Mercurial > repos > nilesh > rseqc
diff RNA_fragment_size.xml @ 63:27e16a30667a draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit d7544582d5599c67a284faf9232cd2ccc4daa1de
| author | iuc |
|---|---|
| date | Tue, 09 Apr 2024 11:24:55 +0000 |
| parents | 5968573462fa |
| children |
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--- a/RNA_fragment_size.xml Wed Feb 22 15:06:01 2023 +0000 +++ b/RNA_fragment_size.xml Tue Apr 09 11:24:55 2024 +0000 @@ -6,49 +6,41 @@ <import>rseqc_macros.xml</import> </macros> <expand macro="bio_tools"/> - - <expand macro="requirements" /> - - <expand macro="stdio" /> - + <expand macro="requirements"/> + <expand macro="stdio"/> <version_command><![CDATA[RNA_fragment_size.py --version]]></version_command> - <command><![CDATA[ @BAM_SAM_INPUTS@ RNA_fragment_size.py -i 'input.${extension}' --refgene='${refgene}' --mapq=${mapq} --frag-num=${fragnum} > '${output}' ]]> </command> - <inputs> - <expand macro="bam_param" /> - <expand macro="refgene_param" /> - <expand macro="mapq_param" /> - <param name="fragnum" type="integer" value="3" label="Minimum number of fragments (default: 3)" help="(--frag-num)" /> + <expand macro="bam_param"/> + <expand macro="refgene_param"/> + <expand macro="mapq_param"/> + <param name="fragnum" type="integer" value="3" label="Minimum number of fragments (default: 3)" help="(--frag-num)"/> </inputs> - <outputs> - <data format="tabular" name="output" /> + <data format="tabular" name="output"/> </outputs> - <tests> - <test> - <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" /> + <test expect_num_outputs="1"> + <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/> <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/> <output name="output"> <assert_contents> - <has_line_matching expression="^chrom\ttx_start\ttx_end\tsymbol\tfrag_count\tfrag_mean\tfrag_median\tfrag_std$" /> - <has_line_matching expression="^chr1\t11873\t14409\tNR_046018\t1\t0\t0\t0$" /> - <has_line_matching expression="^chr1\t14361\t29370\tNR_024540\t14\t66.5\t51.0\t41.119599080\d+$" /> - <has_line_matching expression="^chr1\t17368\t17436\tNR_106918\t0\t0\t0\t0$" /> - <has_line_matching expression="^chr1\t17368\t17436\tNR_107062\t0\t0\t0\t0$" /> - <has_line_matching expression="^chr1\t34610\t36081\tNR_026818\t0\t0\t0\t0$" /> - <has_line_matching expression="^chr1\t34610\t36081\tNR_026820\t0\t0\t0\t0$" /> - <has_line_matching expression="^chr1\t69090\t70008\tNM_001005484\t0\t0\t0\t0$" /> + <has_line_matching expression="^chrom\ttx_start\ttx_end\tsymbol\tfrag_count\tfrag_mean\tfrag_median\tfrag_std$"/> + <has_line_matching expression="^chr1\t11873\t14409\tNR_046018\t1\t0\t0\t0$"/> + <has_line_matching expression="^chr1\t14361\t29370\tNR_024540\t14\t66.5\t51.0\t41.119599080\d+$"/> + <has_line_matching expression="^chr1\t17368\t17436\tNR_106918\t0\t0\t0\t0$"/> + <has_line_matching expression="^chr1\t17368\t17436\tNR_107062\t0\t0\t0\t0$"/> + <has_line_matching expression="^chr1\t34610\t36081\tNR_026818\t0\t0\t0\t0$"/> + <has_line_matching expression="^chr1\t34610\t36081\tNR_026820\t0\t0\t0\t0$"/> + <has_line_matching expression="^chr1\t69090\t70008\tNM_001005484\t0\t0\t0\t0$"/> </assert_contents> </output> </test> </tests> - <help><![CDATA[ RNA_fragment_size.py ++++++++++++++++++++ @@ -80,7 +72,5 @@ ]]> </help> - - <expand macro="citations" /> - + <expand macro="citations"/> </tool>