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comparison infer_experiment.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_infer_experiment" name="Infer Experiment" version="@TOOL_VERSION@.1"> 1 <tool id="rseqc_infer_experiment" name="Infer Experiment" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
2 <description>speculates how RNA-seq were configured</description> 2 <description>speculates how RNA-seq were configured</description>
3 <expand macro="bio_tools"/> 3 <expand macro="bio_tools"/>
4 <macros> 4 <macros>
5 <import>rseqc_macros.xml</import> 5 <import>rseqc_macros.xml</import>
6 </macros> 6 </macros>
10 <expand macro="stdio" /> 10 <expand macro="stdio" />
11 11
12 <version_command><![CDATA[infer_experiment.py --version]]></version_command> 12 <version_command><![CDATA[infer_experiment.py --version]]></version_command>
13 13
14 <command><![CDATA[ 14 <command><![CDATA[
15 infer_experiment.py -i '${input}' -r '${refgene}' 15 @BAM_SAM_INPUTS@
16 infer_experiment.py -i 'input.${extension}' -r '${refgene}'
16 --sample-size ${sample_size} 17 --sample-size ${sample_size}
17 --mapq ${mapq} 18 --mapq ${mapq}
18 > '${output}' 19 > '${output}'
19 ]]> 20 ]]>
20 </command> 21 </command>
25 <expand macro="sample_size_param" /> 26 <expand macro="sample_size_param" />
26 <expand macro="mapq_param" /> 27 <expand macro="mapq_param" />
27 </inputs> 28 </inputs>
28 29
29 <outputs> 30 <outputs>
30 <data format="txt" name="output" /> 31 <data format="txt" name="output" label="${tool.name} on ${on_string}: RNA-seq experiment configuration" />
31 </outputs> 32 </outputs>
32 33
33 <tests> 34 <tests>
34 <test> 35 <test>
35 <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"/>