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comparison hapog.xml @ 3:5287036a797a draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit 8e54473840ee1238da9cb8a77cf136f00b40e4e7
author iuc
date Fri, 05 Apr 2024 09:39:36 +0000
parents ee0d6e789958
children
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2:ee0d6e789958 3:5287036a797a
1 <tool id="hapog" name="Hapo-G" profile="21.05" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> 1 <tool id="hapog" name="Hapo-G" profile="21.05" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>genome polishing</description> 2 <description>genome polishing</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">1.3.7</token> 4 <token name="@TOOL_VERSION@">1.3.8</token>
5 <token name="@VERSION_SUFFIX@">0</token> 5 <token name="@VERSION_SUFFIX@">0</token>
6 </macros> 6 </macros>
7 <xrefs> 7 <xrefs>
8 <xref type="bio.tools">hapog</xref> 8 <xref type="bio.tools">hapog</xref>
9 </xrefs> 9 </xrefs>
63 </when> 63 </when>
64 <when value="bam"> 64 <when value="bam">
65 <param name="bam" type="data" format="bam" label="Pre-aligned reads"/> 65 <param name="bam" type="data" format="bam" label="Pre-aligned reads"/>
66 </when> 66 </when>
67 </conditional> 67 </conditional>
68 <param argument="-u" type="boolean" truevalue="-u" falsevalue="" checked="False" label="Include unpolished sequences in final output" /> 68 <param argument="-u" type="boolean" truevalue="-u" falsevalue="" checked="False" label="Include unpolished sequences in final output"/>
69 </inputs> 69 </inputs>
70 <outputs> 70 <outputs>
71 <data format="fasta" name="output" label="${tool.name}: polished assembly from ${on_string}" from_work_dir="output/hapog_results/hapog.fasta"/> 71 <data format="fasta" name="output" label="${tool.name}: polished assembly from ${on_string}" from_work_dir="output/hapog_results/hapog.fasta"/>
72 <data format="tsv" name="changes" label="${tool.name}: report of changes" from_work_dir="output/hapog_results/hapog.changes"/> 72 <data format="tsv" name="changes" label="${tool.name}: report of changes" from_work_dir="output/hapog_results/hapog.changes"/>
73 </outputs> 73 </outputs>
74 <tests> 74 <tests>
75 <test> 75 <test>
76 <param name="genome" value="genome.fa" /> 76 <param name="genome" value="genome.fa"/>
77 <conditional name="reads"> 77 <conditional name="reads">
78 <param name="type" value="short" /> 78 <param name="type" value="short"/>
79 <param name="pe1" value="fastq1.fq" /> 79 <param name="pe1" value="fastq1.fq"/>
80 <param name="pe2" value="fastq2.fq" /> 80 <param name="pe2" value="fastq2.fq"/>
81 </conditional> 81 </conditional>
82 <output name="output" file="hapog_short.fasta" /> 82 <output name="output" file="hapog_short.fasta"/>
83 <output name="changes" file="hapog_short.changes" /> 83 <output name="changes" file="hapog_short.changes"/>
84 </test> 84 </test>
85 <test> 85 <test>
86 <param name="genome" value="genome.fa" /> 86 <param name="genome" value="genome.fa"/>
87 <conditional name="reads"> 87 <conditional name="reads">
88 <param name="type" value="short" /> 88 <param name="type" value="short"/>
89 <param name="pe1" value="fastq1.fq.gz" /> 89 <param name="pe1" value="fastq1.fq.gz"/>
90 <param name="pe2" value="fastq2.fq.gz" /> 90 <param name="pe2" value="fastq2.fq.gz"/>
91 </conditional> 91 </conditional>
92 <output name="output" file="hapog_short.fasta"/> 92 <output name="output" file="hapog_short.fasta"/>
93 <output name="changes" file="hapog_short.changes" /> 93 <output name="changes" file="hapog_short.changes"/>
94 </test> 94 </test>
95 <test> 95 <test>
96 <param name="genome" value="genome.fa" /> 96 <param name="genome" value="genome.fa"/>
97 <conditional name="reads"> 97 <conditional name="reads">
98 <param name="type" value="long" /> 98 <param name="type" value="long"/>
99 <param name="single" value="fastq1.fq" /> 99 <param name="single" value="fastq1.fq"/>
100 </conditional> 100 </conditional>
101 <output name="output" file="hapog_long.fasta" /> 101 <output name="output" file="hapog_long.fasta"/>
102 <output name="changes" file="hapog_long.changes" /> 102 <output name="changes" file="hapog_long.changes"/>
103 </test> 103 </test>
104 <test> 104 <test>
105 <param name="genome" value="genome.fa" /> 105 <param name="genome" value="genome.fa"/>
106 <conditional name="reads"> 106 <conditional name="reads">
107 <param name="type" value="long" /> 107 <param name="type" value="long"/>
108 <param name="single" value="fastq1.fq.gz" /> 108 <param name="single" value="fastq1.fq.gz"/>
109 </conditional> 109 </conditional>
110 <output name="output" file="hapog_long.fasta"/> 110 <output name="output" file="hapog_long.fasta"/>
111 <output name="changes" file="hapog_long.changes" /> 111 <output name="changes" file="hapog_long.changes"/>
112 </test> 112 </test>
113 <test> 113 <test>
114 <param name="genome" value="genome.fa" /> 114 <param name="genome" value="genome.fa"/>
115 <conditional name="reads"> 115 <conditional name="reads">
116 <param name="type" value="bam" /> 116 <param name="type" value="bam"/>
117 <param name="bam" value="input.bam" /> 117 <param name="bam" value="input.bam"/>
118 </conditional> 118 </conditional>
119 <output name="output" file="hapog_bam.fasta"/> 119 <output name="output" file="hapog_bam.fasta"/>
120 <output name="changes" file="hapog_bam.changes" /> 120 <output name="changes" file="hapog_bam.changes"/>
121 </test> 121 </test>
122 </tests> 122 </tests>
123 <help><![CDATA[ 123 <help><![CDATA[
124 Hapo-G uses alignments produced by BWA (or any other aligner that produces SAM files) to polish the consensus of a genome assembly. 124 Hapo-G uses alignments produced by BWA (or any other aligner that produces SAM files) to polish the consensus of a genome assembly.
125 ]]></help> 125 ]]></help>