comparison hisat2.xml @ 3:b1e25f9b5eab draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 9a9d44116b21d9a155b5cc274475e78c14915059

2:c37b4554f794

    <macros>
        <import>hisat2_macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="2.0">hisat</requirement>
        <requirement type="package" version="1.2">samtools</requirement>
    </requirements>
    <stdio>
        <regex match="hisat2-align exited with value 1" source="both" level="fatal"/>
        <exit_code range="1:" />
    </stdio>
    <version_command>hisat2 --version</version_command>
    <command>
        <![CDATA[

        #else:
            #set index_path = $reference_genome.index.fields.path
        #end if
        hisat2 -p \${GALAXY_SLOTS:-1} -x "${index_path}"
        #if str($input_format.paired.paired_selector) == 'paired':
            -1 "${reads_f}" -2 "${reads_r}"
            @paired_end_options@
        #else if str($input_format.paired.paired_selector) == 'paired_collection':
            -1 "${input_format.paired.reads.forward}" -2 "${input_format.paired.reads.reverse}"
            @paired_end_options@
        #else:

        #end if
        #if str($paired_options.paired_options_selector) == "advanced":
            --minins ${paired_options.minins} --maxins ${paired_options.maxins} ${paired_options.no_mixed} ${paired_options.no_discordant}
            ${paired_options.dovetail} ${paired_options.contain} ${paired_options.overlap}
        #end if
        | samtools view -bS - | samtools sort - -o hsbam > "${output_alignments}"
        ]]>
    </command>
    <inputs>
        <conditional name="input_format">
            <param label="Input data format" name="input_format_selector" type="select">

                <param argument="--no-overlap" falsevalue="" help="If one mate alignment overlaps the other at all, consider that to be non-concordant." label="Mates cannot overlap" name="overlap" truevalue="--no-overlap" type="boolean" />
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="bam" name="output_alignments" />
    </outputs>
    <tests>
        <test>
            <param name="input_format_selector" value="fastq" />
            <param name="paired_selector" value="paired" />

3:b1e25f9b5eab

    <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"/>
        <exit_code range="1:" />
    </stdio>
    <version_command>hisat2 --version</version_command>
    <command>
        <![CDATA[

        #else:
            #set index_path = $reference_genome.index.fields.path
        #end if
        hisat2 -p \${GALAXY_SLOTS:-1} -x "${index_path}"
        #if str($input_format.paired.paired_selector) == 'paired':
            -1 "${input_format.paired.reads_f}" -2 "${input_format.paired.reads_r}"
            @paired_end_options@
        #else if str($input_format.paired.paired_selector) == 'paired_collection':
            -1 "${input_format.paired.reads.forward}" -2 "${input_format.paired.reads.reverse}"
            @paired_end_options@
        #else:

        #end if
        #if str($paired_options.paired_options_selector) == "advanced":
            --minins ${paired_options.minins} --maxins ${paired_options.maxins} ${paired_options.no_mixed} ${paired_options.no_discordant}
            ${paired_options.dovetail} ${paired_options.contain} ${paired_options.overlap}
        #end if
        | samtools sort - -@ \${GALAXY_SLOTS:-2} -l 6 -o hsbam > "${output_alignments}"
        ]]>
    </command>
    <inputs>
        <conditional name="input_format">
            <param label="Input data format" name="input_format_selector" type="select">

                <param argument="--no-overlap" falsevalue="" help="If one mate alignment overlaps the other at all, consider that to be non-concordant." label="Mates cannot overlap" name="overlap" truevalue="--no-overlap" type="boolean" />
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="bam" name="output_alignments">
            <actions>
              <conditional name="reference_genome.reference_genome_source">
                <when value="indexed">
                  <action type="metadata" name="dbkey">
                    <option type="from_data_table" name="hisat2_indexes" column="1" offset="0">
                      <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
                      <filter type="param_value" ref="reference_genome.index" column="0"/>
                    </option>
                  </action>
                </when>
                <when value="history">
                  <action type="metadata" name="dbkey">
                    <option type="from_param" name="reference_genome.history_item" param_attribute="dbkey" />
                  </action>
                </when>
              </conditional>
            </actions>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="input_format_selector" value="fastq" />
            <param name="paired_selector" value="paired" />