Mercurial > repos > iuc > bandage
changeset 8:ddddce450736 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit 2b3b163bbe36bb648c17c9b0bf808d41d92078c0
| author | iuc |
|---|---|
| date | Mon, 28 Nov 2022 08:20:19 +0000 |
| parents | 21e491ad532a |
| children | |
| files | bandage_image.xml bandage_info.xml macros.xml test-data/gfa.tabular test-data/out.jpg test-data/out.png test-data/out.svg test-data/out.tab test-data/out_fontsize.jpg test-data/out_labels.svg test-data/out_standard.tab |
| diffstat | 11 files changed, 69 insertions(+), 60347 deletions(-) [+] |
line wrap: on
line diff
--- a/bandage_image.xml Tue Nov 01 15:09:04 2022 +0000 +++ b/bandage_image.xml Mon Nov 28 08:20:19 2022 +0000 @@ -7,10 +7,13 @@ <expand macro="requirements"/> <expand macro="version_command"/> <command detect_errors="exit_code"> <![CDATA[ + +ln -s '$input_file' input.gfa && + @HEADLESS@ Bandage image - '$input_file' + input.gfa 'out.$output_format' #if $height: --height '$height' @@ -22,13 +25,13 @@ --fontsize '$fontsize' #end if #if $nodewidth: - --nodewidth '$nodewidth' + --nodewidth '$nodewidth' #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 name="input_file" type="data" format="gfa1,gfa2,fastg,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?"/> @@ -52,27 +55,43 @@ </outputs> <tests> <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"/> + <param name="input_file" ftype="txt" value="bandage_input.txt"/> + <output name="outfile" ftype="jpg"> + <assert_contents> + <has_size value="47168" delta="15000"/> + </assert_contents> + </output> </test> <test><!-- test with width and height parameters --> - <param name="input_file" ftype="tabular" value="gfa.tabular"/> + <param name="input_file" ftype="txt" value="bandage_input.txt"/> <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"/> + <output name="outfile" ftype="png"> + <assert_contents> + <has_size value="2000" delta="1500"/> + </assert_contents> + </output> </test> <test><!-- test svg output --> - <param name="input_file" ftype="tabular" value="gfa.tabular"/> + <param name="input_file" ftype="txt" value="bandage_input.txt"/> <param name="output_format" value="svg"/> - <output name="outfile" ftype="svg" file="out.svg" compare="sim_size" delta="120000"/> + <output name="outfile" ftype="svg"> + <assert_contents> + <has_size value="15154" delta="5000"/> + </assert_contents> + </output> </test> <test><!-- test with node name and length labels --> - <param name="input_file" ftype="txt" value="gfa.tabular"/> + <param name="input_file" ftype="txt" value="bandage_input.txt"/> <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"/> + <output name="outfile" ftype="svg"> + <assert_contents> + <has_size value="49566" delta="15000"/> + </assert_contents> + </output> </test> <test><!-- test with node name, length labels and fontsize--> <param name="input_file" ftype="txt" value="bandage_input.txt"/> @@ -80,10 +99,17 @@ <param name="names" value="--names"/> <param name="lengths" value="--lengths"/> <param name="fontsize" value="5"/> - <output name="outfile" ftype="jpg" file="out_fontsize.jpg" compare="sim_size" delta="250000"/> + <output name="outfile" ftype="jpg"> + <assert_contents> + <has_size value="45286" delta="15000"/> + </assert_contents> + </output> </test> </tests> <help><![CDATA[ + +*THE NEW BANDAGE: As of version 2022.09, the Bandage tool is now built on `Bandage-NG <https://github.com/asl/BandageNG>`_. This fork of the original Bandage is better maintained with additional features and performance upgrades.* + @BANDAGE_OVERVIEW@ **Command Documentation** @@ -96,4 +122,3 @@ ]]></help> <expand macro="citations"/> </tool> -
--- a/bandage_info.xml Tue Nov 01 15:09:04 2022 +0000 +++ b/bandage_info.xml Mon Nov 28 08:20:19 2022 +0000 @@ -8,16 +8,18 @@ <expand macro="version_command"/> <command detect_errors="exit_code"> <![CDATA[ +ln -s '$input_file' input.gfa && + @HEADLESS@ Bandage info - '$input_file' + input.gfa $tsv | sed 's/:\s\+/:\t/g' > out.tab ]]></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 name="input_file" type="data" format="gfa1,gfa2,fastg,txt" label="Graphical Fragment Assembly" help="Supports multiple assembly graph formats: LastGraph (Velvet), FASTG (SPAdes), Trinity.fasta, ASQG and GFA."/> <param argument="--tsv" type="boolean" checked="false" truevalue="--tsv" falsevalue="" label="Output the information in a single tab-delimited line starting with the graph file"/> </inputs> <outputs> @@ -25,22 +27,24 @@ </outputs> <tests> <test> - <param name="input_file" ftype="tabular" value="gfa.tabular"/> + <param name="input_file" ftype="txt" value="bandage_input.txt"/> <param name="tsv" value="True"/> <output name="outfile" ftype="tabular" file="out.tab" compare="contains"/> </test> <test> - <param name="input_file" ftype="tabular" value="gfa.tabular"/> + <param name="input_file" ftype="txt" value="bandage_input.txt"/> <output name="outfile" ftype="tabular" file="out_standard.tab"/> </test> </tests> <help><