graphlan_import: import2graphlan.xml annotate

annotate import2graphlan.xml @ 27:252c242518f2 draft

Uploaded

author	george-weingart
date	Thu, 04 Sep 2014 20:04:01 -0400
parents	4c76917ae3d7
children	3b2b6c5e38e2

rev	line source
23 01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	1 <tool id="import2graphlan" name="import2graphlan" version="1.0.0">
25 9ecf8701f72f Uploaded george-weingart parents: 23 diff changeset	2 <description>Import to Graphlan</description>
23 01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	3 <command interpreter="python">
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	4 export2graphlan.py
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	5 -i $inp_data
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	6 -o $out_data
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	7 -t $output_tree_file
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	8 -a $output_annot_file
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	9
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	10 --annotations $export_annotations
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	11 --external_annotations $export_external_annotations
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	12 --background_levels $background_levels
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	13 #if $str($background_clades) != " ":
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	14 --background_clades $background_clades
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	15 #end if
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	16 #if $str($background_colors) != " ":
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	17 --background_colors $background_colors
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	18 #end if
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	19 #if $str($export_title) != " ":
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	20 --title $export_title
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	21 #end if
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	22 --title_font_size $title_font_size
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	23 --def_clade_size $def_clade_size
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	24 --min_clade_size $min_clade_size
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	25 --max_clade_size $max_clade_size
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	26 --def_font_size $def_font_size
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	27 --min_font_size $min_font_size
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	28 --max_font_size $max_font_size
26 4c76917ae3d7 Uploaded george-weingart parents: 25 diff changeset	29 --annotation_legend_font_size $annotation_legend_font_size
23 01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	30 --abundance_threshold $abundance_threshold
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	31 --least_biomarkers $least_biomarkers
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	32
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	33 --skip_rows 1,2
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	34 </command>
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	35
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	36 <inputs>
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	37 <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"/>
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	38 <param format="lefse_internal_res" name="out_data" type="data" label="Output of Lefse" help="This is the Lefse output file"/>
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	39 <param name="export_annotations" type="text" format="text" label="Annotations" value="2,3"/>
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	40 <param name="export_external_annotations" type="text" format="text" label="External Annotations" value="4,5,6"/>
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	41 <param name="background_levels" type="text" format="text" label="Background Levels" value="1,2,3"/>
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	42 <param name="background_clades" type="text" format="text" label="Background Clades" value=" " />
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	43 <param name="background_colors" type="text" format="text" label="Background Colors" value=" " />
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	44 <param name="export_title" type="text" format="text" label="Title" value=" "/>
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	45 <param name="title_font_size" type="integer" size="4" value="15" label="Title font size"/>
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	46 <param name="def_clade_size" type="integer" size="4" value="0" label="Default Clade size"/>
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	47 <param name="min_clade_size" type="integer" size="4" value="20" label="Minimum Clade size that are Biomarkers"/>
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	48 <param name="max_clade_size" type="integer" size="4" value="200" label="Maximum Clade size that are Biomarkers"/>
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	49 <param name="def_font_size" type="integer" size="4" value="10" label="Default font size"/>
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	50 <param name="min_font_size" type="integer" size="4" value="8" label="Minimum font size "/>
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	51 <param name="max_font_size" type="integer" size="4" value="12" label="Maximum font size "/>
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	52 <param name="annotation_legend_font_size" type="integer" size="4" value="10" label="Annotation legend font size "/>
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	53 <param name="abundance_threshold" type="float" value="20.0" label="Abundance threshold: minimun abundace value for a clade to be annotated"/>
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	54 <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 "/>
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	55 <param name="least_biomarkers" type="integer" size="4" value="0" label="Minimum number of biomarkers to extract "/>
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	56
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	57 </inputs>
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	58 <outputs>
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	59 <data name="output_annot_file" format="circl" />
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	60 <data name="output_tree_file" format="circl" />
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	61 </outputs>
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	62
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	63 <help>
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	64 Overview
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	65 ========
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	66 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.
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	67
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	68 The aim of this tool is to support biologists, helping them by provide the tree and the annotation file for GraPhlAn, automatically.
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	69
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	70 Input files
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	71 -----------
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	72
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	73 As shown in the image below, export2graphlan can work with just one of the following files or with both of them.
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	74
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	75 * 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.
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	76
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	77 * 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.
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	78
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	79 Input parameters
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	80 ----------------
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	81
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	82 --annotations ANNOTATIONS
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	83 List which levels should be annotated in the tree. Use
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	84 a comma separate values form, e.g.,
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	85 --annotation_levels 1,2,3. Default is None
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	86 --external_annotations EXTERNAL_ANNOTATIONS
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	87 List which levels should use the external legend for
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	88 the annotation. Use a comma separate values form,
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	89 e.g., --annotation_levels 1,2,3. Default is None
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	90 --background_levels BACKGROUND_LEVELS
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	91 List which levels should be highlight with a shaded
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	92 background. Use a comma separate values form, e.g.,
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	93 --background_levels 1,2,3
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	94 --background_clades BACKGROUND_CLADES
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	95 Specify the clades that should be highlight with a
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	96 shaded background. Use a comma separate values form
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	97 and surround the string with " if it contains spaces.
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	98 Example: --background_clades "Bacteria.Actinobacteria,
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	99 Bacteria.Bacteroidetes.Bacteroidia,
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	100 Bacteria.Firmicutes.Clostridia.Clostridiales"
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	101 --background_colors BACKGROUND_COLORS
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	102 Set the color to use for the shaded background. Colors
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	103 can be either in RGB or HSV (using a semi-colon to
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	104 separate values, surrounded with ()) format. Use a
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	105 comma separate values form and surround the string
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	106 with " if it contains spaces. Example:
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	107 --background_colors "#29cc36, (150; 100; 100), (280;
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	108 80; 88)"
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	109 --title TITLE If specified set the title of the GraPhlAn plot.
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	110 Surround the string with " if it contains spaces,
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	111 e.g., --title "Title example"
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	112 --title_font_size TITLE_FONT_SIZE
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	113 Set the title font size. Default is 15
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	114 --def_clade_size DEF_CLADE_SIZE
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	115 Set a default size for clades that are not found as
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	116 biomarkers by LEfSe. Default is 10
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	117 --min_clade_size MIN_CLADE_SIZE
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	118 Set the minimum value of clades that are biomarkers.
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	119 Default is 20
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	120 --max_clade_size MAX_CLADE_SIZE
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	121 Set the maximum value of clades that are biomarkers.
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	122 Default is 200
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	123 --def_font_size DEF_FONT_SIZE
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	124 Set a default font size. Default is 10
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	125 --min_font_size MIN_FONT_SIZE
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	126 Set the minimum font size to use. Default is 8
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	127 --max_font_size MAX_FONT_SIZE
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	128 Set the maximum font size. Default is 12
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	129 --annotation_legend_font_size ANNOTATION_LEGEND_FONT_SIZE
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	130 Set the font size for the annotation legend. Default
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	131 is 10
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	132 --abundance_threshold ABUNDANCE_THRESHOLD
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	133 Set the minimun abundace value for a clade to be
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	134 annotated. Default is 20.0
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	135 --most_abundant MOST_ABUNDANT
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	136 When only lefse_input is provided, you can specify how
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	137 many clades highlight. Since the biomarkers are
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	138 missing, they will be chosen from the most abundant
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	139 --least_biomarkers LEAST_BIOMARKERS
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	140 When only lefse_input is provided, you can specify the
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	141 minimum number of biomarkers to extract. The taxonomy
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	142 is parsed, and the level is choosen in order to have
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	143 at least the specified number of biomarkers
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	144 --discard_otus If specified the OTU ids will be discarde from the
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	145 taxonmy. Default behavior keep OTU ids in taxonomy
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	146 --internal_levels If specified sum-up from leaf to root the abundances
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	147 values. Default behavior do not sum-up abundances on
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	148 the internal nodes
25 9ecf8701f72f Uploaded george-weingart parents: 23 diff changeset	149
23 01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	150
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	151 output parameters:
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	152
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	153 -t TREE, --tree TREE Output filename where save the input tree for GraPhlAn
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	154
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	155 -a ANNOTATION, --annotation ANNOTATION : This is the Output filename where to save GraPhlAn annotation
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	156
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	157 Input data matrix parameters:
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	158 --sep SEP
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	159 --out_table OUT_TABLE : This is where to write the processed data matrix to file
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	160
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	161 --fname_row FNAME_ROW : Row number containing the names of the features (default 0, specify -1 if no names are present in the matrix)
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	162
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	163 --sname_row SNAME_ROW
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	164 column number containing the names of the samples (default 0, specify -1 if no names are present in the matrix)
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	165 --metadata_rows METADATA_ROWS
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	166 Row numbers to use as metadata[default None, meaning
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	167 no metadata
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	168 --skip_rows SKIP_ROWS
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	169 Row numbers to skip (0-indexed, comma separated) from
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	170 the input file[default None, meaning no rows skipped
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	171 --sperc SPERC Percentile of sample value distribution for sample
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	172 selection
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	173 --fperc FPERC Percentile of feature value distribution for sample
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	174 selection
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	175 --stop STOP Number of top samples to select (ordering based on
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	176 percentile specified by --sperc)
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	177 --ftop FTOP Number of top features to select (ordering based on
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	178 percentile specified by --fperc)
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	179 --def_na DEF_NA Set the default value for missing values [default None
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	180 which means no replacement]
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	181
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	182 Integration
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	183 ===========
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	184
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	185 A graphical representation of how export2graphlan can be integrated in the analysis pipeline:
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	186
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	187 .. image:: https://bitbucket.org/repo/oL6bEG/images/3364692296-graphlan_integration.png
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	188 :height: 672
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	189 :width: 800
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	190
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	191 Want to know more?
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	192 ==================
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	193
27 252c242518f2 Uploaded george-weingart parents: 26 diff changeset	194 If you want to know more about export2graphlan please have a look at the tutorial `here`_
26 4c76917ae3d7 Uploaded george-weingart parents: 25 diff changeset	195
4c76917ae3d7 Uploaded george-weingart parents: 25 diff changeset	196
27 252c242518f2 Uploaded george-weingart parents: 26 diff changeset	197 .. _here: https://bitbucket.org/nsegata/graphlan/wiki/export2graphlan%20-%20tutorial
23 01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	198 </help>
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	199 </tool>

Mercurial > repos > george-weingart > graphlan_import

annotate import2graphlan.xml @ 27:252c242518f2 draft