comparison macros.xml @ 14:c9944a2600f1 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 20eabb7209eb447bc66450e955291143694b419a

13:e32b215b7c04

<macros>
    <token name="@TOOL_VERSION@">1.10.1</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <token name="@IDX_VERSION@">q7</token>
    <token name="@PROFILE_VERSION@">20.01</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">salmon</requirement>
            <requirement type="package" version="1.3">seqtk</requirement>
            <requirement type="package" version="1.16.1">samtools</requirement>

        <!--Salmon quant type select: reads-based or alignment-based-->
        <param name="discardOrphansQuasi" type="boolean" truevalue="--discardOrphansQuasi" falsevalue="" checked="False"
        label="Discard orphan quasi"
        help="Discard orphan mappings in quasi-mapping mode. If this flag is passed then only paired mappings will be considered toward quantification estimates.  The default behavior is to consider orphan mappings if no valid paired mappings exist."/>
        <conditional name="validmap">
            <param name="validateMappings" type="boolean" truevalue="--validateMappings" falsevalue="" checked="False"
            label="Validate mappings"
            help="Validate mappings using alignment-based verifcation. If this flag is passed, quasi-mappings will be validated to ensure that they could give rise to a reasonable alignment before they are further used for quantification."/>
            <when value="--validateMappings">
                <param name="minScoreFraction" type="float" value="0.65" min="0.0" max="0.99"
                label="Min Score Fraction"
                help="The fraction of the optimal possible alignment score that a mapping must achieve in order to be considered valid. Should be in (0,1]."/>
                <param name="maxMMPExtension" type="integer" optional="True"

                #end if
                #set $ext = 'fastq'
            #end if
            ln -s '${quant_type.input.single_or_paired.input_1.forward}' ./mate1.$ext &&
            ln -s '${quant_type.input.single_or_paired.input_1.reverse}' ./mate2.$ext &&
        #else if '$quant_type.input.single_or_paired.single_or_paired_opts' == 'paired_interleaved':
            #if $quant_type.input.single_or_paired.input_1.ext == 'fasta':
                #set $ext = 'fasta'
            #else:
                #if $quant_type.input.single_or_paired.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
                    #set compressed = 'GZ'

14:c9944a2600f1

<macros>
    <token name="@TOOL_VERSION@">1.10.1</token>
    <token name="@VERSION_SUFFIX@">2</token>
    <token name="@IDX_VERSION@">q7</token>
    <token name="@PROFILE_VERSION@">20.01</token>
    <xml name="xrefs">
        <xrefs>
            <xref type="bio.tools">salmon</xref>
        </xrefs>
    </xml>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">salmon</requirement>
            <requirement type="package" version="1.3">seqtk</requirement>
            <requirement type="package" version="1.16.1">samtools</requirement>

        <!--Salmon quant type select: reads-based or alignment-based-->
        <param name="discardOrphansQuasi" type="boolean" truevalue="--discardOrphansQuasi" falsevalue="" checked="False"
        label="Discard orphan quasi"
        help="Discard orphan mappings in quasi-mapping mode. If this flag is passed then only paired mappings will be considered toward quantification estimates.  The default behavior is to consider orphan mappings if no valid paired mappings exist."/>
        <conditional name="validmap">
            <param name="validateMappings" type="select" label="Validate mappings" help="Validate mappings using alignment-based verifcation. If this flag is passed, quasi-mappings will be validated to ensure that they could give rise to a reasonable alignment before they are further used for quantification.">
                <option value="--validateMappings">True</option>
                <option value="" selected="true">False</option>
            </param>
            <when value="--validateMappings">
                <param name="minScoreFraction" type="float" value="0.65" min="0.0" max="0.99"
                label="Min Score Fraction"
                help="The fraction of the optimal possible alignment score that a mapping must achieve in order to be considered valid. Should be in (0,1]."/>
                <param name="maxMMPExtension" type="integer" optional="True"

                #end if
                #set $ext = 'fastq'
            #end if
            ln -s '${quant_type.input.single_or_paired.input_1.forward}' ./mate1.$ext &&
            ln -s '${quant_type.input.single_or_paired.input_1.reverse}' ./mate2.$ext &&
        #else if $quant_type.input.single_or_paired.single_or_paired_opts == 'paired_interleaved':
            #if $quant_type.input.single_or_paired.input_1.ext == 'fasta':
                #set $ext = 'fasta'
            #else:
                #if $quant_type.input.single_or_paired.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
                    #set compressed = 'GZ'