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annotate 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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58124285e462 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit 87337151f2f9ae1946db8b3a6da1c4f512ae135d
iuc
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1 <tool id="bandage_image" name="Bandage Image" version="@TOOL_VERSION@+galaxy1">
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2 <description>visualize de novo assembly graphs</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
067592b6b312 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
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6 <expand macro="requirements"/>
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7 <expand macro="version_command"/>
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58124285e462 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit 87337151f2f9ae1946db8b3a6da1c4f512ae135d
iuc
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8 <command detect_errors="exit_code"> <![CDATA[
58124285e462 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit 87337151f2f9ae1946db8b3a6da1c4f512ae135d
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9 ## set headless mode
58124285e462 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit 87337151f2f9ae1946db8b3a6da1c4f512ae135d
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10 export QT_QPA_PLATFORM='offscreen' &&
58124285e462 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit 87337151f2f9ae1946db8b3a6da1c4f512ae135d
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11
0
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12 Bandage
067592b6b312 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
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13 image
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14 '$input_file'
067592b6b312 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
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15 'out.$output_format'
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16 #if $height:
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17 --height '$height'
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18 #end if
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19 #if $width:
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20 --width '$width'
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21 #end if
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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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22 $names
58124285e462 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit 87337151f2f9ae1946db8b3a6da1c4f512ae135d
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23 $lengths
0
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24 ]]></command>
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25 <inputs>
1
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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."/>
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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."/>
067592b6b312 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
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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."/>
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58124285e462 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit 87337151f2f9ae1946db8b3a6da1c4f512ae135d
iuc
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29 <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
iuc
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30 <param argument="--lengths" type="boolean" truevalue="--lengths" falsevalue="" label="Node length labels?"/>
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31 <param name="output_format" type="select" label="Produce jpg, png or svg file?">
067592b6b312 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
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32 <option selected="True" value="jpg">.jpg</option>
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33 <option value="png">.png</option>
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34 <option value="svg">.svg</option>
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35 </param>
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36
0
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37 </inputs>
067592b6b312 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
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38 <outputs>
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39 <data name="outfile" format="jpg" from_work_dir="out.*" label="${tool.name} on ${on_string}: Assembly Graph Image">
067592b6b312 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
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40 <change_format>
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41 <when input="output_format" value="png" format="png"/>
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42 <when input="output_format" value="svg" format="svg"/>
067592b6b312 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
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43 </change_format>
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44 </data>
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45 </outputs>
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46 <tests>
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47 <test><!-- test with default settings -->
0
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48 <param name="input_file" ftype="tabular" value="gfa.tabular"/>
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49 <output name="outfile" ftype="jpg" file="out.jpg" compare="sim_size" delta="70000"/>
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50 </test>
2
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51 <test><!-- test with width and height parameters -->
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52 <param name="input_file" ftype="tabular" value="gfa.tabular"/>
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53 <param name="height" value="100"/>
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54 <param name="width" value="100"/>
067592b6b312 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
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55 <param name="output_format" value="png"/>
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56 <output name="outfile" ftype="png" file="out.png" compare="sim_size" delta="120000"/>
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57 </test>
2
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58 <test><!-- test svg output -->
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59 <param name="input_file" ftype="tabular" value="gfa.tabular"/>
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60 <param name="output_format" value="svg"/>
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61 <output name="outfile" ftype="svg" file="out.svg" compare="sim_size" delta="120000"/>
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62 </test>
2
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63 <test><!-- test with node name and length labels -->
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64 <param name="input_file" ftype="txt" value="gfa.tabular"/>
58124285e462 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit 87337151f2f9ae1946db8b3a6da1c4f512ae135d
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65 <param name="output_format" value="svg"/>
58124285e462 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit 87337151f2f9ae1946db8b3a6da1c4f512ae135d
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66 <param name="names" value="--names"/>
58124285e462 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit 87337151f2f9ae1946db8b3a6da1c4f512ae135d
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67 <param name="lengths" value="--lengths"/>
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68 <output name="outfile" ftype="svg" file="out_labels.svg" compare="sim_size" delta="250000"/>
58124285e462 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit 87337151f2f9ae1946db8b3a6da1c4f512ae135d
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69 </test>
0
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70 </tests>
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71 <help><![CDATA[
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72 @BANDAGE_OVERVIEW@
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73
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74 **Command Documentation**
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75
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76 ``Bandage image`` will generate an image file of the graph visualisation.
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77
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78 .. image:: $PATH_TO_IMAGES/bandage_graph.png
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79 :alt: example bandage plot
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80
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81 ]]></help>
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82 <expand macro="citations"/>
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83 </tool>
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84