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comparison summarize_run.xml @ 0:9e0453df1745 draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
author jvolkening
date Sat, 02 Mar 2024 07:43:50 +0000
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1 <tool id="b2b_summarize_run" name="Summarize run" version="0.002">
2
3 <description>Summarize sequencing run and assembly statistics</description>
4
5 <!-- ***************************************************************** -->
6
7 <requirements>
8 <!--
9 <requirement type="package" version="0.003">b2b-utils</requirement>
10 -->
11 <requirement type="package" version="0.7.17">bwa</requirement>
12 <requirement type="package" version="0.008009">perl-biox-seq</requirement>
13 <requirement type="package" version="1.23">perl-file-which</requirement>
14 </requirements>
15
16 <!-- ***************************************************************** -->
17
18 <version_command>echo "0.002"</version_command>
19
20 <!-- ***************************************************************** -->
21
22 <command detect_errors="aggressive">
23 <![CDATA[
24 perl $__tool_directory__/frag_lens
25 --forward "$in_filt1"
26 --reverse "$in_filt2"
27 --ref "$in_ref"
28 --threads "\${GALAXY_SLOTS:-1}"
29 --max_aln 100000
30 | perl $__tool_directory__/summarize_run.pl
31 --raw_1 $in_raw1
32 --raw_2 $in_raw2
33 --filt_1 $in_filt1
34 --filt_2 $in_filt2
35 --consensus $in_ref
36 --bedgraph $in_bg
37 --fastqc_1 $in_fqc1
38 --fastqc_2 $in_fqc2
39 --out $report
40 --threads "\${GALAXY_SLOTS:-1}"
41 ;
42
43 ]]>
44 </command>
45
46 <!-- ***************************************************************** -->
47
48 <inputs>
49 <param format="fastqsanger,fastq" name="in_raw1" type="data" label="Raw forward reads" />
50 <param format="fastqsanger,fastq" name="in_raw2" type="data" label="Raw reverse reads" />
51 <param format="fastqsanger,fastq" name="in_filt1" type="data" label="Filtered/synced forward reads" />
52 <param format="fastqsanger,fastq" name="in_filt2" type="data" label="Filtered/synced reverse reads" />
53 <param format="fasta" name="in_ref" type="data" label="Consensus (FASTA)" />
54 <param format="bedgraph" name="in_bg" type="data" label="Coverage (bedgraph)" />
55 <param format="txt" name="in_fqc1" type="data" label="Raw FastQC (forward reads)" />
56 <param format="txt" name="in_fqc2" type="data" label="Raw FastQC (reverse reads)" />
57 </inputs>
58
59 <!-- ***************************************************************** -->
60
61 <outputs>
62 <data format="tabular" name="report" label="Run/assembly summary" />
63 </outputs>
64
65 <!-- ***************************************************************** -->
66
67 <tests>
68 <test>
69 <param name="in_raw1" value="sumrun_R1.fq" ftype="fastq" />
70 <param name="in_raw2" value="sumrun_R2.fq" ftype="fastq" />
71 <param name="in_filt1" value="sumrun_sync_R1.fq" ftype="fastq" />
72 <param name="in_filt2" value="sumrun_sync_R2.fq" ftype="fastq" />
73 <param name="in_ref" value="sumrun_ref.fa" ftype="fasta" />
74 <param name="in_bg" value="sumrun_ref.bg" ftype="bedgraph" />
75 <param name="in_fqc1" value="sumrun_R1.fastqc" ftype="txt" />
76 <param name="in_fqc2" value="sumrun_R2.fastqc" ftype="txt" />
77 <output name="report" file="sumrun.report.tsv" compare="diff" />
78 </test>
79 </tests>
80
81 <!-- ***************************************************************** -->
82
83 <help>
84
85 `summarize_run` is a Galaxy-only utility from BASE2BIO that reports a
86 number of summary statistics for a sequencing run and assembly. It was
87 written to support workflows at the USDA Southeast Poultry Research
88 Laboratory and may be of limited general-purpose application.
89
90 </help>
91
92 <!-- ***************************************************************** -->
93
94 <citations>
95 </citations>
96
97 </tool>
98