Mercurial > repos > iuc > bandage
view bandage_image.xml @ 1:ebe4463404b4 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit 5badd53c6fdaf43796ffacff94852356696d30d0
author | iuc |
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date | Wed, 15 May 2019 04:11:22 -0400 |
parents | 067592b6b312 |
children | 58124285e462 |
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<tool id="bandage_image" name="Bandage Image" version="@TOOL_VERSION@+galaxy0"> <description>visualize de novo assembly graphs</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <expand macro="version_command"/> <command detect_errors="exit_code"> <![CDATA[ Bandage image '$input_file' 'out.$output_format' #if $height: --height '$height' #end if #if $width: --width '$width' #end if ]]></command> <inputs> <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."/> <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."/> <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."/> <param name="output_format" type="select" label="Produce jpg, png or svg file?"> <option selected="True" value="jpg">.jpg</option> <option value="png">.png</option> <option value="svg">.svg</option> </param> </inputs> <outputs> <data name="outfile" format="jpg" from_work_dir="out.*" label="${tool.name} on ${on_string}: Assembly Graph Image"> <change_format> <when input="output_format" value="png" format="png"/> <when input="output_format" value="svg" format="svg"/> </change_format> </data> </outputs> <tests> <test> <param name="input_file" ftype="tabular" value="gfa.tabular"/> <output name="outfile" ftype="jpg" file="out.jpg" compare="sim_size" delta="70000"/> </test> <test> <param name="input_file" ftype="tabular" value="gfa.tabular"/> <param name="height" value="100"/> <param name="width" value="100"/> <param name="output_format" value="png"/> <output name="outfile" ftype="png" file="out.png" compare="sim_size" delta="120000"/> </test> <test> <param name="input_file" ftype="tabular" value="gfa.tabular"/> <param name="output_format" value="svg"/> <output name="outfile" ftype="svg" file="out.svg" compare="sim_size" delta="120000"/> </test> </tests> <help><![CDATA[ @BANDAGE_OVERVIEW@ **Command Documentation** ``Bandage image`` will generate an image file of the graph visualisation. .. image:: $PATH_TO_IMAGES/bandage_graph.png :alt: example bandage plot ]]></help> <expand macro="citations"/> </tool>