Mercurial > repos > iuc > gatk4_mutect2
diff macros.xml @ 3:287c4af133e6 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
| author | iuc |
|---|---|
| date | Sun, 10 May 2020 17:58:00 -0400 |
| parents | 3be27a9a7313 |
| children | 1cea23583655 |
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--- a/macros.xml Fri Apr 10 14:10:55 2020 -0400 +++ b/macros.xml Sun May 10 17:58:00 2020 -0400 @@ -1,7 +1,7 @@ <?xml version="1.0"?> <macros> - <token name="@VERSION@">4.1.4.0</token> - <token name="@WRAPPER_VERSION@">@VERSION@+galaxy</token> + <token name="@VERSION@">4.1.7.0</token> + <token name="@WRAPPER_VERSION@">@VERSION@+galaxy0</token> <xml name="requirements"> <requirements> @@ -290,45 +290,58 @@ </xml> <!--BAM input--> - <template name="picard_bam_input"> - --INPUT input.bam - </template> - - <template name="gatk_bam_input"> - --input input.bam + <template name="picard_tumor_bam_input"> + --INPUT tumor.bam </template> - <template name="bam_index_pre_chth"><![CDATA[ + <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 + "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 + #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_bam_req_params"> - <param argument="--input" type="data" format="bam,sam" label="Input BAM/SAM/CRAM file" /> + <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_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 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