Mercurial > repos > george-weingart > graphlan_import
annotate import2graphlan.xml @ 60:39126c375dd4 draft default tip
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| author | george-weingart |
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| date | Sat, 06 Sep 2014 15:42:27 -0400 |
| parents | 000d65b33ecd |
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| 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 | |
| 57 | 116 **--external_annotations** EXTERNAL_ANNOTATIONS 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 | 117 |
| 118 | |
| 57 | 119 **--background_levels** BACKGROUND_LEVELS List which levels should be highlight with a shaded background. Use a comma separate values form, e.g.,--background_levels 1,2,3 |
| 42 | 120 |
| 46 | 121 |
| 43 | 122 **--background_clades** BACKGROUND_CLADES |
| 42 | 123 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 | 124 |
| 56 | 125 Example: --background_clades "Bacteria.Actinobacteria,Bacteria.Bacteroidetes.Bacteroidia,Bacteria.Firmicutes.Clostridia.Clostridiales" |
| 42 | 126 |
| 46 | 127 |
| 60 | 128 **--background_colors** BACKGROUND_COLORS 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. Use a comma separate values form and surround the string with " if it contains spaces. Example: #29cc36, (150; 100; 100), (280;80; 88) |
| 54 | 129 |
| 130 | |
| 58 | 131 **--title TITLE** If specified set the title of the GraPhlAn plot. Surround the string with " if it contains spaces, e.g., --title "Title example" |
| 132 | |
| 133 **--title_font_size** TITLE_FONT_SIZE Set the title font size. Default is 15 | |
| 42 | 134 |
| 46 | 135 |
| 58 | 136 **--def_clade_size** DEF_CLADE_SIZE Set a default size for clades that are not found as biomarkers by LEfSe. Default is 10 |
| 43 | 137 |
| 46 | 138 |
| 59 | 139 **--min_clade_size** MIN_CLADE_SIZE Set the minimum value of clades that are biomarkers. Default is 20 |
| 43 | 140 |
| 47 | 141 |
| 59 | 142 **--max_clade_size** MAX_CLADE_SIZE Set the maximum value of clades that are biomarkers. Default is 200 |
| 43 | 143 |
| 46 | 144 |
| 59 | 145 **--def_font_size** DEF_FONT_SIZE Set a default font size. Default is 10 |
| 54 | 146 |
| 147 | |
| 59 | 148 **--min_font_size** MIN_FONT_SIZE Set the minimum font size to use. Default is 8 |
| 43 | 149 |
| 46 | 150 |
| 59 | 151 **--max_font_size** MAX_FONT_SIZE Set the maximum font size. Default is 12 |
| 43 | 152 |
| 46 | 153 |
| 59 | 154 **--annotation_legend_font_size** ANNOTATION_LEGEND_FONT_SIZE Set the font size for the annotation legend. Default is 10 |
| 43 | 155 |
| 59 | 156 **--abundance_threshold** ABUNDANCE_THRESHOLD Set the minimun abundace value for a clade to be annotated. Default is 20.0 |
| 46 | 157 |
| 54 | 158 |
| 59 | 159 **--most_abundant** MOST_ABUNDANT When only lefse_input is provided, you can specify how many clades highlight. Since the biomarkers are missing, they will be chosen from the most abundant |
| 54 | 160 |
| 161 | |
| 59 | 162 **--least_biomarkers** LEAST_BIOMARKERS When only lefse_input is provided, you can specify the minimum number of biomarkers to extract. The taxonomy is parsed, and the level is choosen in order to have at least the specified number of biomarkers |
| 54 | 163 |
| 164 | |
| 59 | 165 **--discard_otus** If specified the OTU ids will be discarded from the taxonmy. Default behavior keep OTU ids in taxonomy |
| 46 | 166 |
| 43 | 167 **--internal_levels** If specified sum-up from leaf to root the abundances values. Default behavior do not sum-up abundances on the internal nodes |
| 59 | 168 |
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169 |
| 41 | 170 Input data matrix parameters |
| 171 ============================ | |
| 39 | 172 |
| 45 | 173 **--sep** SEP |
| 41 | 174 |
| 45 | 175 **--out_table** OUT_TABLE : This is where to write the processed data matrix to file |
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176 |
| 45 | 177 **--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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178 |
| 45 | 179 **--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 | 180 |
| 45 | 181 **--metadata_rows** METADATA_ROWS Row numbers to use as metadata[default None, meaning no metadata |
| 41 | 182 |
| 45 | 183 **--skip_rows** SKIP_ROWS Row numbers to skip (0-indexed, comma separated) from the input file[default None, meaning no rows skipped |
| 41 | 184 |
| 45 | 185 **--sperc** SPERC Percentile of sample value distribution for sample selection |
| 41 | 186 |
| 45 | 187 **--fperc** FPERC Percentile of feature value distribution for sample selection |
| 41 | 188 |
| 45 | 189 **--stop** STOP Number of top samples to select (ordering based on percentile specified by --sperc) |
| 41 | 190 |
| 45 | 191 **--ftop** FTOP Number of top features to select (ordering based on percentile specified by --fperc) |
| 41 | 192 |
| 45 | 193 **--def_na** DEF_NA Set the default value for missing values [default None which means no replacement] |
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194 |
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195 Integration |
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196 =========== |
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197 |
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198 A graphical representation of how **export2graphlan** can be integrated in the analysis pipeline: |
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199 |
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200 .. image:: https://bitbucket.org/repo/oL6bEG/images/3364692296-graphlan_integration.png |
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201 :height: 672 |
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202 :width: 800 |
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203 |
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204 Want to know more? |
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205 ================== |
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206 |
| 27 | 207 If you want to know more about **export2graphlan** please have a look at the tutorial `here`_ |
| 26 | 208 |
| 209 | |
| 27 | 210 .. _here: https://bitbucket.org/nsegata/graphlan/wiki/export2graphlan%20-%20tutorial |
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211 </help> |
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212 </tool> |
| 54 | 213 |