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comparison TEfinder.xml @ 1:9b4cda05001c draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit 5d19bf766a0ac0121ce45b5c532ea5e43825082b
author iuc
date Fri, 23 Sep 2022 10:59:34 +0000
parents 2b3fade73a41
children
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0:2b3fade73a41 1:9b4cda05001c
1 <tool id="te_finder" name="TEfinder" version="1.0.1" profile="21.05"> 1 <tool id="te_finder" name="TEfinder" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
2 <description>Transposable element insertions finder</description> 2 <description>Transposable element insertions finder</description>
3 3 <macros>
4 <requirements> 4 <import>macros.xml</import>
5 <requirement type="package" version="1.15.1">samtools</requirement> 5 </macros>
6 <requirement type="package" version="2.30.0">bedtools</requirement> 6 <expand macro="xrefs"/>
7 <requirement type="package" version="2.27.4">picard</requirement> 7 <expand macro="requirements"/>
8 <requirement type="package" version="3.4">grep</requirement>
9 <requirement type="package" version="1.07.1">bc</requirement>
10 </requirements>
11
12 <command> 8 <command>
13 <![CDATA[ 9 <![CDATA[
14 '$__tool_directory__/TEfinder' -fa '$required_inputs.FastaFile' 10 '$__tool_directory__/TEfinder' -fa '$required_inputs.FastaFile'
15 -alignment '$required_inputs.alignmentFile' 11 -alignment '$required_inputs.alignmentFile'
16 -gtf '$required_inputs.TransposonsInGenome' 12 -gtf '$required_inputs.TransposonsInGenome'
30 26
31 <inputs> 27 <inputs>
32 <!-- <param format="fasta" name="input" type="data" label="Source file"/> --> 28 <!-- <param format="fasta" name="input" type="data" label="Source file"/> -->
33 <section name="required_inputs" title="Required Inputs" expanded="True"> 29 <section name="required_inputs" title="Required Inputs" expanded="True">
34 <param name="FastaFile" type="data" format="fasta" label="Select reference genome FASTA index (FA/FASTA file)" /> 30 <param name="FastaFile" type="data" format="fasta" label="Select reference genome FASTA index (FA/FASTA file)" />
35 <param name="alignmentFile" type="data" format="bam" label="Select sample reads aligned to reference genome (BAM/SAM file)" /> 31 <param name="alignmentFile" type="data" format="bam,sam" label="Select sample reads aligned to reference genome (BAM/SAM file)" />
36 <param name="TransposonsInGenome" type="data" format="gtf" label="Select reference genome TE annotation (GFF/GTF file)" /> 32 <param name="TransposonsInGenome" type="data" format="gtf,gff" label="Select reference genome TE annotation (GFF/GTF file)" />
37 <param name="TransposonsToSearch" type="data" format="text" label="Select TE names" help="Single column text file" /> 33 <param name="TransposonsToSearch" type="data" format="txt" label="Select TE names" help="Single column text file" />
38 </section> 34 </section>
39 <!-- Advanced Options --> 35 <!-- Advanced Options -->
40 <section name="advanced_options" title="Advanced Options" expanded="False"> 36 <section name="advanced_options" title="Advanced Options" expanded="False">
41 <param name="FragmentInsertSize" argument="-fis" type="integer" min="0" value="400" label="Short-read sequencing fragment insert size" /> 37 <param name="FragmentInsertSize" argument="-fis" type="integer" min="0" value="400" label="Short-read sequencing fragment insert size" />
42 <param name="MaxDistanceForMerge" argument="-md" type="integer" min="0" value="150" label="Maximum distance between reads for bedtools merge" /> 38 <param name="MaxDistanceForMerge" argument="-md" type="integer" min="0" value="150" label="Maximum distance between reads for bedtools merge" />