comparison hisat2.xml @ 8:4d0a3173cde0 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 379063161020578e1bd306769116c1b691216b35

7:5ba8e317529a

<?xml version="1.0"?>
<tool id="hisat2" name="HISAT2" version="2.0.3.2">
    <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="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"/>
        <exit_code range="1:" />
    </stdio>
    <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":

                #set right = str($output_aligned_reads_l).replace(".dat", ".2.dat")
                && mv '${left}' '${output_aligned_reads_l}'
                && mv '${right}' '${output_aligned_reads_r}'
            #end if
        #end if
        ]]>
    </command>
    <inputs>
        <conditional name="input_format">
            <param label="Input data format" name="input_format_selector" type="select">
                <option selected="true" value="fastq">FASTQ</option>
                <option value="fasta">FASTA</option>

            </param>
            <when value="defaults" />
            <when value="advanced">
                <param argument="-s" min="0" label="Skip the first N reads or pairs in the input" name="skip" type="integer" value="0" />
                <param argument="-u" min="0" help="Align the first N reads or read pairs from the input (after the first N reads or pairs have been skipped), then stop." label="Stop after aligning N reads" name="stop_after" type="integer" value="0" />
                <param argument="-5" min="0" help="Trim N bases from 5' (left) end of each read before alignment" label="Trim 5' end" name="trim_five" type="integer" value="0" />
                <param argument="-3" min="0" help="Trim N bases from 3' (right) end of each read before alignment" label="Trim 3' end" name="trim_three" type="integer" value="0" />
            </when>
        </conditional>
        <conditional name="scoring_options">
            <param label="Scoring options" name="scoring_options_selector" type="select">
                <option value="defaults">Use default values</option>

8:4d0a3173cde0

<?xml version="1.0"?>
<tool id="hisat2" name="HISAT2" version="2.0.3.3">
    <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"/>
        <exit_code range="1:" />
    </stdio>
    <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":

                #set right = str($output_aligned_reads_l).replace(".dat", ".2.dat")
                && mv '${left}' '${output_aligned_reads_l}'
                && mv '${right}' '${output_aligned_reads_r}'
            #end if
        #end if
    ]]></command>
    <inputs>
        <conditional name="input_format">
            <param label="Input data format" name="input_format_selector" type="select">
                <option selected="true" value="fastq">FASTQ</option>
                <option value="fasta">FASTA</option>

            </param>
            <when value="defaults" />
            <when value="advanced">
                <param argument="-s" min="0" label="Skip the first N reads or pairs in the input" name="skip" type="integer" value="0" />
                <param argument="-u" min="0" help="Align the first N reads or read pairs from the input (after the first N reads or pairs have been skipped), then stop." label="Stop after aligning N reads" name="stop_after" type="integer" value="0" />
                <param name="trim_five" argument="-5" min="0" help="Trim N bases from 5' (left) end of each read before alignment" label="Trim 5' end" type="integer" value="0" />
                <param name="trim_three" argument="-3" min="0" help="Trim N bases from 3' (right) end of each read before alignment" label="Trim 3' end" type="integer" value="0" />
            </when>
        </conditional>
        <conditional name="scoring_options">
            <param label="Scoring options" name="scoring_options_selector" type="select">
                <option value="defaults">Use default values</option>