annotate bandage_info.xml @ 8:ddddce450736 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit 2b3b163bbe36bb648c17c9b0bf808d41d92078c0

<tool id="bandage_info" name="Bandage Info" version="@TOOL_VERSION@+galaxy2" profile="18.01">
    <description>determine statistics of de novo assembly graphs</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tools"/>
    <expand macro="requirements"/>
    <expand macro="version_command"/>
    <command detect_errors="exit_code">
    <![CDATA[
ln -s '$input_file' input.gfa &&

@HEADLESS@
Bandage
    info
    input.gfa
    $tsv
    | sed 's/:\s\+/:\t/g'
    > out.tab
    ]]></command>
    <inputs>
        <param name="input_file" type="data" format="gfa1,gfa2,fastg,txt" label="Graphical Fragment Assembly" help="Supports multiple assembly graph formats: LastGraph (Velvet), FASTG (SPAdes), Trinity.fasta, ASQG and GFA."/>
        <param argument="--tsv" type="boolean" checked="false" truevalue="--tsv" falsevalue="" label="Output the information in a single tab-delimited line starting with the graph file"/>
    </inputs>
    <outputs>
        <data name="outfile" format="tabular" from_work_dir="out.tab" label="${tool.name} on ${on_string}: Assembly Graph Information"/>
    </outputs>
    <tests>
        <test>
            <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="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 (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.
- **Total length:** The total number of base pairs in the graph.
- **Dead ends:** The number of instances where an end of a node does not connect to any other nodes.
- **Percentage dead ends:** The proportion of possible dead ends. The maximum number of dead ends is twice the number of nodes (occurs when there are no edges), so this value is the number of dead ends divided by twice the node count.
- **Connected components:** The number of regions of the graph which are disconnected from each other.
- **Largest component:** The total number of base pairs in the largest connected component.
- **N50:** Nodes that are this length or greater will collectively add up to at least half of the total length.
- **Shortest node:** The length of the shortest node in the graph.
- **Lower quartile node:** The median node length for the shorter half of the nodes.
- **Median node:** The median node length for the graph.
- **Upper quartile node:** The median node length for the longer half of the nodes.
- **Longest node:** The length of the longest node in the graph.

Example output::

    Node count:               561
    Edge count:               734
    Total length (bp):        4878380
    Dead ends:                33
    Percentage dead ends:     2.94118%
    Connected components:     19
    Largest component (bp):   4821329
    N50 (bp):                 90360
    Shortest node (bp):       1
    Lower quartile node (bp): 17
    Median node (bp):         87
    Upper quartile node (bp): 404
    Longest node (bp):        205425

    ]]></help>
    <expand macro="citations"/>
</tool>