Mercurial > repos > iuc > bandage

annotate bandage_image.xml @ 8:ddddce450736 draft default tip

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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
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21e491ad532a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit c7fe7b3a7c6e1f2109868093b9ce5321c2979a24
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1 <tool id="bandage_image" name="Bandage Image" version="@TOOL_VERSION@+galaxy4" profile="21.05">
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2 <description>visualize de novo assembly graphs</description>
067592b6b312 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
6
b9e31c5c01c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit fd23651fa43e8eefb7f55032c9ea645083042455"
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6 <expand macro="bio_tools"/>
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067592b6b312 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
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7 <expand macro="requirements"/>
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8 <expand macro="version_command"/>
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9 <command detect_errors="exit_code"> <![CDATA[
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ddddce450736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit 2b3b163bbe36bb648c17c9b0bf808d41d92078c0
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11 ln -s '$input_file' input.gfa &&
ddddce450736 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit 2b3b163bbe36bb648c17c9b0bf808d41d92078c0
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12
3
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13 @HEADLESS@
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14 Bandage
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15 image
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16 input.gfa
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17 'out.$output_format'
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18 #if $height:
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19 --height '$height'
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20 #end if
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21 #if $width:
067592b6b312 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
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22 --width '$width'
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23 #end if
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24 #if $fontsize:
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25 --fontsize '$fontsize'
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26 #end if
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27 #if $nodewidth:
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28 --nodewidth '$nodewidth'
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29 #end if
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30 $names
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31 $lengths
0
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32 ]]></command>
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33 <inputs>
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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."/>
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067592b6b312 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
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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."/>
067592b6b312 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
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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."/>
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58124285e462 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit 87337151f2f9ae1946db8b3a6da1c4f512ae135d
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37 <param argument="--names" type="boolean" truevalue="--names" falsevalue="" label="Node name labels?"/>
58124285e462 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit 87337151f2f9ae1946db8b3a6da1c4f512ae135d
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38 <param argument="--lengths" type="boolean" truevalue="--lengths" falsevalue="" label="Node length labels?"/>
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94fe43e75ddc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit 585f5fa2d2714638c84b3c9ddaeb5a9557159a95"
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39 <param argument="--fontsize" type="integer" min="5" optional="true" label="Font size" help="Node font size?"/>
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40 <param argument="--nodewidth" type="float" min="5" optional="true" label="Node width" help="Node width for graph image?" />
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41 <param name="output_format" type="select" label="Produce jpg, png or svg file?">
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42 <option selected="True" value="jpg">.jpg</option>
067592b6b312 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
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43 <option value="png">.png</option>
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44 <option value="svg">.svg</option>
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45 </param>
2
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46
0
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47 </inputs>
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48 <outputs>
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49 <data name="outfile" format="jpg" from_work_dir="out.*" label="${tool.name} on ${on_string}: Assembly Graph Image">
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50 <change_format>
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51 <when input="output_format" value="png" format="png"/>
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52 <when input="output_format" value="svg" format="svg"/>
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53 </change_format>
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54 </data>
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55 </outputs>
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56 <tests>
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57 <test><!-- test with default settings -->
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58 <param name="input_file" ftype="txt" value="bandage_input.txt"/>
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59 <output name="outfile" ftype="jpg">
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60 <assert_contents>
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61 <has_size value="47168" delta="15000"/>
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62 </assert_contents>
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63 </output>
0
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64 </test>
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65 <test><!-- test with width and height parameters -->
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66 <param name="input_file" ftype="txt" value="bandage_input.txt"/>
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67 <param name="height" value="100"/>
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68 <param name="width" value="100"/>
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69 <param name="output_format" value="png"/>
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70 <output name="outfile" ftype="png">
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71 <assert_contents>
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72 <has_size value="2000" delta="1500"/>
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73 </assert_contents>
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74 </output>
0
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75 </test>
2
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76 <test><!-- test svg output -->
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77 <param name="input_file" ftype="txt" value="bandage_input.txt"/>
0
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78 <param name="output_format" value="svg"/>
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79 <output name="outfile" ftype="svg">
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80 <assert_contents>
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81 <has_size value="15154" delta="5000"/>
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82 </assert_contents>
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83 </output>
0
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84 </test>
2
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85 <test><!-- test with node name and length labels -->
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86 <param name="input_file" ftype="txt" value="bandage_input.txt"/>
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87 <param name="output_format" value="svg"/>
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88 <param name="names" value="--names"/>
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89 <param name="lengths" value="--lengths"/>
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90 <output name="outfile" ftype="svg">
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91 <assert_contents>
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92 <has_size value="49566" delta="15000"/>
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93 </assert_contents>
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94 </output>
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95 </test>
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96 <test><!-- test with node name, length labels and fontsize-->
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97 <param name="input_file" ftype="txt" value="bandage_input.txt"/>
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98 <param name="output_format" value="jpg"/>
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99 <param name="names" value="--names"/>
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100 <param name="lengths" value="--lengths"/>
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101 <param name="fontsize" value="5"/>
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102 <output name="outfile" ftype="jpg">
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103 <assert_contents>
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104 <has_size value="45286" delta="15000"/>
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105 </assert_contents>
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106 </output>
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107 </test>
0
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108 </tests>
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109 <help><![CDATA[
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110
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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.*
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112
0
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113 @BANDAGE_OVERVIEW@
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114
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115 **Command Documentation**
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116
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117 ``Bandage image`` will generate an image file of the graph visualisation.
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118
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119 .. image:: $PATH_TO_IMAGES/bandage_graph.png
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120 :alt: example bandage plot
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121
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122 ]]></help>
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123 <expand macro="citations"/>
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124 </tool>