comparison hisat2.xml @ 4:2d449a1bb5ab draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit f33b04533bca91242b8a0a4077e1d593f5a874e0

3:b1e25f9b5eab

<?xml version="1.0"?>
<tool id="hisat2" name="HISAT2" version="1.0.1">
    <description>A fast and sensitive alignment program</description>
    <macros>
        <import>hisat2_macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="2.0">hisat</requirement>
        <!-- Conda dependency -->
        <requirement type="package" version="2.0.0beta">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"/>

            <param name="paired_selector" value="paired" />
            <param name="reference_genome_source" value="history" />
            <param ftype="fasta" name="history_item" value="phiX.fa" />
            <param ftype="fastqsanger" name="reads_f" value="hisat_input_1_forward.fastq" />
            <param ftype="fastqsanger" name="reads_r" value="hisat_input_1_reverse.fastq" />
            <output file="hisat_output_1.bam" ftype="bam" name="output_alignments" />
        </test>
        <test>
            <param name="input_format_selector" value="fastq" />
            <param name="paired_selector" value="paired" />
            <param name="reference_genome_source" value="history" />

            <param name="input_options_selector" value="advanced" />
            <param name="trim_three" value="15" />
            <param name="trim_five" value="15" />
            <param ftype="fastqsanger" name="reads_f" value="hisat_input_2_forward.fastq" />
            <param ftype="fastqsanger" name="reads_r" value="hisat_input_2_reverse.fastq" />
            <output file="hisat_output_2.bam" ftype="bam" name="output_alignments" />
        </test>
        <test>
            <param name="input_format_selector" value="fastq" />
            <param name="paired_selector" value="paired" />
            <param name="reference_genome_source" value="history" />

            <param name="reads_f" ftype="fastqsanger" value="hisat_input_2_forward.fastq" />
            <param name="reads_r" ftype="fastqsanger" value="hisat_input_2_reverse.fastq" />
            <param name="paired_end_options_selector" value="advanced" />
            <param name="no_mixed" value="True" />
            <param name="no_discordant" value="True" />
            <output name="output_alignments" ftype="bam" file="hisat_output_3.bam" />
        </test>
    </tests>
    <help>
        <![CDATA[
Introduction

4:2d449a1bb5ab

<?xml version="1.0"?>
<tool id="hisat2" name="HISAT" version="2.0.3">
    <description>A fast and sensitive alignment program</description>
    <macros>
        <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"/>

            <param name="paired_selector" value="paired" />
            <param name="reference_genome_source" value="history" />
            <param ftype="fasta" name="history_item" value="phiX.fa" />
            <param ftype="fastqsanger" name="reads_f" value="hisat_input_1_forward.fastq" />
            <param ftype="fastqsanger" name="reads_r" value="hisat_input_1_reverse.fastq" />
            <output file="hisat_output_1.bam" ftype="bam" name="output_alignments" lines_diff="2" />
        </test>
        <test>
            <param name="input_format_selector" value="fastq" />
            <param name="paired_selector" value="paired" />
            <param name="reference_genome_source" value="history" />

            <param name="input_options_selector" value="advanced" />
            <param name="trim_three" value="15" />
            <param name="trim_five" value="15" />
            <param ftype="fastqsanger" name="reads_f" value="hisat_input_2_forward.fastq" />
            <param ftype="fastqsanger" name="reads_r" value="hisat_input_2_reverse.fastq" />
            <output file="hisat_output_2.bam" ftype="bam" name="output_alignments" lines_diff="2" />
        </test>
        <test>
            <param name="input_format_selector" value="fastq" />
            <param name="paired_selector" value="paired" />
            <param name="reference_genome_source" value="history" />

            <param name="reads_f" ftype="fastqsanger" value="hisat_input_2_forward.fastq" />
            <param name="reads_r" ftype="fastqsanger" value="hisat_input_2_reverse.fastq" />
            <param name="paired_end_options_selector" value="advanced" />
            <param name="no_mixed" value="True" />
            <param name="no_discordant" value="True" />
            <output name="output_alignments" ftype="bam" file="hisat_output_3.bam" lines_diff="2" />
        </test>
    </tests>
    <help>
        <![CDATA[
Introduction