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comparison minimap2.xml @ 3:1650a97189be draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 1672eb3642d19c8502322115b86846297cd5a6b0
author iuc
date Fri, 17 Nov 2017 08:11:42 -0500
parents 4070f129540a
children 6f50f36e4481
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2:4070f129540a 3:1650a97189be
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="minimap2" name="Map with minimap2" version="2.4.1" profile="17.01"> 2 <tool id="minimap2" name="Map with minimap2" version="2.5" profile="17.01">
3 <description>A fast pairwise aligner for genomic and spliced nucleotide sequences</description> 3 <description>A fast pairwise aligner for genomic and spliced nucleotide sequences</description>
4 <requirements> 4 <requirements>
5 <requirement type="package" version="2.4">minimap2</requirement> 5 <requirement type="package" version="2.5">minimap2</requirement>
6 <requirement type="package" version="1.6">samtools</requirement> 6 <requirement type="package" version="1.6">samtools</requirement>
7 </requirements> 7 </requirements>
8 <version_command>minimap2 --version</version_command> 8 <version_command>minimap2 --version</version_command>
9 <command> 9 <command>
10 <![CDATA[ 10 <![CDATA[
87 $io_options.Q 87 $io_options.Q
88 $io_options.L 88 $io_options.L
89 #if $io_options.cs: 89 #if $io_options.cs:
90 --cs $io_options.cs 90 --cs $io_options.cs
91 #end if 91 #end if
92 $io_options.Y
92 #if $io_options.K: 93 #if $io_options.K:
93 -K $io_options.K 94 -K $io_options.K
94 #end if 95 #end if
95 -t \${GALAXY_SLOTS:-4} 96 -t \${GALAXY_SLOTS:-4}
96 reference.fa 97 reference.fa
209 <param argument="--cs" type="select" optional="true" label="Output cs tag?" help="The cs tag is a more compact standalone representation of the MD tag, see help below."> 210 <param argument="--cs" type="select" optional="true" label="Output cs tag?" help="The cs tag is a more compact standalone representation of the MD tag, see help below.">
210 <option value="none">no</option> 211 <option value="none">no</option>
211 <option value="short">short</option> 212 <option value="short">short</option>
212 <option value="long">long</option> 213 <option value="long">long</option>
213 </param> 214 </param>
215 <param argument="-Y" type="boolean" truevalue="-Y" falsevalue="" label="use soft clipping for supplementary alignments ?"/>
214 </section> 216 </section>
215 </inputs> 217 </inputs>
216 <outputs> 218 <outputs>
217 <data format="bam" name="alignment_output" label="${tool.name} on ${on_string} (mapped reads in ${io_options.output_format} format)"> 219 <data format="bam" name="alignment_output" label="${tool.name} on ${on_string} (mapped reads in ${io_options.output_format} format)">
218 <actions> 220 <actions>