Mercurial > repos > nilesh > rseqc

comparison RPKM_saturation.xml @ 50:f242ee103277 draft

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planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit 91ad241aa3f34b70649d13a5f18611da7577a5ee
author lparsons
date Tue, 03 May 2016 16:36:57 -0400
parents 6b33e31bda10
children 09846d5169fa
comparison
equal deleted inserted replaced
49:6b33e31bda10 50:f242ee103277
75 <data format="xls" name="outputrawxls" from_work_dir="output.rawCount.xls" label="${tool.name} on ${on_string} (Raw Count XLS)"/> 75 <data format="xls" name="outputrawxls" from_work_dir="output.rawCount.xls" label="${tool.name} on ${on_string} (Raw Count XLS)"/>
76 <data format="txt" name="outputr" from_work_dir="output.saturation.r" label="${tool.name} on ${on_string} (R Script)"/> 76 <data format="txt" name="outputr" from_work_dir="output.saturation.r" label="${tool.name} on ${on_string} (R Script)"/>
77 <data format="pdf" name="outputpdf" from_work_dir="output.saturation.pdf" label="${tool.name} on ${on_string} (PDF)"/> 77 <data format="pdf" name="outputpdf" from_work_dir="output.saturation.pdf" label="${tool.name} on ${on_string} (PDF)"/>
78 </outputs> 78 </outputs>
79 79
80 <!-- Unable to succefully run this script with test data
81 <tests> 80 <tests>
82 <test> 81 <test>
83 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/> 82 <param name="input" value="pairend_strandspecific_51mer_hg19_random.bam"/>
84 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed"/> 83 <param name="refgene" value="hg19.HouseKeepingGenes_30.bed"/>
85 <output name="outputxls" file="output.eRPKM.xls"/> 84 <output name="outputxls">
86 <output name="outputrawxls" file="output.rawCount.xls"/> 85 <assert_contents>
87 <output name="outputr" file="output.saturation.r"/> 86 <has_n_columns n="26" />
87 <has_line_matching expression="chr1\t16174358\t16266950\tNM_015001.*" />
88 </assert_contents>
89 </output>
90 <output name="outputrawxls">
91 <assert_contents>
92 <has_n_columns n="26" />
93 <has_line_matching expression="chr1\t16174358\t16266950\tNM_015001.*" />
94 </assert_contents>
95 </output>
96 <output name="outputr">
97 <assert_contents>
98 <has_text text="pdf('output.saturation.pdf')" />
99 <has_line_matching expression="S5=c\(\d+\.\d+\)" />
100 </assert_contents>
101 </output>
88 </test> 102 </test>
89 </tests> 103 </tests>
90 -->
91 104
92 <help><![CDATA[ 105 <help><![CDATA[
93 RPKM_saturation.py 106 RPKM_saturation.py
94 ++++++++++++++++++ 107 ++++++++++++++++++
95 108