Mercurial > repos > galaxy-australia > purge_haplotigs
comparison purge_haplotigs_cov.xml @ 0:af9c15ba501f draft default tip
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
author | galaxy-australia |
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date | Wed, 20 Apr 2022 06:46:59 +0000 |
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-1:000000000000 | 0:af9c15ba501f |
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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> |