comparison hisat2.xml @ 19:fbf98f24097b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 9bbf35d7f47e5ab6b78248c9907b71446d4e7b0c

18:764756ab0eb5

        <regex level="fatal" match="hisat2: not found" source="both" />
        <exit_code range="1:" />
    </stdio>
    <version_command>hisat2 --version</version_command>
    <command><![CDATA[

## Prepare HISAT2 index

#if $reference_genome.source == "history":
    ln -s '$reference_genome.history_item' genome.fa &&

19:fbf98f24097b

        <regex level="fatal" match="hisat2: not found" source="both" />
        <exit_code range="1:" />
    </stdio>
    <version_command>hisat2 --version</version_command>
    <command><![CDATA[
## Use pipefail if available to quit with first non-zero exit code
set -o | grep -q pipefail && set -o pipefail;

## Prepare HISAT2 index

#if $reference_genome.source == "history":
    ln -s '$reference_genome.history_item' genome.fa &&