Hello,
I have a tool that issues a warning:
/galaxy-central/tools/graphlan/src/graphlan_lib.py:981: UserWarning: You passed a edgecolor/edgecolors ([‘blue’, ‘blue’, ‘blue’, ‘blue’, ‘blue’, ‘blue’, ‘blue’]) for an unfilled marker (’+’). Matplotlib is ignoring the edgecolor in favor of the facecolor. This behavior may change in the future.
zorder=12)
and the job is flagged in red.
I wnt it to show as completed successfully in green.
How can I do it ?
Below is my xml.
Thanks!
=====================================================================
graphlan_prepare_annotations.py
–input $inp_data
–output_annot_file $output_annot_file
–selclades $cond.cls_n
–clade_marker_size $clade_marker_size
–clade_marker_color ‘$clade_marker_color’
–clade_marker_edge_width ‘$clade_marker_edge_width’
–annotation_font_size $annotation_font_size
–annotation_background_color ‘$annotation_background_color’
–annotation_background_edge_color ‘$annotation_background_edge_color’
–annotation ‘$annotation’
–annotation_label_clade_selector $annotation_label_clade_selector
–annotation_abbreviation ‘$annotation_abbreviation’
–clade_marker_shape ‘$clade_marker_shape’
–clade_marker_edge_color ‘$clade_marker_edge_color’
–ignore_branch_len $gchoice.ignore_branch_len
–total_plotted_degrees $gchoice.total_plotted_degrees
–start_rotation $gchoice.start_rotation
–clade_separation $gchoice.clade_separation
–branch_bracket_width $gchoice.branch_bracket_width
–branch_bracket_depth $gchoice.branch_bracket_depth
–annotation_background_width $gchoice.annotation_background_width
–annotation_background_alpha $gchoice.annotation_background_alpha
–annotation_background_separation $gchoice.annotation_background_separation
–annotation_background_offset $gchoice.annotation_background_offset
–annotation_legend_font_size $gchoice.annotation_legend_font_size
–branch_thickness $gchoice.branch_thickness
–branch_color “$gchoice.branch_color”
–branch_ancestor_clade_color “$gchoice.branch_ancestor_clade_color”
–label_font_strech $gchoice.label_font_strech
–taxo_sel $cond.taxo_sel
–root_dir $GALAXY_ROOT_DIR
<conditional name="cond" type="data_column" data_ref="inp_data" accept_default="true">
<param name="taxo_sel" type="select" data_ref="inp_data" label="Select Full Taxonomy">
<option value="0" selected="True">No</option>
<option value="1">Yes</option>
</param>
<when value="0">
<param name="cls_n" type="select" label="Select clade(s)" multiple="True" size ="70" dynamic_options="get_cols(inp_data,'0')"/>
</when>
<when value="1">
<param name="cls_n" type="select" label="Select clade(s)" multiple="True" size ="70" dynamic_options="get_cols(inp_data,'1')"/>
</when>
</conditional>
<param name="clade_marker_color" type="text" format="text" label="Clade Fill Color (e.g. r, red, or #FF0000)"/>
<param name="clade_marker_size" type="float" size="4" value="20" label ="Clade Size"/>
<param name="annotation_font_size" type="integer" size="4" value="7" min="0" label="Label Font Size (pixels) > 1 "/>
<param name="clade_marker_edge_color" type="text" format="text" label="Clade Edge Color (e.g. r, red, or #FF0000)"/>
<param name="annotation_background_edge_color" type="text" format="text" label="Annotation Edge Color (e.g. r, red, or #FF0000)"/>
<param name="clade_marker_edge_width" type="float" size="4" value="0.5" label="Clade Edge Line Width"/>
<param name="clade_marker_shape" type="select" format="text" >
<label>Clade Marker Style</label>
<option value=" "> </option>
<option value="o">o</option>
<option value="+">+</option>
<option value="*">*</option>
<option value="x">x</option>
<option value=".">.</option>
<option value="v">v</option>
<option value="^">^</option>
<option value="d">d</option>
<option value="h">h</option>
<option value="H">H</option>
<option value="v">v</option>
<option value="v">v</option>
<option value="_">_</option>
<option value="p">p</option>
<option value="s">s</option>
</param>
<param name="annotation_background_color" type="text" format="text" label="Annotation Color (e.g. r, red, or #FF0000)"/>
<param name="annotation" type="text" format="text" label="Annotation Label - Use * to use clade name "/>
<param name="annotation_abbreviation" type="text" format="text" label="Annotation Abbreviation - Use * for automatic abbreviations"/>
<param name="annotation_label_clade_selector" type="select" format="text">
<label>Annotation Label Clade Selector</label>
<option value="?">Clade only</option>
<option value="-">Clade and descendant nodes</option>
<option value="+">Clade and its leaf nodes</option>
<option value="^">Clade leaf nodes</option>
</param>
<conditional name="gchoice">
<param name="global_choice" type="select" label="Select Global Choices" help="Select choices which apply to all Clades">
<option value="d" selected='True'>Default</option>
<option value="a">Advanced</option>
</param>
<when value="d">
<param name="ignore_branch_len" type="hidden" value="0"/>
<param name="total_plotted_degrees" type="hidden" value="360"/>
<param name="start_rotation" type="hidden" value="180"/>
<param name="clade_separation" type="hidden" value=""/>
<param name="branch_bracket_width" type="hidden" value="0.25"/>
<param name="branch_bracket_depth" type="hidden" value="1"/>
<param name="annotation_background_width" type="hidden" value="0.1"/>
<param name="annotation_background_alpha" type="hidden" value="0.2"/>
<param name="annotation_background_separation" type="hidden" value="0.02"/>
<param name="annotation_background_offset" type="hidden" value="0.02"/>
<param name="annotation_legend_font_size" type="hidden" value="7"/>
<param name="branch_thickness" type="hidden" value="0.75"/>
<param name="branch_color" type="hidden" value=""/>
<param name="branch_ancestor_clade_color" type="hidden" value=""/>
<param name="label_font_strech" type="hidden" value="0"/>
</when>
<when value="a">
<param name="ignore_branch_len" type="select" value="1" format="text" >
<label>Ignore Branch Length</label>
<option value="1">No</option>
<option value="0">Yes</option>
</param>
<param name="total_plotted_degrees" type="float" size="4" value="360" min="0" max="360" label="Total Rotation (float: 0 to 360)" />
<param name="start_rotation" type="float" size="4" value="180" min="0" max="360" label="Start Rotation (float: 0 to 360) "/>
<param name="clade_separation" type="float" size="4" value="0" min="0" label="Clade Separation (float >= 0)"/>
<param name="branch_bracket_width" type="float" size="4" min="0" max="1" value="0.25" label="Sub Branches Angle Reduction (float: 0 to 1)"/>
<param name="branch_bracket_depth" type="float" size="4" min="0" max="1" value="1" label="Sub Branches Opening Point (float: 0 to 1)"/>
<param name="annotation_background_width" type="float" size="4" min="0" value="0.1" label="Annotation Wings Width (float >=0)"/>
<param name="annotation_background_alpha" type="float" size="4" min="0" max="1" value="0.2" label="Annotation Wings Alpha (float: 0 to 1)"/>
<param name="annotation_background_separation" type="float" size="4" min="0" value="0.02" label="Annotation Wing Offset (float >= 0)"/>
<param name="annotation_background_offset" type="float" size="4" min="0" value="0.02" label="Annotation Ext Offset (float >= 0)"/>
<param name="annotation_legend_font_size" type="integer" size="4" min="0" value="7" label="Annotation Legend Font Size (pixels, integer > 1)"/>
<param name="branch_thickness" type="float" min="0" value="0.75" size="4" label="Branch Line Width (float >= 0)"/>
<param name="branch_color" type="text" format="text" label="Branch Default Color (e.g. r, red, or #FF0000)"/>
<param name="branch_ancestor_clade_color" type="text" format="text" label="Branch Ancestor Clade Color (e.g. r, red, or #FF0000)"/>
<param name="label_font_strech" type="integer" size="4" value="0" min="0" max="1000" label="Label Font Strech (integer 0 to 1000)"/>
</when>
</conditional>
</page>
</inputs>
<outputs>
<data name="output_annot_file" format="circl" />
</outputs>
<requirements>
<requirement type="package" version="1.63">biopython</requirement>
</requirements>
.. class:: infomark
What it does
GraPhlAn annotates and visualizes phylogenetic and taxonomic trees with labels, colors, heatmaps, and other graphical features. The figure at the bottom of this page summarizes the kinds of graphical features you can apply on a taxonomic tree.
GraPhlAn can also be used as a command line program. You can find the updated source code and manual here1_
The first step consists of uploading your input dataset. This can be done from the Galaxy Get-Data / Load-file. Be sure you choose File-Format: circl
Input examples: You can try out GraPhlAn using uploading two toy examples of a taxonomic trees guide.txt_ and a phylogenetic tree phylo_small.xml_. You can also copy-and-paste their full address or content into the text field.
Input:
The input data consists in a tree file in Newick, Nexus, or simple text file and it has to be loaded into Galaxy from the present module.
(Final) Output:
Image in svg, png, pdf or ps format
The process consists of four steps (Galaxy modules):
1) “Load input tree” from file or URL - Use the Galaxy / Get Data / Upload file and IMPORTANT sure you select File Format: circl
2) “Annotate tree” adds all graphical features but the external “rings” (optional, can be applied recursively)
3) “Add rings to the tree” adds the external “rings” in a circular heatmap or barplot fashion (optional, can be applied recursively)
4) “Plot tree” generates the output image file from the annotated tree.
Below are four examples of quite large phylogenetic trees visualized with GraPhlAn. You can also open the four corresponding high-resolution images for the PhyloPhlAn tree of life, the HMP+MetaHit gut microbiome, the 7-bodysites HMP tree, and the Archaeal tree.
… image:: https://bitbucket.org/nsegata/graphlan/wiki/four_exes.png
Graphlan Annotation (Step 2)
This module graphycally annotates trees. Please refer to the “Load input tree” Galaxy module above for an introduction to GraPhlAn, and to the extensive textual manual available here2_
This annotation step can be recursively applied. This means that multiple annotations can be sequentially added to the same tree simply re-running this galaxy module on the output of the previous application.
… image:: https://bitbucket.org/nsegata/graphlan/wiki/four_exes.png
The scheme below summarizes the different types of graphical options that you can apply to the input tree with the “Annotate tree” and “Add rings to the tree” modules.
… image:: https://bitbucket.org/nsegata/graphlan/wiki/GraPhlAn_Fig1_small.png
… _guide.txt: https://bitbucket.org/nsegata/graphlan/wiki/guide.txt
… _phylo_small.xml: https://bitbucket.org/nsegata/graphlan/wiki/phylo_small.xml
… _PhyloPhlAn tree of life: https://bitbucket.org/nsegata/graphlan/wiki/ppa_tol.png
… _HMP+MetaHit gut microbiome: https://bitbucket.org/nsegata/graphlan/wiki/gut_microbiome.png
… _7-bodysites HMP tree: https://bitbucket.org/nsegata/graphlan/wiki/hmptree.png
… _Archaeal tree: https://bitbucket.org/nsegata/graphlan/wiki/archaea.png
… _here1: https://bitbucket.org/nsegata/graphlan/
… _here2: https://bitbucket.org/nsegata/graphlan/src/2fb8ce095bde/readme.txt
… _Nicola Segata: nsegata@hsph.harvard.edu
… _Curtis Huttenhower: chuttenh@hsph.harvard.edu
Citation and contacts
If you find GraphAn useful in your research, please cite our paper:
| Francesco Asnicar, George Weingart, Timothy L. Tickle, Curtis Huttenhower, Nicola Segata.
| "Compact graphical representation of phylogenetic data and metadata with GraPhlAn"
| Compact graphical representation of phylogenetic data and metadata with GraPhlAn [PeerJ]
|
