Mercurial > repos > nilesh > rseqc
comparison FPKM_count.xml @ 62:473382134e56 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit ccb6f7edba5492f4750ef8a59c4f91eb67fdbbec
author | iuc |
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date | Wed, 22 Feb 2023 15:06:01 +0000 |
parents | 5968573462fa |
children | 27e16a30667a |
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61:5968573462fa | 62:473382134e56 |
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13 <version_command><![CDATA[FPKM_count.py --version]]></version_command> | 13 <version_command><![CDATA[FPKM_count.py --version]]></version_command> |
14 | 14 |
15 <command><![CDATA[ | 15 <command><![CDATA[ |
16 @BAM_SAM_INPUTS@ | 16 @BAM_SAM_INPUTS@ |
17 FPKM_count.py -i 'input.${extension}' -o output -r '${refgene}' | 17 FPKM_count.py -i 'input.${extension}' -o output -r '${refgene}' |
18 | |
19 #if str($strand_type.strand_specific) == "pair" | 18 #if str($strand_type.strand_specific) == "pair" |
20 -d | 19 -d |
21 #if str($strand_type.pair_type) == "sd" | 20 #if str($strand_type.pair_type) == "sd" |
22 '1++,1--,2+-,2-+' | 21 '1++,1--,2+-,2-+' |
23 #else | 22 #else |
24 '1+-,1-+,2++,2--' | 23 '1+-,1-+,2++,2--' |
25 #end if | 24 #end if |
26 #end if | 25 #end if |
27 | |
28 #if str($strand_type.strand_specific) == "single" | 26 #if str($strand_type.strand_specific) == "single" |
29 -d | 27 -d |
30 #if str($strand_type.single_type) == "s" | 28 #if str($strand_type.single_type) == "s" |
31 '++,--' | 29 '++,--' |
32 #else | 30 #else |
33 '+-,-+' | 31 '+-,-+' |
34 #end if | 32 #end if |
35 #end if | 33 #end if |
36 | |
37 @MULTIHITS@ | 34 @MULTIHITS@ |
38 | |
39 $onlyexonic | 35 $onlyexonic |
40 --single-read="${singleread}" | 36 --single-read="${singleread}" |
41 ]]> | 37 ]]> |
42 </command> | 38 </command> |
43 | 39 |
53 <option value="0">Ignore it (0)</option> | 49 <option value="0">Ignore it (0)</option> |
54 </param> | 50 </param> |
55 </inputs> | 51 </inputs> |
56 | 52 |
57 <outputs> | 53 <outputs> |
58 <data format="xls" name="outputxls" from_work_dir="output.FPKM.xls"/> | 54 <data format="tabular" name="output" from_work_dir="output.FPKM.xls" label="${tool.name} on ${on_string}: FPKM counts"/> |
59 </outputs> | 55 </outputs> |
60 | 56 |
61 <tests> | 57 <tests> |
62 <test> | 58 <test> |
63 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/> | 59 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/> |
64 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/> | 60 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/> |
65 <output name="outputxls" file="output.FPKM.xls"/> | 61 <output name="output" file="output01.tab"/> |
62 </test> | |
63 <test> | |
64 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/> | |
65 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/> | |
66 <conditional name="multihits_type"> | |
67 <param name="multihits_type_selector" value="skip_multihits"/> | |
68 <param name="mapq" value="20"/> | |
69 </conditional> | |
70 <output name="output" file="output02.tab"/> | |
71 <assert_command> | |
72 <has_text text="--mapq=20" /> | |
73 </assert_command> | |
66 </test> | 74 </test> |
67 </tests> | 75 </tests> |
68 | 76 |
69 <help><![CDATA[ | 77 <help><![CDATA[ |
70 FPKM_count.py | 78 FPKM_count.py |