comparison macros.xml @ 8:c124315e2b88 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"

7:fbf3f04324a1

        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">samtools</requirement>
            <yield/>
        </requirements>
    </xml>
    <token name="@TOOL_VERSION@">1.9</token>
    <token name="@FLAGS@">#set $flags = sum(map(int, str($filter).split(',')))</token>
    <token name="@PREPARE_IDX@"><![CDATA[
        ##prepare input and indices 
        ln -s '$input' infile &&
        #if $input.is_of_type('bam'):
            #if str( $input.metadata.bam_index ) != "None":
                ln -s '${input.metadata.bam_index}' infile.bai &&
            #else:

                samtools index infile infile.crai &&
            #end if
        #end if
    ]]></token>
    <token name="@PREPARE_IDX_MULTIPLE@"><![CDATA[
        ##prepare input and indices 
        #for $i, $bam in enumerate( $input_bams ):
            ln -s '$bam' '${i}' &&
            #if $bam.is_of_type('bam'):
                #if str( $bam.metadata.bam_index ) != "None":
                    ln -s '${bam.metadata.bam_index}' '${i}.bai' &&

        #else
            #set reffa=None
            #set reffai=None
        #end if
    ]]></token>
    <token name="@ADDTHREADS@"><![CDATA[
        ##compute the number of ADDITIONAL threads to be used by samtools (-@)
        addthreads=\${GALAXY_SLOTS:-1} && (( addthreads-- )) &&
    ]]></token>
    <token name="@ADDMEMORY@"><![CDATA[
        ##compute the number of memory available to samtools sort (-m)
        ##use only 75% of available: https://github.com/samtools/samtools/issues/831
        addmemory=\${GALAXY_MEMORY_MB_PER_SLOT:-768} && 
        ((addmemory=addmemory*75/100)) &&
    ]]></token>
    <xml name="seed_input">
       <param name="seed" type="integer" optional="True" label="Seed for random number generator" help="If empty a random seed is used." /> 
    </xml>
    <xml name="flag_options">
        <option value="1">read is paired</option>
        <option value="2">read is mapped in a proper pair</option>
        <option value="4">read is unmapped</option>
        <option value="8">mate is unmapped</option>
        <option value="16">read reverse strand</option>
        <option value="32">mate reverse strand</option>
        <option value="64">read is the first in a pair</option>
        <option value="128">read is the second in a pair</option>
        <option value="256">alignment or read is not primary</option>
        <option value="512">read fails platform/vendor quality checks</option>
        <option value="1024">read is a PCR or optical duplicate</option>
        <option value="2048">supplementary alignment</option>
    </xml>

    <!-- region specification macros and tokens for tools that allow the specification 
         of region by bed file / space separated list of regions -->
    <token name="@REGIONS_FILE@"><![CDATA[
        #if $cond_region.select_region == 'tab':
            -t '$cond_region.targetregions'
        #end if

8:c124315e2b88

        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">samtools</requirement>
            <yield/>
        </requirements>
    </xml>
    <token name="@TOOL_VERSION@">1.13</token>
    <token name="@PROFILE@">20.05</token>
    <token name="@FLAGS@"><![CDATA[
        #set $flags = 0
        #if $filter
            #set $flags = sum(map(int, str($filter).split(',')))
        #end if
    ]]></token>
    <token name="@PREPARE_IDX@"><![CDATA[
        ##prepare input and indices
        ln -s '$input' infile &&
        #if $input.is_of_type('bam'):
            #if str( $input.metadata.bam_index ) != "None":
                ln -s '${input.metadata.bam_index}' infile.bai &&
            #else:

                samtools index infile infile.crai &&
            #end if
        #end if
    ]]></token>
    <token name="@PREPARE_IDX_MULTIPLE@"><![CDATA[
        ##prepare input and indices
        #for $i, $bam in enumerate( $input_bams ):
            ln -s '$bam' '${i}' &&
            #if $bam.is_of_type('bam'):
                #if str( $bam.metadata.bam_index ) != "None":
                    ln -s '${bam.metadata.bam_index}' '${i}.bai' &&

        #else
            #set reffa=None
            #set reffai=None
        #end if
    ]]></token>

    <xml name="optional_reference">
        <conditional name="addref_cond">
            <param name="addref_select" type="select" label="Use a reference sequence">
                <help>@HELP@</help>
                <option value="no">No</option>
                <option value="history">Use a genome/index from the history</option>
                <option value="cached">Use a built-in genome</option>
            </param>
            <when value="no"/>
            <when value="history">
                <param name="ref" argument="@ARGUMENT@" type="data" format="fasta,fasta.gz" label="Reference"/>
            </when>
            <when value="cached">
                <param name="ref" argument="@ARGUMENT@" type="select" label="Reference">
                    <options from_data_table="fasta_indexes">
                        <filter type="data_meta" ref="input" key="dbkey" column="dbkey"/>
                    </options>
                    <validator  type="no_options" message="No reference genome is available for the build associated with the selected input dataset"/>
                </param>
            </when>
        </conditional>
    </xml>
    <xml name="mandatory_reference" token_help="" token_argument="">
        <conditional name="addref_cond">
            <param name="addref_select" type="select" label="Use a reference sequence">
                <help>@HELP@</help>
                <option value="history">Use a genome/index from the history</option>
                <option value="cached">Use a built-in genome</option>
            </param>
            <when value="history">
                <param name="ref" argument="@ARGUMENT@" type="data" format="fasta,fasta.gz" label="Reference"/>
            </when>
            <when value="cached">
                <param name="ref" argument="@ARGUMENT@" type="select" label="Reference">
                    <options from_data_table="fasta_indexes">
                        <filter type="data_meta" ref="input" key="dbkey" column="dbkey"/>
                        <validator message="No reference genome is available for the build associated with the selected input dataset" type="no_options" />
                    </options>
                </param>
            </when>
        </conditional>
    </xml>


    <token name="@ADDTHREADS@"><![CDATA[
        ##compute the number of ADDITIONAL threads to be used by samtools (-@)
        addthreads=\${GALAXY_SLOTS:-1} && (( addthreads-- )) &&
    ]]></token>
    <token name="@ADDMEMORY@"><![CDATA[
        ##compute the number of memory available to samtools sort (-m)
        ##use only 75% of available: https://github.com/samtools/samtools/issues/831
        addmemory=\${GALAXY_MEMORY_MB_PER_SLOT:-768} &&
        ((addmemory=addmemory*75/100)) &&
    ]]></token>
    <xml name="seed_input">
       <param name="seed" type="integer" optional="True" label="Seed for random number generator" help="If empty a random seed is used." />
    </xml>
    <xml name="flag_options" token_s1="false" token_s2="false" token_s4="false" token_s8="false" token_s16="false" token_s32="false" token_s64="false" token_s128="false" token_s256="false" token_s512="false" token_s1024="false" token_s2048="false">
        <option value="1" selected="@S1@">Read is paired</option>
        <option value="2" selected="@S2@">Read is mapped in a proper pair</option>
        <option value="4" selected="@S4@">Read is unmapped</option>
        <option value="8" selected="@S8@">Mate is unmapped</option>
        <option value="16" selected="@S16@">Read is mapped to the reverse strand of the reference</option>
        <option value="32" selected="@S32@">Mate is mapped to the reverse strand of the reference</option>
        <option value="64" selected="@S64@">Read is the first in a pair</option>
        <option value="128" selected="@S128@">Read is the second in a pair</option>
        <option value="256" selected="@S256@">Alignment of the read is not primary</option>
        <option value="512" selected="@S512@">Read fails platform/vendor quality checks</option>
        <option value="1024" selected="@S1024@">Read is a PCR or optical duplicate</option>
        <option value="2048" selected="@S2048@">Alignment is supplementary</option>
    </xml>

    <!-- region specification macros and tokens for tools that allow the specification
         of region by bed file / space separated list of regions -->
    <token name="@REGIONS_FILE@"><![CDATA[
        #if $cond_region.select_region == 'tab':
            -t '$cond_region.targetregions'
        #end if