Mercurial > repos > nilesh > rseqc
diff FPKM_count.xml @ 62:473382134e56 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit ccb6f7edba5492f4750ef8a59c4f91eb67fdbbec
| author | iuc |
|---|---|
| date | Wed, 22 Feb 2023 15:06:01 +0000 |
| parents | 5968573462fa |
| children | 27e16a30667a |
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--- a/FPKM_count.xml Sat Dec 10 11:23:05 2022 +0000 +++ b/FPKM_count.xml Wed Feb 22 15:06:01 2023 +0000 @@ -15,7 +15,6 @@ <command><![CDATA[ @BAM_SAM_INPUTS@ FPKM_count.py -i 'input.${extension}' -o output -r '${refgene}' - #if str($strand_type.strand_specific) == "pair" -d #if str($strand_type.pair_type) == "sd" @@ -24,7 +23,6 @@ '1+-,1-+,2++,2--' #end if #end if - #if str($strand_type.strand_specific) == "single" -d #if str($strand_type.single_type) == "s" @@ -33,9 +31,7 @@ '+-,-+' #end if #end if - @MULTIHITS@ - $onlyexonic --single-read="${singleread}" ]]> @@ -55,14 +51,26 @@ </inputs> <outputs> - <data format="xls" name="outputxls" from_work_dir="output.FPKM.xls"/> + <data format="tabular" name="output" from_work_dir="output.FPKM.xls" label="${tool.name} on ${on_string}: FPKM counts"/> </outputs> <tests> <test> <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/> <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/> - <output name="outputxls" file="output.FPKM.xls"/> + <output name="output" file="output01.tab"/> + </test> + <test> + <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/> + <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/> + <conditional name="multihits_type"> + <param name="multihits_type_selector" value="skip_multihits"/> + <param name="mapq" value="20"/> + </conditional> + <output name="output" file="output02.tab"/> + <assert_command> + <has_text text="--mapq=20" /> + </assert_command> </test> </tests>