Mercurial > repos > iuc > bandage

annotate bandage_image.xml @ 8:97e44e92e5b9 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit c7fe7b3a7c6e1f2109868093b9ce5321c2979a24
author iuc
date Tue, 01 Nov 2022 15:08:26 +0000
parents 53ccc02313e0
children
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8
97e44e92e5b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit c7fe7b3a7c6e1f2109868093b9ce5321c2979a24
iuc
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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>
221c0d23467b 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>
7
53ccc02313e0 "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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221c0d23467b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
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7 <expand macro="requirements"/>
221c0d23467b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
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8 <expand macro="version_command"/>
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9 <command detect_errors="exit_code"> <![CDATA[
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10 @HEADLESS@
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11 Bandage
221c0d23467b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
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12 image
221c0d23467b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
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13 '$input_file'
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14 'out.$output_format'
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15 #if $height:
221c0d23467b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
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16 --height '$height'
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17 #end if
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18 #if $width:
221c0d23467b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
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19 --width '$width'
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20 #end if
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21 #if $fontsize:
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22 --fontsize '$fontsize'
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23 #end if
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24 #if $nodewidth:
97e44e92e5b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit c7fe7b3a7c6e1f2109868093b9ce5321c2979a24
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25 --nodewidth '$nodewidth'
97e44e92e5b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit c7fe7b3a7c6e1f2109868093b9ce5321c2979a24
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26 #end if
2
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27 $names
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28 $lengths
0
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29 ]]></command>
221c0d23467b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
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30 <inputs>
1
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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."/>
0
221c0d23467b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
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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."/>
221c0d23467b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
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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."/>
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34 <param argument="--names" type="boolean" truevalue="--names" falsevalue="" label="Node name labels?"/>
42348f95138d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit 87337151f2f9ae1946db8b3a6da1c4f512ae135d
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35 <param argument="--lengths" type="boolean" truevalue="--lengths" falsevalue="" label="Node length labels?"/>
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36 <param argument="--fontsize" type="integer" min="5" optional="true" label="Font size" help="Node font size?"/>
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97e44e92e5b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit c7fe7b3a7c6e1f2109868093b9ce5321c2979a24
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37 <param argument="--nodewidth" type="float" min="5" optional="true" label="Node width" help="Node width for graph image?" />
0
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38 <param name="output_format" type="select" label="Produce jpg, png or svg file?">
221c0d23467b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
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39 <option selected="True" value="jpg">.jpg</option>
221c0d23467b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
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40 <option value="png">.png</option>
221c0d23467b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
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41 <option value="svg">.svg</option>
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42 </param>
2
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43
0
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44 </inputs>
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45 <outputs>
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46 <data name="outfile" format="jpg" from_work_dir="out.*" label="${tool.name} on ${on_string}: Assembly Graph Image">
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47 <change_format>
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48 <when input="output_format" value="png" format="png"/>
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49 <when input="output_format" value="svg" format="svg"/>
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50 </change_format>
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51 </data>
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52 </outputs>
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53 <tests>
2
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54 <test><!-- test with default settings -->
0
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55 <param name="input_file" ftype="tabular" value="gfa.tabular"/>
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56 <output name="outfile" ftype="jpg" file="out.jpg" compare="sim_size" delta="70000"/>
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57 </test>
2
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58 <test><!-- test with width and height parameters -->
0
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59 <param name="input_file" ftype="tabular" value="gfa.tabular"/>
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60 <param name="height" value="100"/>
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61 <param name="width" value="100"/>
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62 <param name="output_format" value="png"/>
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63 <output name="outfile" ftype="png" file="out.png" compare="sim_size" delta="120000"/>
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64 </test>
2
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65 <test><!-- test svg output -->
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66 <param name="input_file" ftype="tabular" value="gfa.tabular"/>
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67 <param name="output_format" value="svg"/>
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68 <output name="outfile" ftype="svg" file="out.svg" compare="sim_size" delta="120000"/>
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69 </test>
2
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70 <test><!-- test with node name and length labels -->
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71 <param name="input_file" ftype="txt" value="gfa.tabular"/>
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72 <param name="output_format" value="svg"/>
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73 <param name="names" value="--names"/>
42348f95138d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit 87337151f2f9ae1946db8b3a6da1c4f512ae135d
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74 <param name="lengths" value="--lengths"/>
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75 <output name="outfile" ftype="svg" file="out_labels.svg" compare="sim_size" delta="250000"/>
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76 </test>
4
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77 <test><!-- test with node name, length labels and fontsize-->
acced764a3ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit 585f5fa2d2714638c84b3c9ddaeb5a9557159a95"
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78 <param name="input_file" ftype="txt" value="bandage_input.txt"/>
acced764a3ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit 585f5fa2d2714638c84b3c9ddaeb5a9557159a95"
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79 <param name="output_format" value="jpg"/>
acced764a3ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit 585f5fa2d2714638c84b3c9ddaeb5a9557159a95"
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80 <param name="names" value="--names"/>
acced764a3ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit 585f5fa2d2714638c84b3c9ddaeb5a9557159a95"
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81 <param name="lengths" value="--lengths"/>
acced764a3ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit 585f5fa2d2714638c84b3c9ddaeb5a9557159a95"
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82 <param name="fontsize" value="5"/>
acced764a3ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit 585f5fa2d2714638c84b3c9ddaeb5a9557159a95"
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83 <output name="outfile" ftype="jpg" file="out_fontsize.jpg" compare="sim_size" delta="250000"/>
acced764a3ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit 585f5fa2d2714638c84b3c9ddaeb5a9557159a95"
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84 </test>
0
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85 </tests>
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86 <help><![CDATA[
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87 @BANDAGE_OVERVIEW@
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88
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89 **Command Documentation**
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90
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91 ``Bandage image`` will generate an image file of the graph visualisation.
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92
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93 .. image:: $PATH_TO_IMAGES/bandage_graph.png
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94 :alt: example bandage plot
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95
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96 ]]></help>
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97 <expand macro="citations"/>
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98 </tool>
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99