Mercurial > repos > iuc > medaka_variant_pipeline

comparison medaka_variant.xml @ 3:148f32860445 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44"
author iuc
date Tue, 01 Sep 2020 03:06:38 -0400
parents ce2bf68a260d
children 5c959a2dde5f
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2:ce2bf68a260d 3:148f32860445
1 <tool id="medaka_variant_pipeline" name="medaka: Variant pipeline" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> 1 <tool id="medaka_variant_pipeline" name="medaka: Variant pipeline" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
2 <description>via neural networks</description> 2 <description>via neural networks</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
30 $S 30 $S
31 ## required 31 ## required
32 -i alignment.bam 32 -i alignment.bam
33 -f reference.fa 33 -f reference.fa
34 34
35 |& tee '$out_log' 35 2>&1 | tee '$out_log'
36 ]]></command> 36 ]]></command>
37 <inputs> 37 <inputs>
38 <param argument="-i" type="data" format="bam" label="Select input reads" help="Read groups are currently ignored, so the bam should only contain reads from a single sample."/> 38 <param argument="-i" type="data" format="bam" label="Select input reads" help="Read groups are currently ignored, so the bam should only contain reads from a single sample."/>
39 <expand macro="reference"/> 39 <expand macro="reference"/>
40 <param argument="-r" type="text" value="" optional="true" label="Set region string(s)" help="If not provided, will process all contigs."/> 40 <param argument="-r" type="text" value="" optional="true" label="Set region string(s)" help="If not provided, will process all contigs."/>