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comparison FPKM_count.xml @ 14:b21f0167e197 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit ccb6f7edba5492f4750ef8a59c4f91eb67fdbbec
author iuc
date Wed, 22 Feb 2023 15:05:13 +0000
parents a7f9084572fe
children
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13:a7f9084572fe 14:b21f0167e197
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