| Previous changeset 1:1d4f065fa0ef (2021-05-17) Next changeset 3:3242dbeea69c (2024-05-18) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 695cbdabe249ed4a72c5d2f345dda439f67a2637 |
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modified:
irissv.xml |
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| diff -r 1d4f065fa0ef -r b4b6b660293a irissv.xml --- a/irissv.xml Mon May 17 17:29:39 2021 +0000 +++ b/irissv.xml Wed Jul 06 07:07:21 2022 +0000 |
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| @@ -1,5 +1,4 @@ -<?xml version="1.0"?> -<tool id="irissv" name="Iris" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> +<tool id="irissv" name="Iris" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@"> <description>Refine insertion sequences</description> <macros> <import>macros.xml</import> @@ -8,13 +7,16 @@ <expand macro="requirements"/> <expand macro="version_command"/> - <command detect_errors="exit_code"><![CDATA[ + <command detect_errors="aggressive"><![CDATA[ @REF_FASTA@ + ln -s '$in_bam' reads.bam && + ln -s '$in_bam.metadata.bam_index' 'reads.bam.bai' && + iris genome_in=reference vcf_in='${in_vcf}' - reads_in='${in_bam}' + reads_in='reads.bam' vcf_out='${out_vcf}' threads=\${GALAXY_SLOTS:-4} padding_before='${padding_before}' |