Mercurial > repos > george-weingart > graphlan_import
comparison export2graphlan.xml @ 21:5ecece9f42dd draft
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| author | george-weingart |
|---|---|
| date | Thu, 04 Sep 2014 16:34:51 -0400 |
| parents | 65bf0d7f535b |
| children |
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| 20:65bf0d7f535b | 21:5ecece9f42dd |
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| 26 --def_font_size $def_font_size | 26 --def_font_size $def_font_size |
| 27 --min_font_size $min_font_size | 27 --min_font_size $min_font_size |
| 28 --max_font_size $max_font_size | 28 --max_font_size $max_font_size |
| 29 --annotation_legend_font_size $annotation_legend_font_size | 29 --annotation_legend_font_size $annotation_legend_font_size |
| 30 --abundance_threshold $abundance_threshold | 30 --abundance_threshold $abundance_threshold |
| 31 #if $most_abundant > 0: | |
| 32 --most_abundant $most_abundant | |
| 33 #end if | |
| 31 --skip_rows 1,2 | 34 --skip_rows 1,2 |
| 32 </command> | 35 </command> |
| 33 | 36 |
| 34 <inputs> | 37 <inputs> |
| 35 <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"/> | 38 <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"/> |
| 47 <param name="def_font_size" type="integer" size="4" value="10" label="Default font size"/> | 50 <param name="def_font_size" type="integer" size="4" value="10" label="Default font size"/> |
| 48 <param name="min_font_size" type="integer" size="4" value="8" label="Minimum font size "/> | 51 <param name="min_font_size" type="integer" size="4" value="8" label="Minimum font size "/> |
| 49 <param name="max_font_size" type="integer" size="4" value="12" label="Maximum font size "/> | 52 <param name="max_font_size" type="integer" size="4" value="12" label="Maximum font size "/> |
| 50 <param name="annotation_legend_font_size" type="integer" size="4" value="10" label="Annotation legend font size "/> | 53 <param name="annotation_legend_font_size" type="integer" size="4" value="10" label="Annotation legend font size "/> |
| 51 <param name="abundance_threshold" type="float" value="20.0" label="Abundance threshold: minimun abundace value for a clade to be annotated"/> | 54 <param name="abundance_threshold" type="float" value="20.0" label="Abundance threshold: minimun abundace value for a clade to be annotated"/> |
| 52 | 55 <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 "/> |
| 53 | 56 |
| 57 least_biomarkers | |
| 54 </inputs> | 58 </inputs> |
| 55 <outputs> | 59 <outputs> |
| 56 <data name="output_annot_file" format="circl" /> | 60 <data name="output_annot_file" format="circl" /> |
| 57 <data name="output_tree_file" format="circl" /> | 61 <data name="output_tree_file" format="circl" /> |
| 58 </outputs> | 62 </outputs> |
| 71 | 75 |
| 72 * **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. | 76 * **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. |
| 73 | 77 |
| 74 * **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. | 78 * **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. |
| 75 | 79 |
| 76 Input parameters6666 | 80 Input parameters |
| 77 -------------------- | 81 ---------------- |
| 78 | 82 |
| 79 --annotations ANNOTATIONS | 83 --annotations ANNOTATIONS |
| 80 List which levels should be annotated in the tree. Use | 84 List which levels should be annotated in the tree. Use |
| 81 a comma separate values form, e.g., | 85 a comma separate values form, e.g., |
| 82 --annotation_levels 1,2,3. Default is None | 86 --annotation_levels 1,2,3. Default is None |
| 143 --internal_levels If specified sum-up from leaf to root the abundances | 147 --internal_levels If specified sum-up from leaf to root the abundances |
| 144 values. Default behavior do not sum-up abundances on | 148 values. Default behavior do not sum-up abundances on |
| 145 the internal nodes | 149 the internal nodes |
| 146 | 150 |
| 147 input parameters: | 151 input parameters: |
| 148 You need to provide at least LEfSe input data | 152 |
| 149 -i LEFSE_INPUT, --lefse_input LEFSE_INPUT | 153 -i LEFSE_INPUT, --lefse_input LEFSE_INPUT |
| 150 | 154 |
| 151 -o LEFSE_OUTPUT, --lefse_output LEFSE_OUTPUT | 155 -o LEFSE_OUTPUT, --lefse_output LEFSE_OUTPUT |
| 152 | 156 |
| 153 output parameters: | 157 output parameters: |