Mercurial > repos > iuc > bandage
diff bandage_image.xml @ 0:067592b6b312 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
author | iuc |
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date | Tue, 18 Sep 2018 05:41:44 -0400 |
parents | |
children | ebe4463404b4 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bandage_image.xml Tue Sep 18 05:41:44 2018 -0400 @@ -0,0 +1,70 @@ +<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="tabular" label="Graphical Fragment Assembly" /> + <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> +