Mercurial > repos > iuc > te_finder
changeset 1:2edb80d68a1b draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit 5d19bf766a0ac0121ce45b5c532ea5e43825082b
| author | iuc |
|---|---|
| date | Fri, 23 Sep 2022 11:00:13 +0000 |
| parents | 838fb3a1678f |
| children | |
| files | TEfinder.xml macros.xml |
| diffstat | 2 files changed, 27 insertions(+), 13 deletions(-) [+] |
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--- a/TEfinder.xml Mon Aug 08 19:41:18 2022 +0000 +++ b/TEfinder.xml Fri Sep 23 11:00:13 2022 +0000 @@ -1,14 +1,10 @@ -<tool id="te_finder" name="TEfinder" version="1.0.1" profile="21.05"> +<tool id="te_finder" name="TEfinder" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <description>Transposable element insertions finder</description> - - <requirements> - <requirement type="package" version="1.15.1">samtools</requirement> - <requirement type="package" version="2.30.0">bedtools</requirement> - <requirement type="package" version="2.27.4">picard</requirement> - <requirement type="package" version="3.4">grep</requirement> - <requirement type="package" version="1.07.1">bc</requirement> - </requirements> - + <macros> + <import>macros.xml</import> + </macros> + <expand macro="xrefs"/> + <expand macro="requirements"/> <command> <![CDATA[ '$__tool_directory__/TEfinder' -fa '$required_inputs.FastaFile' @@ -32,9 +28,9 @@ <!-- <param format="fasta" name="input" type="data" label="Source file"/> --> <section name="required_inputs" title="Required Inputs" expanded="True"> <param name="FastaFile" type="data" format="fasta" label="Select reference genome FASTA index (FA/FASTA file)" /> - <param name="alignmentFile" type="data" format="bam" label="Select sample reads aligned to reference genome (BAM/SAM file)" /> - <param name="TransposonsInGenome" type="data" format="gtf" label="Select reference genome TE annotation (GFF/GTF file)" /> - <param name="TransposonsToSearch" type="data" format="text" label="Select TE names" help="Single column text file" /> + <param name="alignmentFile" type="data" format="bam,sam" label="Select sample reads aligned to reference genome (BAM/SAM file)" /> + <param name="TransposonsInGenome" type="data" format="gtf,gff" label="Select reference genome TE annotation (GFF/GTF file)" /> + <param name="TransposonsToSearch" type="data" format="txt" label="Select TE names" help="Single column text file" /> </section> <!-- Advanced Options --> <section name="advanced_options" title="Advanced Options" expanded="False">
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri Sep 23 11:00:13 2022 +0000 @@ -0,0 +1,18 @@ +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="1.15.1">samtools</requirement> + <requirement type="package" version="2.30.0">bedtools</requirement> + <requirement type="package" version="2.27.4">picard</requirement> + <requirement type="package" version="3.4">grep</requirement> + <requirement type="package" version="1.07.1">bc</requirement> + </requirements> + </xml> + <token name="@TOOL_VERSION@">1.0.1</token> + <token name="@VERSION_SUFFIX@">1</token> + <xml name="xrefs"> + <xrefs> + <xref type="bio.tools">tefinder</xref> + </xrefs> + </xml> +</macros>