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comparison bandage_info.xml @ 8:ddddce450736 draft default tip

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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 b9e31c5c01c7
children
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7:21e491ad532a 8:ddddce450736
6 <expand macro="bio_tools"/> 6 <expand macro="bio_tools"/>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
8 <expand macro="version_command"/> 8 <expand macro="version_command"/>
9 <command detect_errors="exit_code"> 9 <command detect_errors="exit_code">
10 <![CDATA[ 10 <![CDATA[
11 ln -s '$input_file' input.gfa &&
12
11 @HEADLESS@ 13 @HEADLESS@
12 Bandage 14 Bandage
13 info 15 info
14 '$input_file' 16 input.gfa
15 $tsv 17 $tsv
16 | sed 's/:\s\+/:\t/g' 18 | sed 's/:\s\+/:\t/g'
17 > out.tab 19 > out.tab
18 ]]></command> 20 ]]></command>
19 <inputs> 21 <inputs>
20 <param name="input_file" type="data" format="txt" label="Graphical Fragment Assembly" help="Supports multiple assembly graph formats: LastGraph (Velvet), FASTG (SPAdes), Trinity.fasta, ASQG and GFA."/> 22 <param name="input_file" type="data" format="gfa1,gfa2,fastg,txt" label="Graphical Fragment Assembly" help="Supports multiple assembly graph formats: LastGraph (Velvet), FASTG (SPAdes), Trinity.fasta, ASQG and GFA."/>
21 <param argument="--tsv" type="boolean" checked="false" truevalue="--tsv" falsevalue="" label="Output the information in a single tab-delimited line starting with the graph file"/> 23 <param argument="--tsv" type="boolean" checked="false" truevalue="--tsv" falsevalue="" label="Output the information in a single tab-delimited line starting with the graph file"/>
22 </inputs> 24 </inputs>
23 <outputs> 25 <outputs>
24 <data name="outfile" format="tabular" from_work_dir="out.tab" label="${tool.name} on ${on_string}: Assembly Graph Information"/> 26 <data name="outfile" format="tabular" from_work_dir="out.tab" label="${tool.name} on ${on_string}: Assembly Graph Information"/>
25 </outputs> 27 </outputs>
26 <tests> 28 <tests>
27 <test> 29 <test>
28 <param name="input_file" ftype="tabular" value="gfa.tabular"/> 30 <param name="input_file" ftype="txt" value="bandage_input.txt"/>
29 <param name="tsv" value="True"/> 31 <param name="tsv" value="True"/>
30 <output name="outfile" ftype="tabular" file="out.tab" compare="contains"/> 32 <output name="outfile" ftype="tabular" file="out.tab" compare="contains"/>
31 </test> 33 </test>
32 <test> 34 <test>
33 <param name="input_file" ftype="tabular" value="gfa.tabular"/> 35 <param name="input_file" ftype="txt" value="bandage_input.txt"/>
34 <output name="outfile" ftype="tabular" file="out_standard.tab"/> 36 <output name="outfile" ftype="tabular" file="out_standard.tab"/>
35 </test> 37 </test>
36 </tests> 38 </tests>
37 <help><![CDATA[ 39 <help><![CDATA[
38 40
41 *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.*
42
39 @BANDAGE_OVERVIEW@ 43 @BANDAGE_OVERVIEW@
40 44
41 **Command Documentation** 45 **Command Documentation**
42 46
43 ``Bandage info`` takes a graph file as input and outputs the following statistics about the graph: 47 ``Bandage info`` takes a graph file (GFA) as input and outputs the following statistics about the graph:
44 48
45 - **Node count:** The number of nodes in the graph. Only positive nodes are counted (i.e. each complementary pair counts as one). 49 - **Node count:** The number of nodes in the graph. Only positive nodes are counted (i.e. each complementary pair counts as one).
46 - **Edge count:** The number of edges in the graph. Only one edge in each complementary pair is counted. 50 - **Edge count:** The number of edges in the graph. Only one edge in each complementary pair is counted.
47 - **Total length:** The total number of base pairs in the graph. 51 - **Total length:** The total number of base pairs in the graph.
48 - **Dead ends:** The number of instances where an end of a node does not connect to any other nodes. 52 - **Dead ends:** The number of instances where an end of a node does not connect to any other nodes.