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comparison samtools_ampliconclip.xml @ 2:b5f87b4cfda6 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_ampliconclip commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
author iuc
date Sun, 08 Sep 2024 03:21:59 +0000
parents d90472d5f10a
children
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1:d90472d5f10a 2:b5f87b4cfda6
1 <tool id="samtools_ampliconclip" name="Samtools ampliconclip" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> 1 <tool id="samtools_ampliconclip" name="Samtools ampliconclip" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>clip primer bases from bam files</description> 2 <description>clip primer bases from bam files</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"/>
27 ]]></command> 27 ]]></command>
28 <inputs> 28 <inputs>
29 <param name="input_bed" type="data" format="bed" label="Genetic intervals (in BED format)" /> 29 <param name="input_bed" type="data" format="bed" label="Genetic intervals (in BED format)" />
30 <param name="input_bam" type="data" format="bam" label="BAM file" /> 30 <param name="input_bam" type="data" format="bam" label="BAM file" />
31 <param name="hard_clip_mode" argument="--hard-clip" type="boolean" checked="false" truevalue="--hard-clip" falsevalue="--soft-clip" label="hard clip" help="hard clip (remove bases), unchekced = default soft-clipping" /> 31 <param name="hard_clip_mode" argument="--hard-clip" type="boolean" checked="false" truevalue="--hard-clip" falsevalue="--soft-clip" label="hard clip" help="hard clip (remove bases), unchekced = default soft-clipping" />
32 <param name="strand" argument="--strand" type="boolean" checked="false" truevalue="--strand" falsevalue="" label="only clip reads that match bed file strand annotation" /> 32 <param argument="--strand" type="boolean" checked="false" truevalue="--strand" falsevalue="" label="only clip reads that match bed file strand annotation" />
33 <param name="both_ends" argument="--both-ends" type="boolean" checked="false" truevalue="--both-ends" falsevalue="" label="clip both ends of reads (false = 5' only)" /> 33 <param argument="--both-ends" type="boolean" checked="false" truevalue="--both-ends" falsevalue="" label="clip both ends of reads (false = 5' only)" />
34 <param name="no_excluded" argument="--no-excluded" type="boolean" checked="false" truevalue="--no-excluded" falsevalue="" label="don't write excluded reads to output (default = write all)" /> 34 <param argument="--no-excluded" type="boolean" checked="false" truevalue="--no-excluded" falsevalue="" label="don't write excluded reads to output (default = write all)" />
35 <param name="min_length" argument="--fail-len" type="integer" min="0" optional="true" label="Min Read length" help="mark reads QCFAIL at this length or shorter after clipping" /> 35 <param name="min_length" argument="--fail-len" type="integer" min="0" optional="true" label="Min Read length" help="mark reads QCFAIL at this length or shorter after clipping" />
36 <param name="tolerance" argument="--tolerance" type="integer" value="5" min="0" label="Tolerance" help="match region within this number of bases, default 5." /> 36 <param argument="--tolerance" type="integer" value="5" min="0" label="Tolerance" help="match region within this number of bases, default 5." />
37 37
38 </inputs> 38 </inputs>
39 <outputs> 39 <outputs>
40 <data name="output_bam" format="bam" /> 40 <data name="output_bam" format="bam" />
41 </outputs> 41 </outputs>