Mercurial > repos > jdv > b2b_summarize_assembly

comparison summarize_assembly.xml @ 0:114353d77370 draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
author jdv
date Wed, 17 Jul 2019 17:49:39 -0400
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1 <tool id="b2b_summarize_assembly" name="Summarize assembly" version="0.02">
2
3 <description>Calculate and print basic assembly summary stats</description>
4
5 <!-- ***************************************************************** -->
6
7 <requirements>
8 <!--
9 <requirement type="package" version="0.003">b2b-utils</requirement>
10 -->
11 <requirement type="package" version="0.006007">perl-biox-seq</requirement>
12 </requirements>
13
14 <!-- ***************************************************************** -->
15
16 <version_command>summarize_assembly --version | perl -wnE'print "$1\n" for /summarize_assembly v(.+)/g'</version_command>
17
18 <!-- ***************************************************************** -->
19
20 <command detect_errors="aggressive">
21 <![CDATA[
22
23 summarize_assembly
24 --fasta $input1
25 --cutoffs $cutoffs
26 #if $split_N:
27 --split_N
28 #end if
29 #if $strip_N:
30 --strip_N
31 #end if
32
33 > $report
34 ;
35
36 ]]>
37 </command>
38
39 <!-- ***************************************************************** -->
40
41 <inputs>
42 <param format="fasta" name="input1" type="data" label="Assembly in FASTA format" />
43 <param name="cutoffs" type="text" size="60" value="50 90" label="Nx cutoffs to calculate (space-separated)">
44 <sanitizer invalid_char="">
45 <valid initial="string.digits"><add value=" " /></valid>
46 </sanitizer>
47 </param>
48 <param name="strip_N" type="boolean" label="Strip Ns prior to calculations" />
49 <param name="split_N" type="boolean" label="Split scaffolds on Ns (e.g. report contig-level summary)" />
50 </inputs>
51
52 <!-- ***************************************************************** -->
53
54 <outputs>
55 <data format="txt" name="report" label="${tool.name} on ${on_string}" />
56 </outputs>
57
58 <!-- ***************************************************************** -->
59
60 <tests>
61 <test>
62 <param name="input1" value="assembly.fa" ftype="fasta" />
63 <param name="cutoffs" value="50 90 95" />
64 <output name="report" file="summarize.txt" compare="diff" />
65 </test>
66 <test>
67 <param name="input1" value="assembly.fa" ftype="fasta" />
68 <param name="cutoffs" value="50 90 95" />
69 <param name="strip_N" value="True" />
70 <output name="report" file="summarize.strip.txt" compare="diff" />
71 </test>
72 <test>
73 <param name="input1" value="assembly.fa" ftype="fasta" />
74 <param name="cutoffs" value="50 90 95" />
75 <param name="split_N" value="True" />
76 <output name="report" file="summarize.split.txt" compare="diff" />
77 </test>
78 </tests>
79
80 <!-- ***************************************************************** -->
81
82 <help>
83
84 summarize_assembly is a utility from b2b-utils. It takes a FASTA file and
85 optionally a list of cutoff values as input and prints out summary
86 information about the contigs/scaffolds contained in the file. You can, of
87 course, supply a FASTA file of any sort of nucleic acid sequences, but the
88 summary information makes most sense for contigs from genomic sequencing
89 assemblies.
90
91 </help>
92
93 <!-- ***************************************************************** -->
94
95 <citations>
96 </citations>
97
98 </tool>
99