Mercurial > repos > galaxy-australia > purge_haplotigs

comparison purge_haplotigs_cov.xml @ 0:af9c15ba501f draft default tip

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"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
author galaxy-australia
date Wed, 20 Apr 2022 06:46:59 +0000
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1 <tool id="purge_haplotigs_cov" name="Purge Haplotigs Cov" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" >
2 <description>Generate a coverage statistic</description>
3 <xrefs>
4 <xref type='bio.tools'>purgehaplotigs</xref>
5 </xrefs>
6 <macros>
7 <import>macros.xml</import>
8 </macros>
9 <expand macro="requirements" />
10 <expand macro="stdio" />
11 <expand macro="version_command" />
12 <command><![CDATA[
13 purge_haplotigs cov
14 #if $options.j:
15 -j '$options.j'
16 #end if
17 #if $options.s:
18 -s '$options.s'
19 #end if
20 -i $genomecov
21 -l $low_cutoff
22 -m $mid_cutoff
23 -h $high_cutoff
24 cp coverage_stats.csv '$output_statistic'
25 2>&1
26
27 ]]></command>
28 <inputs>
29 <param name="genomecov" type="data" format="tabular" label="Coverage file" help="Coverage file"/>
30 <param name="low_cutoff" type="integer" value="10" label="read depth low cutoff" help="obtain from the histogram"/>
31 <param name="mid_cutoff" type="integer" value="20" label="read depth high cutoff" help="Coverage file"/>
32 <param name="high_cutoff" type="integer" value="30" label="read depth mid cutoff" help="The low point between the haploid and diploid peaks"/>
33 <section name="options" title="Options" expanded="False">
34 <param argument="-j" type="integer" value="80" label="Auto-assign contig as j (junk)"/>
35 <param argument="-s" type="integer" value="80" label="Auto-assign contig as s (suspected haplogit)"/>
36 </section>
37 </inputs>
38 <outputs>
39 <data name="output_statistic" format="csv" label="${tool.name} on ${on_string}: Coverage Statistic" from_work_dir="coverage_stats.csv"/>
40 </outputs>
41
42 <tests>
43 <test>
44 <!-- #1 test with common parameters -->
45 <param name="genomecov" value="aligned.bam.gencov" ftype="tabular"/>
46 <param name="low_cutoff" value="10" />
47 <param name="mid_cutoff" value="20" />
48 <param name="high_cutoff" value="30" />
49 <output name="output_statistic" file="coverage_stats.csv" ftype="csv"/>
50 </test>
51 </tests>
52 <help><![CDATA[
53
54 .. class:: infomark
55
56 **What it does**
57
58 Analyze the coverage on a contig by contig basis.
59
60 **Input**
61
62 - input file: a genemecov output file (tabular format) that was produced from purge_haplotigs hist.
63
64 **Parameters**
65
66 - l : The read depth low cutoff (use the histogram to eyeball these cutoffs)
67
68 - m : The low point between the haploid and diploid peaks
69
70 - h : The read depth high cutoff
71
72 - junk : Auto-assign contig as "j" (junk) if this percentage or greater of the contig is low/high coverage (DEFAULT = 80, > 100 = don't junk anything)
73
74 - suspect : Auto-assign contig as "s" (suspected haplotig) if this percentage or less of the contig is diploid level of coverage (DEFAULT = 80)
75
76 **Output**
77
78 - coverage_stats.csv
79
80 .. class:: infomark
81
82 **References**
83 ]]></help>
84 <citations>
85 <citation type="doi">DOI: 10.1186/s12859-018-2485-7</citation>
86 </citations>
87 </tool>