Mercurial > repos > jdv > b2b_summarize_run

comparison summarize_run.xml @ 0:bd599efae04d 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 17:48:19 -0400
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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="0.006007">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
25 perl $__tool_directory__/summarize_run.pl
26 --raw_1 $in_raw1
27 --raw_2 $in_raw2
28 --filt_1 $in_filt1
29 --filt_2 $in_filt2
30 --consensus $in_ref
31 --bedgraph $in_bg
32 --fastqc_1 $in_fqc1
33 --fastqc_2 $in_fqc2
34 --out $report
35 --threads "\${GALAXY_SLOTS:-1}"
36 ;
37
38 ]]>
39 </command>
40
41 <!-- ***************************************************************** -->
42
43 <inputs>
44 <param format="fastqsanger,fastq" name="in_raw1" type="data" label="Raw forward reads" />
45 <param format="fastqsanger,fastq" name="in_raw2" type="data" label="Raw reverse reads" />
46 <param format="fastqsanger,fastq" name="in_filt1" type="data" label="Filtered/synced forward reads" />
47 <param format="fastqsanger,fastq" name="in_filt2" type="data" label="Filtered/synced reverse reads" />
48 <param format="fasta" name="in_ref" type="data" label="Consensus (FASTA)" />
49 <param format="bedgraph" name="in_bg" type="data" label="Coverage (bedgraph)" />
50 <param format="txt" name="in_fqc1" type="data" label="Raw FastQC (forward reads)" />
51 <param format="txt" name="in_fqc2" type="data" label="Raw FastQC (reverse reads)" />
52 </inputs>
53
54 <!-- ***************************************************************** -->
55
56 <outputs>
57 <data format="tabular" name="report" label="Run/assembly summary" />
58 </outputs>
59
60 <!-- ***************************************************************** -->
61
62 <tests>
63 <test>
64 <param name="in_raw1" value="sumrun_R1.fq" ftype="fastq" />
65 <param name="in_raw2" value="sumrun_R2.fq" ftype="fastq" />
66 <param name="in_filt1" value="sumrun_sync_R1.fq" ftype="fastq" />
67 <param name="in_filt2" value="sumrun_sync_R2.fq" ftype="fastq" />
68 <param name="in_ref" value="sumrun_ref.fa" ftype="fasta" />
69 <param name="in_bg" value="sumrun_ref.bg" ftype="bedgraph" />
70 <param name="in_fqc1" value="sumrun_R1.fastqc" ftype="txt" />
71 <param name="in_fqc2" value="sumrun_R2.fastqc" ftype="txt" />
72 <output name="report" file="sumrun.report.tsv" compare="diff" />
73 </test>
74 </tests>
75
76 <!-- ***************************************************************** -->
77
78 <help>
79
80 `summarize_run` is a Galaxy-only utility from BASE2BIO that reports a
81 number of summary statistics for a sequencing run and assembly. It was
82 written to support workflows at the USDA Southeast Poultry Research
83 Laboratory and may be of limited general-purpose application.
84
85 </help>
86
87 <!-- ***************************************************************** -->
88
89 <citations>
90 </citations>
91
92 </tool>
93