Mercurial > repos > galaxy-australia > purge_haplotigs

comparison purge_haplotigs_hist.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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-1:000000000000 0:af9c15ba501f
1 <tool id="purge_haplotigs_hist" name="Purge Haplotigs Hist" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" >
2 <description>Generate a coverage histogram</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 cp $input_bam input.bam &&
14 purge_haplotigs hist
15 -t \${GALAXY_SLOTS:-4}
16 #if $options.depth
17 --depth '$options.depth'
18 #end if
19 -b input.bam
20 -g $genome &&
21 cp input.bam.histogram.png '$output_histogram' &&
22 cp input.bam.gencov '$output_coverage'
23 2>&1
24
25 ]]></command>
26 <inputs>
27 <param name="input_bam" type="data" format="bam" label="BAM file" help="Input BAM file"/>
28 <param name="genome" type="data" format="fasta" label="FASTA file" help="Input Genome File"/>
29 <section name="options" title="Options" expanded="False">
30 <param name="depth" argument="--depth" type="integer" value="200" label="Maximum cutoff for depth" help="default=200, increase if needed."/>
31 </section>
32 </inputs>
33 <outputs>
34 <data name="output_histogram" format="png" label="${tool.name} on ${on_string}: histogram"/>
35 <data name="output_coverage" format="tabular" label="${tool.name} on ${on_string}: Coverage"/>
36 </outputs>
37
38 <tests>
39 <test>
40 <!-- #1 test with common parameters -->
41 <param name="input_bam" value="aligned.bam" ftype="bam"/>
42 <param name="genome" value="contigs.fa" ftype="fasta"/>
43 <output name="output_histogram" file="aligned.bam.histogram.png" ftype="png">
44 <assert_content>
45 <has_size value="135878" delta="100"/>
46 </assert_content>
47 </output>
48 <output name="output_coverage">
49 <assert_contents>
50 <has_n_lines n="2613"/>
51 </assert_contents>
52 </output>
53 </test>
54 </tests>
55 <help><![CDATA[
56
57 .. class:: infomark
58
59 **What it does**
60
61 Purge Haplotigs Histogram is part of purge_haplotigs for generate a coverage histogram.
62
63 **Input**
64
65 - input file 1 - BAM file.
66 - input file 2 - FASTA file.
67
68 **Example:**
69
70 - purge_haplotigs hist -b input.bam -g genome.fa
71
72 **Output**
73
74 - input.bam.histogram.png
75 - input.bam.gencov
76
77 .. class:: infomark
78
79 **References**
80
81 ]]></help>
82 <citations>
83 <citation type="doi">DOI: 10.1186/s12859-018-2485-7</citation>
84 </citations>
85 </tool>