Mercurial > repos > iuc > bandage
diff bandage_info.xml @ 8:ddddce450736 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit 2b3b163bbe36bb648c17c9b0bf808d41d92078c0
author | iuc |
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date | Mon, 28 Nov 2022 08:20:19 +0000 |
parents | b9e31c5c01c7 |
children |
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--- 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><![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** -``Bandage info`` takes a graph file as input and outputs the following statistics about the graph: +``Bandage info`` takes a graph file (GFA) as input and outputs the following statistics about the graph: - **Node count:** The number of nodes in the graph. Only positive nodes are counted (i.e. each complementary pair counts as one). - **Edge count:** The number of edges in the graph. Only one edge in each complementary pair is counted.