comparison macros.xml @ 3:d2c0c2698f58 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"

2:5f71f3690b95

<?xml version="1.0"?>
<macros>
    <token name="@VERSION@">4.1.4.0</token>
    <token name="@WRAPPER_VERSION@">@VERSION@+galaxy</token>

    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@VERSION@">gatk4</requirement>
            <requirement type="package" version="0.2.5">tabix</requirement>

            <when value="no_seq_dict" />
        </conditional>
    </xml>

    <!--BAM input-->
    <template name="picard_bam_input">
        --INPUT input.bam
    </template>

    <template name="gatk_bam_input">
        --input input.bam
    </template>

    <template name="bam_index_pre_chth"><![CDATA[
    #for $sect in $sections
        #if $varExists($sect + "input")
            #if $getVar($sect + "input").is_of_type("bam")
                ln -s $getVar($sect + "input") input.bam &&
                samtools index input.bam &&
            #else
                ln -s $getVar($sect + "input") input.sam &&
                samtools view -bS input.sam -o input.bam &&
                samtools index input.bam &&
            #end if
        #end if
    #end for
    ]]></template>

    <xml name="gatk_bam_req_params">
        <param argument="--input" type="data" format="bam,sam" label="Input BAM/SAM/CRAM file" />
    </xml>

    <template name="picard_bam_index"><![CDATA[
        #if $input.is_of_type("bam")
            ln -s $INPUT input.bam &&
            samtools index input.bam &&
        #else
            ln -s $INPUT input.sam &&
            samtools view -bS input.sam -o input.bam &&
            samtools index input.bam &&
        #end if
    ]]></template>


    <!--Output goes to stdout, no output parameter exists.-->
    <template name="stdout_to_output">
        > output.txt
    </template>

3:d2c0c2698f58

<?xml version="1.0"?>
<macros>
    <token name="@VERSION@">4.1.7.0</token>
    <token name="@WRAPPER_VERSION@">@VERSION@+galaxy0</token>

    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@VERSION@">gatk4</requirement>
            <requirement type="package" version="0.2.5">tabix</requirement>

            <when value="no_seq_dict" />
        </conditional>
    </xml>

    <!--BAM input-->
    <template name="picard_tumor_bam_input">
        --INPUT tumor.bam
    </template>

    <template name="gatk_tumor_bam_input">
        --input tumor.bam
    </template>

    <template name="tumor_bam_index_pre_chth"><![CDATA[
    #for $sect in $sections
        #if $varExists($sect + "tumor")
            ln -s $getVar($sect + "tumor") tumor.bam &&
            ln -s '${tumor.metadata.bam_index}' tumor.bam.bai &&
        #end if
    #end for
    ]]></template>

    <xml name="gatk_tumor_bam_req_params">
        <param name="tumor" argument="--tumor" type="data" format="bam" label="Input Tumor BAM file" />
    </xml>

    <template name="picard_tumor_bam_index"><![CDATA[
        ln -s $INPUT tumor.bam &&
        ln -s $INPUT tumor.bam.bai &&
    ]]></template>

    <template name="picard_normal_bam_input">
        --INPUT normal.bam
    </template>

    <template name="gatk_normal_bam_input">
        --input normal.bam
    </template>

    <template name="normal_bam_index_pre_chth"><![CDATA[
    #for $sect in $sections
        #if $varExists($sect + "normal")
            ln -s $getVar($sect + "normal") normal.bam &&
            ln -s '${normal.metadata.bam_index}' normal.bam.bai &&
        #end if
    #end for
    ]]></template>

    <xml name="gatk_normal_bam_req_params">
        <param name="normal" argument="--normal" type="data" format="bam" label="Input Normal BAM file" />
    </xml>

    <template name="picard_normal_bam_index"><![CDATA[
        ln -s $INPUT normal.bam &&
        ln -s $INPUT normal.bam.bai &&
    ]]></template>
    
    <!--Output goes to stdout, no output parameter exists.-->
    <template name="stdout_to_output">
        > output.txt
    </template>