Mercurial > repos > nilesh > rseqc

comparison read_duplication.xml @ 61:5968573462fa draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
author iuc
date Sat, 10 Dec 2022 11:23:05 +0000
parents 1421603cc95b
children 473382134e56
comparison
equal deleted inserted replaced
60:1421603cc95b 61:5968573462fa
1 <tool id="rseqc_read_duplication" name="Read Duplication" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@"> 1 <tool id="rseqc_read_duplication" name="Read Duplication" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
2 <description>determines reads duplication rate with sequence-based and mapping-based strategies</description> 2 <description>determines reads duplication rate with sequence-based and mapping-based strategies</description>
3 <expand macro="bio_tools"/>
4 <macros> 3 <macros>
5 <import>rseqc_macros.xml</import> 4 <import>rseqc_macros.xml</import>
6 </macros> 5 </macros>
6 <expand macro="bio_tools"/>
7 7
8 <expand macro="requirements" /> 8 <expand macro="requirements" />
9 9
10 <expand macro="stdio" /> 10 <expand macro="stdio" />
11 11
23 <expand macro="mapq_param" /> 23 <expand macro="mapq_param" />
24 <expand macro="rscript_output_param" /> 24 <expand macro="rscript_output_param" />
25 </inputs> 25 </inputs>
26 26
27 <outputs> 27 <outputs>
28 <expand macro="pdf_output_data" filename="output.DupRate_plot.pdf" /> 28 <expand macro="pdf_output_data" filename="output.DupRate_plot.pdf" label="${tool.name} on ${on_string}: plot (PDF)"/>
29 <data format="xls" name="outputxls" from_work_dir="output.pos.DupRate.xls" label="${tool.name} on ${on_string} (Position xls)"/> 29 <data format="xls" name="outputxls" from_work_dir="output.pos.DupRate.xls" label="${tool.name} on ${on_string}: positon (XLS)"/>
30 <data format="xls" name="outputseqxls" from_work_dir="output.seq.DupRate.xls" label="${tool.name} on ${on_string} (Sequence xls)"/> 30 <data format="xls" name="outputseqxls" from_work_dir="output.seq.DupRate.xls" label="${tool.name} on ${on_string}: sequences (XLS)"/>
31 <expand macro="rscript_output_data" filename="output.DupRate_plot.r" /> 31 <expand macro="rscript_output_data" filename="output.DupRate_plot.r" label="${tool.name} on ${on_string}: Rscript"/>
32 </outputs> 32 </outputs>
33 33
34 <tests> 34 <tests>
35 <test> 35 <test>
36 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" /> 36 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" />