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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
author iuc
date Fri, 16 Sep 2022 13:48:16 +0000
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-1:000000000000 0:b58c3bd71ff9
1 <tool id="hapog" name="Hapo-G" profile="21.05" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>genome polishing</description>
3 <macros>
4 <token name="@TOOL_VERSION@">1.3.3</token>
5 <token name="@VERSION_SUFFIX@">0</token>
6 </macros>
7 <requirements>
8 <requirement type="package" version="@TOOL_VERSION@">hapog</requirement>
9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[
11 hapog
12 --genome '${genome}'
13 --output output/
14
15 --threads \${GALAXY_SLOTS:-1}
16
17 #if str( $reads.type ) == "short":
18 #for $i in $reads.pe1
19 --pe1 '${i}'
20 #end for
21 #for $i in $reads.pe2
22 --pe2 '${i}'
23 #end for
24 #elif str( $reads.type ) == "short_collection":
25 #for $i in $reads.pecol
26 --pe1 '${i.forward}'
27 --pe2 '${i.reverse}'
28 #end for
29 #elif str( $reads.type ) == "long":
30 --single '${single}'
31 #elif str( $reads.type ) == "bam":
32 -b '${bam}'
33 #end if
34
35 $u
36 ]]></command>
37 <inputs>
38 <param argument="--genome" type="data" format="fasta" label="Genome assembly to polish"/>
39 <conditional name="reads">
40 <param name="type" type="select" label="Type of data used for polishing">
41 <option value="short">Short (paired) reads</option>
42 <option value="short_collection">Short (paired) reads collection</option>
43 <option value="long">Long reads</option>
44 <option value="bam">Pre-aligned reads (BAM)</option>
45 </param>
46 <when value="short">
47 <param argument="--pe1" type="data" format="fastq,fastq.gz" multiple="true" label="First set of short reads"/>
48 <param argument="--pe2" type="data" format="fastq,fastq.gz" multiple="true" label="Second set of short reads"/>
49 </when>
50 <when value="short_collection">
51 <param name="pecol" type="data_collection" collection_type="paired" format="fastq,fastq.gz" label="Paired collection of short reads"/>
52 </when>
53 <when value="long">
54 <param argument="--single" type="data" format="fastq,fastq.gz" label="Long reads"/>
55 </when>
56 <when value="bam">
57 <param name="bam" type="data" format="bam" label="Pre-aligned reads"/>
58 </when>
59 </conditional>
60 <param argument="-u" type="boolean" truevalue="-u" falsevalue="" checked="False" label="Include unpolished sequences in final output" />
61 </inputs>
62 <outputs>
63 <data format="fasta" name="output" from_work_dir="output/hapog_results/hapog.fasta"/>
64 <data format="tsv" name="changes" from_work_dir="output/hapog_results/hapog.changes"/>
65 </outputs>
66 <tests>
67 <test>
68 <param name="genome" value="genome.fa" />
69 <conditional name="reads">
70 <param name="type" value="short" />
71 <param name="pe1" value="fastq1.fq" />
72 <param name="pe2" value="fastq2.fq" />
73 </conditional>
74 <output name="output" file="hapog_short.fasta" />
75 <output name="changes" file="hapog_short.changes" />
76 </test>
77 <test>
78 <param name="genome" value="genome.fa" />
79 <conditional name="reads">
80 <param name="type" value="short" />
81 <param name="pe1" value="fastq1.fq.gz" />
82 <param name="pe2" value="fastq2.fq.gz" />
83 </conditional>
84 <output name="output" file="hapog_short.fasta"/>
85 <output name="changes" file="hapog_short.changes" />
86 </test>
87 <test>
88 <param name="genome" value="genome.fa" />
89 <conditional name="reads">
90 <param name="type" value="long" />
91 <param name="single" value="fastq1.fq" />
92 </conditional>
93 <output name="output" file="hapog_long.fasta" />
94 <output name="changes" file="hapog_long.changes" />
95 </test>
96 <test>
97 <param name="genome" value="genome.fa" />
98 <conditional name="reads">
99 <param name="type" value="long" />
100 <param name="single" value="fastq1.fq.gz" />
101 </conditional>
102 <output name="output" file="hapog_long.fasta"/>
103 <output name="changes" file="hapog_long.changes" />
104 </test>
105 <test>
106 <param name="genome" value="genome.fa" />
107 <conditional name="reads">
108 <param name="type" value="bam" />
109 <param name="bam" value="input.bam" />
110 </conditional>
111 <output name="output" file="hapog_bam.fasta"/>
112 <output name="changes" file="hapog_bam.changes" />
113 </test>
114 </tests>
115 <help><![CDATA[
116 Hapo-G uses alignments produced by BWA (or any other aligner that produces SAM files) to polish the consensus of a genome assembly.
117 ]]></help>
118 <citations>
119 <citation type="doi">10.1093/nargab/lqab034</citation>
120 </citations>
121 </tool>