Mercurial > repos > george-weingart > graphlan_import
annotate import2graphlan.xml @ 56:96f335baf256 draft
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| author | george-weingart |
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| date | Sat, 06 Sep 2014 15:29:52 -0400 |
| parents | 5f8d50842c4f |
| children | f9b9ad419acf |
| rev | line source |
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1 <tool id="import2graphlan" name="import2graphlan" version="1.0.0"> |
| 25 | 2 <description>Import to Graphlan</description> |
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3 <command interpreter="python"> |
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4 export2graphlan.py |
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5 -i $inp_data |
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6 -o $out_data |
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7 -t $output_tree_file |
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8 -a $output_annot_file |
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9 |
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10 --annotations $export_annotations |
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11 --external_annotations $export_external_annotations |
| 37 | 12 --background_levels $background_levels |
| 38 | 13 |
| 14 | |
| 15 #if $str($gchoice.global_choice) == "a": | |
| 16 | |
| 17 #if $str($gchoice.background_clades) != " ": | |
| 18 --background_clades $gchoice.background_clades | |
| 19 #end if | |
| 20 #if $str($gchoice.background_colors) != " ": | |
| 21 --background_colors $gchoice.background_colors | |
| 22 #end if | |
| 23 | |
| 24 #if $str($gchoice.export_title) != " ": | |
| 25 --title $gchoice.export_title | |
| 26 #end if | |
| 27 | |
| 28 | |
| 39 | 29 |
| 30 | |
| 38 | 31 --title_font_size $gchoice.title_font_size |
| 32 --def_clade_size $gchoice.def_clade_size | |
| 33 --min_clade_size $gchoice.min_clade_size | |
| 34 --max_clade_size $gchoice.max_clade_size | |
| 35 --def_font_size $gchoice.def_font_size | |
| 36 --min_font_size $gchoice.min_font_size | |
| 37 --max_font_size $gchoice.max_font_size | |
| 38 --annotation_legend_font_size $gchoice.annotation_legend_font_size | |
| 39 --abundance_threshold $gchoice.abundance_threshold | |
| 39 | 40 --least_biomarkers $gchoice.least_biomarkers |
| 41 | |
| 42 #if $str($gchoice.discard_otus ) == "1": | |
| 43 --discard_otus | |
| 44 #end if | |
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45 #end if |
| 38 | 46 |
| 47 | |
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48 |
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49 --skip_rows 1,2 |
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50 </command> |
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51 |
| 29 | 52 <inputs> |
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53 <param format="tabular" name="inp_data" type="data" label="Input used to run Lefse" help="This is the file that was used as input for Lefse"/> |
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54 <param format="lefse_internal_res" name="out_data" type="data" label="Output of Lefse" help="This is the Lefse output file"/> |
| 29 | 55 <param name="export_annotations" type="text" format="text" label="Annotations" value="2,3"/> |
| 56 <param name="export_external_annotations" type="text" format="text" label="External Annotations" value="4,5,6"/> | |
| 37 | 57 <param name="background_levels" type="text" format="text" label="Background Levels" value="1,2,3"/> |
| 30 | 58 |
| 59 <conditional name="gchoice"> | |
| 60 <param name="global_choice" type="select" label="Select Global Choices" help="Select choices"> | |
| 61 <option value="d" selected='True'>Default</option> | |
| 62 <option value="a">Advanced</option> | |
| 63 </param> | |
| 44 | 64 <when value="d"> |
| 65 <param name="background_clades" type="hidden" format="text" label="Background Clades" value="" /> | |
| 66 </when> | |
| 30 | 67 <when value="a"> |
| 68 <param name="background_clades" type="text" format="text" label="Background Clades" value=" " /> | |
| 69 <param name="background_colors" type="text" format="text" label="Background Colors" value=" " /> | |
| 70 <param name="export_title" type="text" format="text" label="Title" value=" "/> | |
| 71 <param name="title_font_size" type="integer" size="4" value="15" label="Title font size"/> | |
| 72 <param name="def_clade_size" type="integer" size="4" value="0" label="Default Clade size"/> | |
| 73 <param name="min_clade_size" type="integer" size="4" value="20" label="Minimum Clade size that are Biomarkers"/> | |
| 74 <param name="max_clade_size" type="integer" size="4" value="200" label="Maximum Clade size that are Biomarkers"/> | |
| 75 <param name="def_font_size" type="integer" size="4" value="10" label="Default font size"/> | |
| 76 <param name="min_font_size" type="integer" size="4" value="8" label="Minimum font size "/> | |
| 77 <param name="max_font_size" type="integer" size="4" value="12" label="Maximum font size "/> | |
| 78 <param name="annotation_legend_font_size" type="integer" size="4" value="10" label="Annotation legend font size "/> | |
| 79 <param name="abundance_threshold" type="float" value="20.0" label="Abundance threshold: minimun abundace value for a clade to be annotated"/> | |
| 80 <param name="most_abundant" type="integer" size="4" value="0" label=" When only lefse_input is provided, you can specify how many clades to highlight "/> | |
| 81 <param name="least_biomarkers" type="integer" size="4" value="0" label="Minimum number of biomarkers to extract "/> | |
| 39 | 82 <param name="discard_otus" type="select" label="If specified the OTU ids will be discarded from the taxonomy" value="0" > |
| 41 | 83 <option value="0">No</option> |
| 84 <option value="1">Yes</option> | |
| 39 | 85 </param> |
| 30 | 86 </when> |
| 87 </conditional> | |
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88 </inputs> |
| 29 | 89 <outputs> |
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90 <data name="output_annot_file" format="circl" /> |
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91 <data name="output_tree_file" format="circl" /> |
| 29 | 92 </outputs> |
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93 |
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94 <help> |
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95 Overview |
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96 ======== |
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97 **export2graphlan** is an *OPTIONAL* tool that automatically convert **LEfSe**, **MetaPhlAn2**, and **HUMAnN** input and/or output files, to **GraPhlAn**. Input file can be also given in BIOM (both 1 and 2) format. |
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98 |
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99 The aim of this tool is to support biologists, helping them by provide the tree and the annotation file for GraPhlAn, automatically. |
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100 |
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101 Input files |
| 39 | 102 =========== |
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103 |
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104 As shown in the image below, export2graphlan can work with just one of the following files or with both of them. |
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105 |
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106 * **Result of MetaPhlAn or HUMAnN analysis**: As depicted in the image below, this file can be the result of a MetaPhlAn analysis or a HUMAnN analysis. Generally, it is a tab separated file that have for each row a taxonomy and an abundance value. |
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107 |
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108 * **Output of LEfSe**: This file is the result of LEfSe execute on the *Result of MetaPhlAn or HUMAnN analysis* file. This file allow GraPhlAn to highlight for you the found biomarkers. |
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109 |
| 56 | 110 Input parameters |
| 111 ================ | |
| 52 | 112 |
| 54 | 113 **--annotations** ANNOTATIONS List which levels should be annotated in the tree. Use a comma separate values form, e.g., -annotation_levels 1,2,3. Default is None |
| 56 | 114 |
| 115 | |
| 42 | 116 **--external_annotations** EXTERNAL_ANNOTATIONS |
| 56 | 117 List which levels should use the external legend for the annotation. Use a comma separate values form, e.g., --annotation_levels 1,2,3. Default is None |
| 54 | 118 |
| 119 | |
| 43 | 120 **--background_levels** BACKGROUND_LEVELS |
| 56 | 121 List which levels should be highlight with a shaded background. Use a comma separate values form, e.g.,--background_levels 1,2,3 |
| 42 | 122 |
| 46 | 123 |
| 43 | 124 **--background_clades** BACKGROUND_CLADES |
| 42 | 125 Specify the clades that should be highlight with a shaded background. Use a comma separate values form and surround the string with " if it contains spaces. |
| 54 | 126 |
| 56 | 127 Example: --background_clades "Bacteria.Actinobacteria,Bacteria.Bacteroidetes.Bacteroidia,Bacteria.Firmicutes.Clostridia.Clostridiales" |
| 42 | 128 |
| 46 | 129 |
| 43 | 130 **--background_colors** BACKGROUND_COLORS |
| 42 | 131 Set the color to use for the shaded background. Colors can be either in RGB or HSV (using a semi-colon to separate values, surrounded with ()) format. |
| 132 Use a comma separate values form and surround the string with " if it contains spaces. | |
| 44 | 133 Example: #29cc36, (150; 100; 100), (280;80; 88) |
| 42 | 134 |
| 46 | 135 |
| 54 | 136 |
| 137 | |
| 138 | |
| 43 | 139 **--title TITLE** If specified set the title of the GraPhlAn plot. |
| 42 | 140 Surround the string with " if it contains spaces, e.g., --title "Title example" |
| 141 | |
| 46 | 142 |
| 43 | 143 **--title_font_size** TITLE_FONT_SIZE |
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144 Set the title font size. Default is 15 |
| 43 | 145 |
| 46 | 146 |
| 43 | 147 **--def_clade_size** DEF_CLADE_SIZE |
| 148 Set a default size for clades that are not found as biomarkers by LEfSe. Default is 10 | |
| 149 | |
| 46 | 150 |
| 43 | 151 **--min_clade_size** MIN_CLADE_SIZE |
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152 Set the minimum value of clades that are biomarkers. |
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153 Default is 20 |
| 43 | 154 |
| 47 | 155 |
| 54 | 156 |
| 43 | 157 **--max_clade_size** MAX_CLADE_SIZE |
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158 Set the maximum value of clades that are biomarkers. |
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159 Default is 200 |
| 43 | 160 |
| 46 | 161 |
| 43 | 162 **--def_font_size** DEF_FONT_SIZE |
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163 Set a default font size. Default is 10 |
| 43 | 164 |
| 46 | 165 |
| 54 | 166 |
| 167 | |
| 43 | 168 **--min_font_size** MIN_FONT_SIZE |
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169 Set the minimum font size to use. Default is 8 |
| 43 | 170 |
| 46 | 171 |
| 54 | 172 |
| 173 | |
| 43 | 174 **--max_font_size** MAX_FONT_SIZE |
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175 Set the maximum font size. Default is 12 |
| 43 | 176 |
| 46 | 177 |
| 45 | 178 **--annotation_legend_font_size** ANNOTATION_LEGEND_FONT_SIZE |
| 43 | 179 Set the font size for the annotation legend. Default is 10 |
| 180 | |
| 46 | 181 |
| 54 | 182 |
| 183 | |
| 43 | 184 **--abundance_threshold** ABUNDANCE_THRESHOLD |
| 185 Set the minimun abundace value for a clade to be annotated. Default is 20.0 | |
| 186 | |
| 46 | 187 |
| 54 | 188 |
| 189 | |
| 43 | 190 **--most_abundant** MOST_ABUNDANT |
| 191 When only lefse_input is provided, you can specify how many clades highlight. | |
| 192 Since the biomarkers are missing, they will be chosen from the most abundant | |
| 193 | |
| 46 | 194 |
| 195 | |
| 54 | 196 |
| 197 | |
| 43 | 198 **--least_biomarkers** LEAST_BIOMARKERS |
| 199 When only lefse_input is provided, you can specify the minimum number of biomarkers to extract. | |
| 200 The taxonomy is parsed, and the level is choosen in order to have at least the specified number of biomarkers | |
| 201 | |
| 54 | 202 |
| 203 | |
| 43 | 204 **--discard_otus** If specified the OTU ids will be discarded from the taxonmy. |
| 205 Default behavior keep OTU ids in taxonomy | |
| 206 | |
| 46 | 207 |
| 43 | 208 **--internal_levels** If specified sum-up from leaf to root the abundances values. Default behavior do not sum-up abundances on the internal nodes |
| 25 | 209 |
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210 |
| 41 | 211 Input data matrix parameters |
| 212 ============================ | |
| 39 | 213 |
| 45 | 214 **--sep** SEP |
| 41 | 215 |
| 45 | 216 **--out_table** OUT_TABLE : This is where to write the processed data matrix to file |
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217 |
| 45 | 218 **--fname_row** FNAME_ROW : Row number containing the names of the features (default 0, specify -1 if no names are present in the matrix) |
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219 |
| 45 | 220 **--sname_row** SNAME_ROW column number containing the names of the samples (default 0, specify -1 if no names are present in the matrix) |
| 41 | 221 |
| 45 | 222 **--metadata_rows** METADATA_ROWS Row numbers to use as metadata[default None, meaning no metadata |
| 41 | 223 |
| 45 | 224 **--skip_rows** SKIP_ROWS Row numbers to skip (0-indexed, comma separated) from the input file[default None, meaning no rows skipped |
| 41 | 225 |
| 45 | 226 **--sperc** SPERC Percentile of sample value distribution for sample selection |
| 41 | 227 |
| 45 | 228 **--fperc** FPERC Percentile of feature value distribution for sample selection |
| 41 | 229 |
| 45 | 230 **--stop** STOP Number of top samples to select (ordering based on percentile specified by --sperc) |
| 41 | 231 |
| 45 | 232 **--ftop** FTOP Number of top features to select (ordering based on percentile specified by --fperc) |
| 41 | 233 |
| 45 | 234 **--def_na** DEF_NA Set the default value for missing values [default None which means no replacement] |
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235 |
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236 Integration |
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237 =========== |
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238 |
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239 A graphical representation of how **export2graphlan** can be integrated in the analysis pipeline: |
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240 |
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241 .. image:: https://bitbucket.org/repo/oL6bEG/images/3364692296-graphlan_integration.png |
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242 :height: 672 |
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243 :width: 800 |
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244 |
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245 Want to know more? |
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246 ================== |
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247 |
| 27 | 248 If you want to know more about **export2graphlan** please have a look at the tutorial `here`_ |
| 26 | 249 |
| 250 | |
| 27 | 251 .. _here: https://bitbucket.org/nsegata/graphlan/wiki/export2graphlan%20-%20tutorial |
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252 </help> |
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253 </tool> |
| 54 | 254 |