| Previous changeset 1:ebe4463404b4 (2019-05-15) Next changeset 3:b2860df42e16 (2019-12-05) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit 87337151f2f9ae1946db8b3a6da1c4f512ae135d |
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modified:
bandage_image.xml macros.xml |
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added:
test-data/out_labels.svg |
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| diff -r ebe4463404b4 -r 58124285e462 bandage_image.xml --- a/bandage_image.xml Wed May 15 04:11:22 2019 -0400 +++ b/bandage_image.xml Fri Jul 05 11:36:09 2019 -0400 |
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| @@ -1,12 +1,14 @@ -<tool id="bandage_image" name="Bandage Image" version="@TOOL_VERSION@+galaxy0"> +<tool id="bandage_image" name="Bandage Image" version="@TOOL_VERSION@+galaxy1"> <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[ + <command detect_errors="exit_code"> <![CDATA[ +## set headless mode +export QT_QPA_PLATFORM='offscreen' && + Bandage image '$input_file' @@ -17,16 +19,21 @@ #if $width: --width '$width' #end if + $names + $lengths ]]></command> <inputs> <param name="input_file" type="data" format="txt" label="Graphical Fragment Assembly" help="Supports multiple assembly graph formats: LastGraph (Velvet), FASTG (SPAdes), Trinity.fasta, ASQG and GFA."/> <param argument="--height" type="integer" min="1" value="1000" optional="True" label="Image height" help="If only height or width is set, the other will be determined automatically. If both are set, the image will be exactly that size. Default: 1000."/> <param argument="--width" type="integer" min="1" optional="True" label="Image width" help="If only height or width is set, the other will be determined automatically. If both are set, the image will be exactly that size. Default: not set."/> + <param argument="--names" type="boolean" truevalue="--names" falsevalue="" label="Node name labels?"/> + <param argument="--lengths" type="boolean" truevalue="--lengths" falsevalue="" label="Node length labels?"/> <param name="output_format" type="select" label="Produce jpg, png or svg file?"> <option selected="True" value="jpg">.jpg</option> <option value="png">.png</option> <option value="svg">.svg</option> </param> + </inputs> <outputs> <data name="outfile" format="jpg" from_work_dir="out.*" label="${tool.name} on ${on_string}: Assembly Graph Image"> @@ -37,22 +44,29 @@ </data> </outputs> <tests> - <test> + <test><!-- test with default settings --> <param name="input_file" ftype="tabular" value="gfa.tabular"/> <output name="outfile" ftype="jpg" file="out.jpg" compare="sim_size" delta="70000"/> </test> - <test> + <test><!-- test with width and height parameters --> <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> + <test><!-- test svg output --> <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> + <test><!-- test with node name and length labels --> + <param name="input_file" ftype="txt" value="gfa.tabular"/> + <param name="output_format" value="svg"/> + <param name="names" value="--names"/> + <param name="lengths" value="--lengths"/> + <output name="outfile" ftype="svg" file="out_labels.svg" compare="sim_size" delta="250000"/> + </test> </tests> <help><