Mercurial > repos > iuc > bandage

comparison bandage_image.xml @ 8:ddddce450736 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit 2b3b163bbe36bb648c17c9b0bf808d41d92078c0
author iuc
date Mon, 28 Nov 2022 08:20:19 +0000
parents 21e491ad532a
children
comparison
equal deleted inserted replaced
7:21e491ad532a 8:ddddce450736
5 </macros> 5 </macros>
6 <expand macro="bio_tools"/> 6 <expand macro="bio_tools"/>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
8 <expand macro="version_command"/> 8 <expand macro="version_command"/>
9 <command detect_errors="exit_code"> <![CDATA[ 9 <command detect_errors="exit_code"> <![CDATA[
10
11 ln -s '$input_file' input.gfa &&
12
10 @HEADLESS@ 13 @HEADLESS@
11 Bandage 14 Bandage
12 image 15 image
13 '$input_file' 16 input.gfa
14 'out.$output_format' 17 'out.$output_format'
15 #if $height: 18 #if $height:
16 --height '$height' 19 --height '$height'
17 #end if 20 #end if
18 #if $width: 21 #if $width:
20 #end if 23 #end if
21 #if $fontsize: 24 #if $fontsize:
22 --fontsize '$fontsize' 25 --fontsize '$fontsize'
23 #end if 26 #end if
24 #if $nodewidth: 27 #if $nodewidth:
25 --nodewidth '$nodewidth' 28 --nodewidth '$nodewidth'
26 #end if 29 #end if
27 $names 30 $names
28 $lengths 31 $lengths
29 ]]></command> 32 ]]></command>
30 <inputs> 33 <inputs>
31 <param name="input_file" type="data" format="txt" label="Graphical Fragment Assembly" help="Supports multiple assembly graph formats: LastGraph (Velvet), FASTG (SPAdes), Trinity.fasta, ASQG and GFA."/> 34 <param name="input_file" type="data" format="gfa1,gfa2,fastg,txt" label="Graphical Fragment Assembly" help="Supports multiple assembly graph formats: LastGraph (Velvet), FASTG (SPAdes), Trinity.fasta, ASQG and GFA."/>
32 <param argument="--height" type="integer" min="1" value="1000" optional="True" label="Image height" help="If only height or width is set, the other will be determined automatically. If both are set, the image will be exactly that size. Default: 1000."/> 35 <param argument="--height" type="integer" min="1" value="1000" optional="True" label="Image height" help="If only height or width is set, the other will be determined automatically. If both are set, the image will be exactly that size. Default: 1000."/>
33 <param argument="--width" type="integer" min="1" optional="True" label="Image width" help="If only height or width is set, the other will be determined automatically. If both are set, the image will be exactly that size. Default: not set."/> 36 <param argument="--width" type="integer" min="1" optional="True" label="Image width" help="If only height or width is set, the other will be determined automatically. If both are set, the image will be exactly that size. Default: not set."/>
34 <param argument="--names" type="boolean" truevalue="--names" falsevalue="" label="Node name labels?"/> 37 <param argument="--names" type="boolean" truevalue="--names" falsevalue="" label="Node name labels?"/>
35 <param argument="--lengths" type="boolean" truevalue="--lengths" falsevalue="" label="Node length labels?"/> 38 <param argument="--lengths" type="boolean" truevalue="--lengths" falsevalue="" label="Node length labels?"/>
36 <param argument="--fontsize" type="integer" min="5" optional="true" label="Font size" help="Node font size?"/> 39 <param argument="--fontsize" type="integer" min="5" optional="true" label="Font size" help="Node font size?"/>
50 </change_format> 53 </change_format>
51 </data> 54 </data>
52 </outputs> 55 </outputs>
53 <tests> 56 <tests>
54 <test><!-- test with default settings --> 57 <test><!-- test with default settings -->
55 <param name="input_file" ftype="tabular" value="gfa.tabular"/> 58 <param name="input_file" ftype="txt" value="bandage_input.txt"/>
56 <output name="outfile" ftype="jpg" file="out.jpg" compare="sim_size" delta="70000"/> 59 <output name="outfile" ftype="jpg">
60 <assert_contents>
61 <has_size value="47168" delta="15000"/>
62 </assert_contents>
63 </output>
57 </test> 64 </test>
58 <test><!-- test with width and height parameters --> 65 <test><!-- test with width and height parameters -->
59 <param name="input_file" ftype="tabular" value="gfa.tabular"/> 66 <param name="input_file" ftype="txt" value="bandage_input.txt"/>
60 <param name="height" value="100"/> 67 <param name="height" value="100"/>
61 <param name="width" value="100"/> 68 <param name="width" value="100"/>
62 <param name="output_format" value="png"/> 69 <param name="output_format" value="png"/>
63 <output name="outfile" ftype="png" file="out.png" compare="sim_size" delta="120000"/> 70 <output name="outfile" ftype="png">
71 <assert_contents>
72 <has_size value="2000" delta="1500"/>
73 </assert_contents>
74 </output>
64 </test> 75 </test>
65 <test><!-- test svg output --> 76 <test><!-- test svg output -->
66 <param name="input_file" ftype="tabular" value="gfa.tabular"/> 77 <param name="input_file" ftype="txt" value="bandage_input.txt"/>
67 <param name="output_format" value="svg"/> 78 <param name="output_format" value="svg"/>
68 <output name="outfile" ftype="svg" file="out.svg" compare="sim_size" delta="120000"/> 79 <output name="outfile" ftype="svg">
80 <assert_contents>
81 <has_size value="15154" delta="5000"/>
82 </assert_contents>
83 </output>
69 </test> 84 </test>
70 <test><!-- test with node name and length labels --> 85 <test><!-- test with node name and length labels -->
71 <param name="input_file" ftype="txt" value="gfa.tabular"/> 86 <param name="input_file" ftype="txt" value="bandage_input.txt"/>
72 <param name="output_format" value="svg"/> 87 <param name="output_format" value="svg"/>
73 <param name="names" value="--names"/> 88 <param name="names" value="--names"/>
74 <param name="lengths" value="--lengths"/> 89 <param name="lengths" value="--lengths"/>
75 <output name="outfile" ftype="svg" file="out_labels.svg" compare="sim_size" delta="250000"/> 90 <output name="outfile" ftype="svg">
91 <assert_contents>
92 <has_size value="49566" delta="15000"/>
93 </assert_contents>
94 </output>
76 </test> 95 </test>
77 <test><!-- test with node name, length labels and fontsize--> 96 <test><!-- test with node name, length labels and fontsize-->
78 <param name="input_file" ftype="txt" value="bandage_input.txt"/> 97 <param name="input_file" ftype="txt" value="bandage_input.txt"/>
79 <param name="output_format" value="jpg"/> 98 <param name="output_format" value="jpg"/>
80 <param name="names" value="--names"/> 99 <param name="names" value="--names"/>
81 <param name="lengths" value="--lengths"/> 100 <param name="lengths" value="--lengths"/>
82 <param name="fontsize" value="5"/> 101 <param name="fontsize" value="5"/>
83 <output name="outfile" ftype="jpg" file="out_fontsize.jpg" compare="sim_size" delta="250000"/> 102 <output name="outfile" ftype="jpg">
103 <assert_contents>
104 <has_size value="45286" delta="15000"/>
105 </assert_contents>
106 </output>
84 </test> 107 </test>
85 </tests> 108 </tests>
86 <help><![CDATA[ 109 <help><![CDATA[
110
111 *THE NEW BANDAGE: As of version 2022.09, the Bandage tool is now built on `Bandage-NG <https://github.com/asl/BandageNG>`_. This fork of the original Bandage is better maintained with additional features and performance upgrades.*
112
87 @BANDAGE_OVERVIEW@ 113 @BANDAGE_OVERVIEW@
88 114
89 **Command Documentation** 115 **Command Documentation**
90 116
91 ``Bandage image`` will generate an image file of the graph visualisation. 117 ``Bandage image`` will generate an image file of the graph visualisation.
94 :alt: example bandage plot 120 :alt: example bandage plot
95 121
96 ]]></help> 122 ]]></help>
97 <expand macro="citations"/> 123 <expand macro="citations"/>
98 </tool> 124 </tool>
99