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comparison deletion_profile.xml @ 60:1421603cc95b draft

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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_deletion_profile" name="Deletion Profile" version="@TOOL_VERSION@"> 1 <tool id="rseqc_deletion_profile" name="Deletion Profile" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
2 <description> 2 <description>
3 calculates the distributions of deleted nucleotides across reads 3 calculates the distributions of deleted nucleotides across reads
4 </description> 4 </description>
5 <expand macro="bio_tools"/> 5 <expand macro="bio_tools"/>
6 <macros> 6 <macros>
12 <expand macro="stdio" /> 12 <expand macro="stdio" />
13 13
14 <version_command><![CDATA[deletion_profile.py --version]]></version_command> 14 <version_command><![CDATA[deletion_profile.py --version]]></version_command>
15 15
16 <command><![CDATA[ 16 <command><![CDATA[
17 deletion_profile.py -i '${input}' -o output -l ${readlength} -n ${readnum} -q ${mapq} 17 @BAM_SAM_INPUTS@
18 deletion_profile.py -i 'input.${extension}' -o output -l ${read_align_length} -n ${read_num} -q ${mapq}
18 ]]> 19 ]]>
19 </command> 20 </command>
20 21
21 <inputs> 22 <inputs>
22 <expand macro="bam_param" /> 23 <expand macro="bam_param" />
33 </outputs> 34 </outputs>
34 35
35 <tests> 36 <tests>
36 <test> 37 <test>
37 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" /> 38 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" />
38 <param name="readlength" value="101" /> 39 <param name="read_align_length" value="101" />
39 <param name="rscript_output" value="true" /> 40 <param name="rscript_output" value="true" />
40 <output name="outputpdf" file="output.deletion_profile.pdf" compare="sim_size" /> 41 <output name="outputpdf" file="output.deletion_profile.pdf" compare="sim_size" />
41 <output name="outputxls" file="output.deletion_profile.txt" /> 42 <output name="outputxls" file="output.deletion_profile.txt" />
42 <output name="outputr" file="output.deletion_profile_r" /> 43 <output name="outputr" file="output.deletion_profile_r" />
43 </test> 44 </test>