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comparison bandage_image.xml @ 2:58124285e462 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit 87337151f2f9ae1946db8b3a6da1c4f512ae135d
author iuc
date Fri, 05 Jul 2019 11:36:09 -0400
parents ebe4463404b4
children b2860df42e16
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1:ebe4463404b4 2:58124285e462
1 <tool id="bandage_image" name="Bandage Image" version="@TOOL_VERSION@+galaxy0"> 1 <tool id="bandage_image" name="Bandage Image" version="@TOOL_VERSION@+galaxy1">
2 <description>visualize de novo assembly graphs</description> 2 <description>visualize de novo assembly graphs</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="version_command"/> 7 <expand macro="version_command"/>
8 <command detect_errors="exit_code"> 8 <command detect_errors="exit_code"> <![CDATA[
9 <![CDATA[ 9 ## set headless mode
10 export QT_QPA_PLATFORM='offscreen' &&
11
10 Bandage 12 Bandage
11 image 13 image
12 '$input_file' 14 '$input_file'
13 'out.$output_format' 15 'out.$output_format'
14 #if $height: 16 #if $height:
15 --height '$height' 17 --height '$height'
16 #end if 18 #end if
17 #if $width: 19 #if $width:
18 --width '$width' 20 --width '$width'
19 #end if 21 #end if
22 $names
23 $lengths
20 ]]></command> 24 ]]></command>
21 <inputs> 25 <inputs>
22 <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."/> 26 <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."/>
23 <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."/> 27 <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."/>
24 <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."/> 28 <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."/>
29 <param argument="--names" type="boolean" truevalue="--names" falsevalue="" label="Node name labels?"/>
30 <param argument="--lengths" type="boolean" truevalue="--lengths" falsevalue="" label="Node length labels?"/>
25 <param name="output_format" type="select" label="Produce jpg, png or svg file?"> 31 <param name="output_format" type="select" label="Produce jpg, png or svg file?">
26 <option selected="True" value="jpg">.jpg</option> 32 <option selected="True" value="jpg">.jpg</option>
27 <option value="png">.png</option> 33 <option value="png">.png</option>
28 <option value="svg">.svg</option> 34 <option value="svg">.svg</option>
29 </param> 35 </param>
36
30 </inputs> 37 </inputs>
31 <outputs> 38 <outputs>
32 <data name="outfile" format="jpg" from_work_dir="out.*" label="${tool.name} on ${on_string}: Assembly Graph Image"> 39 <data name="outfile" format="jpg" from_work_dir="out.*" label="${tool.name} on ${on_string}: Assembly Graph Image">
33 <change_format> 40 <change_format>
34 <when input="output_format" value="png" format="png"/> 41 <when input="output_format" value="png" format="png"/>
35 <when input="output_format" value="svg" format="svg"/> 42 <when input="output_format" value="svg" format="svg"/>
36 </change_format> 43 </change_format>
37 </data> 44 </data>
38 </outputs> 45 </outputs>
39 <tests> 46 <tests>
40 <test> 47 <test><!-- test with default settings -->
41 <param name="input_file" ftype="tabular" value="gfa.tabular"/> 48 <param name="input_file" ftype="tabular" value="gfa.tabular"/>
42 <output name="outfile" ftype="jpg" file="out.jpg" compare="sim_size" delta="70000"/> 49 <output name="outfile" ftype="jpg" file="out.jpg" compare="sim_size" delta="70000"/>
43 </test> 50 </test>
44 <test> 51 <test><!-- test with width and height parameters -->
45 <param name="input_file" ftype="tabular" value="gfa.tabular"/> 52 <param name="input_file" ftype="tabular" value="gfa.tabular"/>
46 <param name="height" value="100"/> 53 <param name="height" value="100"/>
47 <param name="width" value="100"/> 54 <param name="width" value="100"/>
48 <param name="output_format" value="png"/> 55 <param name="output_format" value="png"/>
49 <output name="outfile" ftype="png" file="out.png" compare="sim_size" delta="120000"/> 56 <output name="outfile" ftype="png" file="out.png" compare="sim_size" delta="120000"/>
50 </test> 57 </test>
51 <test> 58 <test><!-- test svg output -->
52 <param name="input_file" ftype="tabular" value="gfa.tabular"/> 59 <param name="input_file" ftype="tabular" value="gfa.tabular"/>
53 <param name="output_format" value="svg"/> 60 <param name="output_format" value="svg"/>
54 <output name="outfile" ftype="svg" file="out.svg" compare="sim_size" delta="120000"/> 61 <output name="outfile" ftype="svg" file="out.svg" compare="sim_size" delta="120000"/>
62 </test>
63 <test><!-- test with node name and length labels -->
64 <param name="input_file" ftype="txt" value="gfa.tabular"/>
65 <param name="output_format" value="svg"/>
66 <param name="names" value="--names"/>
67 <param name="lengths" value="--lengths"/>
68 <output name="outfile" ftype="svg" file="out_labels.svg" compare="sim_size" delta="250000"/>
55 </test> 69 </test>
56 </tests> 70 </tests>
57 <help><![CDATA[ 71 <help><![CDATA[
58 @BANDAGE_OVERVIEW@ 72 @BANDAGE_OVERVIEW@
59 73