comparison macros.xml @ 6:fd17362def4f draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6

5:a490494875c7

<?xml version="1.0"?>
<macros>
    <token name="@TOOL_VERSION@">2.1.0</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <token name="@PROFILE@">21.01</token>
    <xml name="biotools">
        <xrefs>
            <xref type="bio.tools">semibin</xref>
        </xrefs>

            <option value="bam">BAM</option>
            <option value="txt">Strobealign-aemb file(s)</option>
        </param>
    </xml>
    <xml name="input-fasta-single">
        <param argument="--input-fasta" type="data" format="fasta,fasta.gz" label="Contig sequences"/>
    </xml>
    <xml name="input-fasta-multi">
        <conditional name="multi_fasta">
            <param name="select" type="select" label="Contig files of the samples">
                <option value="concatenated" selected="true">1 concatenated file (created using the dedicated tool) with all sample contigs </option>
                <option value="multi">1 contig file per sample</option>
            </param>
            <when value="concatenated">
                <param argument="--input-fasta" type="data" format="fasta,fasta.gz" label="Combined contig sequences"/>
                <expand macro="separator"/>
            </when>
            <when value="multi">
                <param argument="--input-fasta" type="data" multiple="true" format="fasta,fasta.gz" label="Contig sequences"/>
                <expand macro="concat_min_len"/>
            </when>
        </conditional>
    </xml>
    <xml name="concat_min_len">
        <param name="min_len" type="integer" min="0" value="0" label="Minimal length for contigs to be kept"/>
    </xml>
    <token name="@SINGLE_FASTA_FILES@"><![CDATA[
#if $input_fasta.ext.endswith(".gz")
gunzip -c '$input_fasta' > 'contigs.fasta' &&
#else
ln -s '$input_fasta' 'contigs.fasta' &&
#end if
    ]]></token>
    <token name="@FASTA_FILES@"><![CDATA[
#if $mode.select == 'single' or $mode.select == 'co'
    #if $mode.input_fasta.ext.endswith(".gz")
gunzip -c '$mode.input_fasta' > 'contigs.fasta' &&
    #else
ln -s '$mode.input_fasta' 'contigs.fasta' &&
    #end if
#else
    #if $mode.multi_fasta.select == 'concatenated'
        #if $mode.multi_fasta.input_fasta.ext.endswith(".gz")
gunzip -c '$mode.multi_fasta.input_fasta' > 'contigs.fasta' &&
        #else
ln -s '$mode.multi_fasta.input_fasta' 'contigs.fasta' &&
        #end if
#set $separator = $mode.multi_fasta.separator
    #else
        #for $e in $mode.multi_fasta.input_fasta
            #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($e.element_identifier))
            #if $e.ext.endswith(".gz")
gunzip -c '$e' > '${identifier}.fasta' &&
            #else
ln -s '$e' '${identifier}.fasta' &&
            #end if
        #end for
#set $separator = ':'
SemiBin2 concatenate_fasta
    --input-fasta *.fasta
    --output 'output'
    --separator '$separator'
    --compression none
    -m $mode.multi_fasta.min_len
&&

    <xml name="input-txt">
        <param argument="--abundance" type="data" format="txt" label="Read mapping to the contigs" multiple="true" help="Strobealign abundance files"/>
    </xml>
    <token name="@BAM_FILES@"><![CDATA[
#if $mode.select == 'single'
#set $identifier = re.sub('[^\s\w\-\\.]', '_', str($mode.input_bam.element_identifier))
ln -s '$mode.input_bam' '${identifier}.bam' &&
#else
    #for $e in $mode.input_bam
        #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($e.element_identifier))
ln -s '$e' '${identifier}.bam' &&
    #end for
#end if
    ]]></token>
    <token name="@STROBEALIGN_FILES@"><![CDATA[
#for $e in $mode.align_select.abundance
    #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($e.element_identifier))
    ln -s '$e' '${identifier}.txt' &&
#end for
    ]]></token>
    <xml name="ref_select_cannot">
        <param name="select" type="select" label="Reference database">

6:fd17362def4f

<?xml version="1.0"?>
<macros>
    <token name="@TOOL_VERSION@">2.1.0</token>
    <token name="@VERSION_SUFFIX@">1</token>
    <token name="@PROFILE@">21.01</token>
    <xml name="biotools">
        <xrefs>
            <xref type="bio.tools">semibin</xref>
        </xrefs>

            <option value="bam">BAM</option>
            <option value="txt">Strobealign-aemb file(s)</option>
        </param>
    </xml>
    <xml name="input-fasta-single">
        <param argument="--input-fasta" type="data" format="fasta,fasta.gz,fasta.bz2" label="Contig sequences"/>
    </xml>
    <xml name="input-fasta-multi">
        <conditional name="multi_fasta">
            <param name="select" type="select" label="Contig files of the samples">
                <option value="concatenated" selected="true">1 concatenated file (created using the dedicated tool) with all sample contigs </option>
                <option value="multi">1 contig file per sample</option>
            </param>
            <when value="concatenated">
                <param argument="--input-fasta" type="data" format="fasta,fasta.gz,fasta.bz2" label="Combined contig sequences"/>
                <expand macro="separator"/>
            </when>
            <when value="multi">
                <param argument="--input-fasta" type="data" multiple="true" format="fasta,fasta.gz,fasta.bz2" label="Contig sequences"/>
                <expand macro="concat_min_len"/>
            </when>
        </conditional>
    </xml>
    <xml name="concat_min_len">
        <param name="min_len" type="integer" min="0" value="0" label="Minimal length for contigs to be kept"/>
    </xml>
    <token name="@SINGLE_FASTA_FILES@"><![CDATA[
ln -s '$input_fasta' 'contigs.$input_fasta.ext' &&
    ]]></token>
    <token name="@FASTA_FILES@"><![CDATA[
#if $mode.select == 'single' or $mode.select == 'co'
ln -s '$input_fasta' 'contigs.$input_fasta.ext' &&
#else
    #if $mode.multi_fasta.select == 'concatenated'
ln -s '$input_fasta' 'contigs.$input_fasta.ext' &&
#set $separator = $mode.multi_fasta.separator
    #else
        #for $e in $mode.multi_fasta.input_fasta
            #set $identifier = re.sub('[^\s\w\-]', '_', str($e.element_identifier))
ln -s '$e' '${identifier}.$e.ext' &&
        #end for
#set $separator = ':'
SemiBin2 concatenate_fasta
    --input-fasta
    #for $e in $mode.multi_fasta.input_fasta
        #set $identifier = re.sub('[^\s\w\-]', '_', str($e.element_identifier))
        '${identifier}.$e.ext'
    #end for
    --output 'output'
    --separator '$separator'
    --compression none
    -m $mode.multi_fasta.min_len
&&

    <xml name="input-txt">
        <param argument="--abundance" type="data" format="txt" label="Read mapping to the contigs" multiple="true" help="Strobealign abundance files"/>
    </xml>
    <token name="@BAM_FILES@"><![CDATA[
#if $mode.select == 'single'
#set $identifier = re.sub('[^\s\w\-]', '_', str($mode.input_bam.element_identifier))
ln -s '$mode.input_bam' '${identifier}.bam' &&
#else
    #for $e in $mode.input_bam
        #set $identifier = re.sub('[^\s\w\-]', '_', str($e.element_identifier))
ln -s '$e' '${identifier}.bam' &&
    #end for
#end if
    ]]></token>
    <token name="@STROBEALIGN_FILES@"><![CDATA[
#for $e in $mode.align_select.abundance
    #set $identifier = re.sub('[^\s\w\-]', '_', str($e.element_identifier))
    ln -s '$e' '${identifier}.txt' &&
#end for
    ]]></token>
    <xml name="ref_select_cannot">
        <param name="select" type="select" label="Reference database">