comparison macros.xml @ 4:1cea23583655 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit ff4bacd218035b7052ceadfadaec81dfd5d07b0e"

3:287c4af133e6

            </when>
            <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>

4:1cea23583655

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

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