Mercurial > repos > iuc > gatk4_mutect2
diff macros.xml @ 4:33da9009065f draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit c9ff247c1f6923be538cae9565ce99975426e94f"
| author | iuc |
|---|---|
| date | Wed, 13 May 2020 20:20:51 +0000 |
| parents | d2c0c2698f58 |
| children | 04253ade1697 |
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--- a/macros.xml Sun May 10 21:57:26 2020 +0000 +++ b/macros.xml Wed May 13 20:20:51 2020 +0000 @@ -289,59 +289,6 @@ </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