Mercurial > repos > nilesh > rseqc
comparison read_hexamer.xml @ 60:1421603cc95b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 1dfe55ca83685cadb0ce8f6ebbd8c13232376d1d
| author | iuc |
|---|---|
| date | Sat, 26 Nov 2022 15:19:14 +0000 |
| parents | dbedfc5f5a3c |
| children | 5968573462fa |
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| 59:dbedfc5f5a3c | 60:1421603cc95b |
|---|---|
| 1 <tool id="rseqc_read_hexamer" name="Hexamer frequency" version="@TOOL_VERSION@"> | 1 <tool id="rseqc_read_hexamer" name="Hexamer frequency" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@"> |
| 2 <description> | 2 <description> |
| 3 calculates hexamer (6mer) frequency for reads, genomes, and mRNA sequences | 3 calculates hexamer (6mer) frequency for reads, genomes, and mRNA sequences |
| 4 </description> | 4 </description> |
| 5 <expand macro="bio_tools"/> | 5 <expand macro="bio_tools"/> |
| 6 <macros> | 6 <macros> |
| 55 <test> | 55 <test> |
| 56 <param name="inputs" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.R1.fastq"/> | 56 <param name="inputs" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.R1.fastq"/> |
| 57 <output name="output"> | 57 <output name="output"> |
| 58 <assert_contents> | 58 <assert_contents> |
| 59 <has_line line="Hexamer	pairend_strandspecific_51mer_hg19_chr1_1-100000_R1_fastq" /> | 59 <has_line line="Hexamer	pairend_strandspecific_51mer_hg19_chr1_1-100000_R1_fastq" /> |
| 60 <has_line line="AAAAAA	0.00217391304348" /> | 60 <has_text text="0.002173913043478261" /> |
| 61 </assert_contents> | 61 </assert_contents> |
| 62 </output> | 62 </output> |
| 63 </test> | 63 </test> |
| 64 <test> | 64 <test> |
| 65 <param name="inputs" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.R1.fastq.gz" ftype="fastqsanger.gz"/> | 65 <param name="inputs" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.R1.fastq.gz" ftype="fastqsanger.gz"/> |
| 66 <output name="output"> | 66 <output name="output"> |
| 67 <assert_contents> | 67 <assert_contents> |
| 68 <has_line line="Hexamer	pairend_strandspecific_51mer_hg19_chr1_1-100000_R1_fastq_gz" /> | 68 <has_line line="Hexamer	pairend_strandspecific_51mer_hg19_chr1_1-100000_R1_fastq_gz" /> |
| 69 <has_line line="AAAAAA	0.00217391304348" /> | 69 <has_text text="0.002173913043478261" /> |
| 70 </assert_contents> | 70 </assert_contents> |
| 71 </output> | 71 </output> |
| 72 </test> | 72 </test> |
| 73 <test> | 73 <test> |
| 74 <param name="inputs" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.R1.fastq,pairend_strandspecific_51mer_hg19_chr1_1-100000.R2.fastq"/> | 74 <param name="inputs" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.R1.fastq,pairend_strandspecific_51mer_hg19_chr1_1-100000.R2.fastq"/> |
| 75 <output name="output"> | 75 <output name="output"> |
| 76 <assert_contents> | 76 <assert_contents> |
| 77 <has_line line="Hexamer	pairend_strandspecific_51mer_hg19_chr1_1-100000_R1_fastq	pairend_strandspecific_51mer_hg19_chr1_1-100000_R2_fastq" /> | 77 <has_line line="Hexamer	pairend_strandspecific_51mer_hg19_chr1_1-100000_R1_fastq	pairend_strandspecific_51mer_hg19_chr1_1-100000_R2_fastq" /> |
| 78 <has_line line="AAAAAA	0.00217391304348	0.00534759358289" /> | 78 <has_text text="0.002173913043478261" /> |
| 79 </assert_contents> | 79 </assert_contents> |
| 80 </output> | 80 </output> |
| 81 </test> | 81 </test> |
| 82 <test> | 82 <test> |
| 83 <param name="inputs" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.R1.fastq,pairend_strandspecific_51mer_hg19_chr1_1-100000.R1.fastq"/> | 83 <param name="inputs" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.R1.fastq,pairend_strandspecific_51mer_hg19_chr1_1-100000.R1.fastq"/> |
| 84 <output name="output"> | 84 <output name="output"> |
| 85 <assert_contents> | 85 <assert_contents> |
| 86 <has_line line="Hexamer	pairend_strandspecific_51mer_hg19_chr1_1-100000_R1_fastq	pairend_strandspecific_51mer_hg19_chr1_1-100000_R1_fastq.1" /> | 86 <has_line line="Hexamer	pairend_strandspecific_51mer_hg19_chr1_1-100000_R1_fastq	pairend_strandspecific_51mer_hg19_chr1_1-100000_R1_fastq.1" /> |
| 87 <has_line line="AAAAAA	0.00217391304348	0.00217391304348" /> | 87 <has_text text="0.002173913043478261" /> |
| 88 </assert_contents> | 88 </assert_contents> |
| 89 </output> | 89 </output> |
| 90 </test> | 90 </test> |
| 91 <!-- Unable to test with collections at the moment (requires type="data_collection" on the input) | 91 <!-- Unable to test with collections at the moment (requires type="data_collection" on the input) |
| 92 <test> | 92 <test> |