comparison hisat2.xml @ 5:1eb21dccc2fa draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d12a2e9dd273b4c23db48bbb747f32700887710e

4:2d449a1bb5ab

        <import>hisat2_macros.xml</import>
    </macros>
    <requirements>
        <!-- Conda dependency -->
        <requirement type="package" version="2.0.3">hisat2</requirement>
        <requirement type="package" version="1.2">samtools</requirement>
    </requirements>
    <stdio>
        <regex match="hisat2-align exited with value 1" source="both" level="fatal"/>
        <regex match="hisat2: not found" source="both" level="fatal"/>

    <version_command>hisat2 --version</version_command>
    <command>
        <![CDATA[
        #if str($spliced_options.spliced_options_selector) == "advanced" and str($spliced_options.known_splice_gtf) != 'None':
            ln -s "${spliced_options.known_splice_gtf}" splice_sites.gtf &&
            extract_splice_sites.py splice_sites.gtf > splice_sites.txt &&
        #end if
        #if $reference_genome.reference_genome_source == "history":
            ln -s "$reference_genome.history_item" genome.fa &&
            hisat2-build genome.fa genome && 
            #set index_path = 'genome'

5:1eb21dccc2fa

        <import>hisat2_macros.xml</import>
    </macros>
    <requirements>
        <!-- Conda dependency -->
        <requirement type="package" version="2.0.3">hisat2</requirement>
        <requirement type="package" version="2.0.3">hisat</requirement>
        <requirement type="package" version="1.2">samtools</requirement>
    </requirements>
    <stdio>
        <regex match="hisat2-align exited with value 1" source="both" level="fatal"/>
        <regex match="hisat2: not found" source="both" level="fatal"/>

    <version_command>hisat2 --version</version_command>
    <command>
        <![CDATA[
        #if str($spliced_options.spliced_options_selector) == "advanced" and str($spliced_options.known_splice_gtf) != 'None':
            ln -s "${spliced_options.known_splice_gtf}" splice_sites.gtf &&
            hisat2_extract_splice_sites.py splice_sites.gtf > splice_sites.txt &&
        #end if
        #if $reference_genome.reference_genome_source == "history":
            ln -s "$reference_genome.history_item" genome.fa &&
            hisat2-build genome.fa genome && 
            #set index_path = 'genome'