output" type="data" format="tabular" label="Input file 107 <param name="lefse_output" type="data" format="tabular" label="Input file corresponding to LEfSe output file (Optional)" help="(--lefse_output)" optional="True"/>
109 corresponding to LEfSe output file (Optional)" help="(--lefse_output)"
110 optional="True"/>
111 108
112 <param name="annotations" type="text" label="List which levels should be 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"/>
113 annotated in the tree (Optional)" help="The levels must be in
114 comma-separated form (--annotations)" optional="True"/>
115 110
116 <param name="external_annotations" type="text" label="List which levels 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"/>
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"/>
120 112
121 <param name="background_levels" type="text" label="List which levels should 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"/>
122 be highlight with a shaded background (Optional)"
123 help="The levels must be in comma-separated form (--background_levels)"
124 optional="True"/>
125 114
126 <param name="background_clades" type="text" label="List of the clades that 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"/>
127 should be highlight with a shaded background (Optional)"
128 help="The clades must be in comma-separated form (--background_clades)"
129 optional="True"/>
130 116
131 <param name="background_colors" type="text" label="List of color to use 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"/>
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"/>
137 118
138 <param name="title" type="text" label="Title of the GraPhlAn plot (Optional)" 119 <param name="title" type="text" label="Title of the GraPhlAn plot (Optional)" help="(--title)" optional="True"/>
139 help="(--title)" optional="True"/>
140 120
141 <param name="title_font_size" type="integer" value="15" label="Title 121 <param name="title_font_size" type="integer" value="15" label="Title font size" help="(--title_font_size)"/>
142 font size" help="(--title_font_size)"/>
143 122
144 <param name="def_clade_size" type="integer" value="10" label="Default 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)"/>
145 size for clades that are not found as biomarkers"
146 help="(--def_clade_size)"/>
147 124
148 <param name="min_clade_size" type="integer" value="20" label="Minimum 125 <param name="min_clade_size" type="integer" value="20" label="Minimum value of clades that are biomarkers" help="(--min_clade_size)"/>
149 value of clades that are biomarkers" help="(--min_clade_size)"/>
150 126
151 <param name="max_clade_size" type="integer" value="200" label="Maximum 127 <param name="max_clade_size" type="integer" value="200" label="Maximum value of clades that are biomarkers" help="(--max_clade_size)"/>
152 value of clades that are biomarkers" help="(--max_clade_size)"/>
153 128
154 <param name="def_font_size" type="integer" value="10" label="Default 129 <param name="def_font_size" type="integer" value="10" label="Default font size" help="(--def_font_size)"/>
155 font size" help="(--def_font_size)"/>
156 130
157 <param name="min_font_size" type="integer" value="8" label="Minimum 131 <param name="min_font_size" type="integer" value="8" label="Minimum font size" help="(--min_font_size)"/>
158 font size" help="(--min_font_size)"/>
159 132
160 <param name="max_font_size" type="integer" value="12" label="Maximum 133 <param name="max_font_size" type="integer" value="12" label="Maximum font size" help="(--max_font_size)"/>
161 font size" help="(--max_font_size)"/>
162 134
163 <param name="annotation_legend_font_size" type="integer" value="10" 135 <param name="annotation_legend_font_size" type="integer" value="10" label="Font size for the annotation legend" help="(--annotation_legend_font_size)"/>
164 label="Font size for the annotation legend"
165 help="(--annotation_legend_font_size)"/>
166 136
167 <param name="abundance_threshold" type="float" value="20.0" 137 <param name="abundance_threshold" type="float" value="20.0" label="Minimun abundance value for a clade to be annotated" help="(--abundance_threshold)"/>
168 label="Minimun abundance value for a clade to be annotated"
169 help="(--abundance_threshold)"/>
170 138
171 <param name="most_abundant" type="integer" label="Number of clades to 139 <param name="most_abundant" type="integer" label="Number of clades to highlight (Optional)" help="(--most_abundant)" optional="True"/>
172 highlight (Optional)" help="(--most_abundant)" optional="True"/>
173 140
174 <param name="least_biomarkers" type="integer" label="Minimum number of 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"/>
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"/>
178 142
179 <param name="fname_row" type="integer" value="0" label="Row number 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)"/>
180 containing the names of the features" help="-1 specifies that no
181 names are present in the matrix (--fname_row)"/>
182 144
183 <param name="sname_row" type="integer" value="0" label="Row number 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)"/>
184 containing the names of the samples" help="-1 specifies that no
185 names are present in the matrix (--sname_row)"/>
186 146
187 <param name="metadata_rows" type="integer" label="Row number 147 <param name="metadata_rows" type="integer" label="Row number to use as metadata (Optional)" help="(--metadata_rows)" optional="True"/>
188 to use as metadata (Optional)" help="(--metadata_rows)" optional="True"/>
189 148
190 <param name="skip_rows" type="text" label="Row number to skip 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"/>
191 from the input file" help="The row numbers ar indexed to 0 and comma
192 separated (--skip_rows)" optional="True"/>
193 150
194 <param name="sperc" type="float" label="Percentile of sample value 151 <param name="sperc" type="float" label="Percentile of sample value
195 distribution for sample selection (Optional)" help="(--sperc)" 152 distribution for sample selection (Optional)" help="(--sperc)"
196 optional="True"/> 153 optional="True"/>
197 154
198 <param name="fperc" type="float" label="Percentile of feature value 155 <param name="fperc" type="float" label="Percentile of feature value distribution for sample selection (Optional)" help="(--fperc)" optional="True"/>
199 distribution for sample selection (Optional)" help="(--fperc)"
200 optional="True"/>
201 156
202 <param name="stop" type="integer" label="Number of top samples to select 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"/>
203 (Optional)" help="The order is based on percentile specified by --sperc
204 (--stop)" optional="True"/>
205 158
206 <param name="ftop" type="integer" label="Number of top features to select 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"/>
207 (Optional)" help="The order is based on percentile specified by --fperc
208 (--ftop)" optional="True"/>
209 </inputs> 160 </inputs>
210 161
211 <outputs> 162 <outputs>
212 <data format="txt" name="tree" 163 <data format="txt" name="tree" label="${tool.name} on ${on_string}: Tree" />
213 label="${tool.name} on ${on_string}: Tree" /> 164 <data format="txt" name="annotation" label="${tool.name} on ${on_string}: Annotation" />
214 <data format="txt" name="annotation"
215 label="${tool.name} on ${on_string}: Annotation" />
216 165
217 </outputs> 166 </outputs>
218 167
219 <tests> 168 <tests>
220 <test> 169 <test>