Mercurial > repos > iuc > bandage

comparison bandage_info.xml @ 5:d8b1027d6ce0 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit 7823462e83ff5efbcfd3161f7d471fd07da51611"
author iuc
date Sun, 12 Sep 2021 08:13:13 +0000
parents b2860df42e16
children b9e31c5c01c7
comparison
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4:94fe43e75ddc 5:d8b1027d6ce0
1 <tool id="bandage_info" name="Bandage Info" version="@TOOL_VERSION@+galaxy1" profile="18.01"> 1 <tool id="bandage_info" name="Bandage Info" version="@TOOL_VERSION@+galaxy2" profile="18.01">
2 <description>determine statistics of de novo assembly graphs</description> 2 <description>determine statistics of de novo assembly graphs</description>
3 <expand macro="bio_tools"/>
3 <macros> 4 <macros>
4 <import>macros.xml</import> 5 <import>macros.xml</import>
5 </macros> 6 </macros>
6 <expand macro="requirements"/> 7 <expand macro="requirements"/>
7 <expand macro="version_command"/> 8 <expand macro="version_command"/>
10 @HEADLESS@ 11 @HEADLESS@
11 Bandage 12 Bandage
12 info 13 info
13 '$input_file' 14 '$input_file'
14 $tsv 15 $tsv
15 > out.txt 16 | sed 's/:\s\+/:\t/g'
17 > out.tab
16 ]]></command> 18 ]]></command>
17 <inputs> 19 <inputs>
18 <param name="input_file" type="data" format="txt" label="Graphical Fragment Assembly" help="Supports multiple assembly graph formats: LastGraph (Velvet), FASTG (SPAdes), Trinity.fasta, ASQG and GFA."/> 20 <param name="input_file" type="data" format="txt" label="Graphical Fragment Assembly" help="Supports multiple assembly graph formats: LastGraph (Velvet), FASTG (SPAdes), Trinity.fasta, ASQG and GFA."/>
19 <param argument="--tsv" type="boolean" checked="false" truevalue="--tsv" falsevalue="" label="Output the information in a single tab-delimited line starting with the graph file"/> 21 <param argument="--tsv" type="boolean" checked="false" truevalue="--tsv" falsevalue="" label="Output the information in a single tab-delimited line starting with the graph file"/>
20 </inputs> 22 </inputs>
21 <outputs> 23 <outputs>
22 <data name="outfile" format="txt" from_work_dir="out.txt" label="${tool.name} on ${on_string}: Assembly Graph Information"/> 24 <data name="outfile" format="tabular" from_work_dir="out.tab" label="${tool.name} on ${on_string}: Assembly Graph Information"/>
23 </outputs> 25 </outputs>
24 <tests> 26 <tests>
25 <test> 27 <test>
26 <param name="input_file" ftype="tabular" value="gfa.tabular"/> 28 <param name="input_file" ftype="tabular" value="gfa.tabular"/>
27 <param name="select_mode" value="info"/> 29 <param name="select_mode" value="info"/>
28 <param name="tsv" value="True"/> 30 <param name="tsv" value="True"/>
29 <output name="outfile" ftype="txt" file="out.txt" compare="contains"/> 31 <output name="outfile" ftype="tabular" file="out.tab" compare="contains"/>
30 </test> 32 </test>
31 <test> 33 <test>
32 <param name="input_file" ftype="tabular" value="gfa.tabular"/> 34 <param name="input_file" ftype="tabular" value="gfa.tabular"/>
33 <param name="select_mode" value="info"/> 35 <param name="select_mode" value="info"/>
34 <output name="outfile" ftype="txt" file="out_standard.txt"/> 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
39 @BANDAGE_OVERVIEW@ 41 @BANDAGE_OVERVIEW@
63 Total length (bp): 4878380 65 Total length (bp): 4878380
64 Dead ends: 33 66 Dead ends: 33
65 Percentage dead ends: 2.94118% 67 Percentage dead ends: 2.94118%
66 Connected components: 19 68 Connected components: 19
67 Largest component (bp): 4821329 69 Largest component (bp): 4821329
68 N50 (bp): 90360 70 N50 (bp): 90360
69 Shortest node (bp): 1 71 Shortest node (bp): 1
70 Lower quartile node (bp): 17 72 Lower quartile node (bp): 17
71 Median node (bp): 87 73 Median node (bp): 87
72 Upper quartile node (bp): 404 74 Upper quartile node (bp): 404
73 Longest node (bp): 205425 75 Longest node (bp): 205425
74 76
75 ]]></help> 77 ]]></help>
76 <expand macro="citations"/> 78 <expand macro="citations"/>
77 </tool> 79 </tool>
78