Mercurial > repos > matthias > stacks2_refmap

comparison stacks_refmap.xml @ 3:93fb82c0fc94 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
author matthias
date Tue, 18 Dec 2018 12:48:09 -0500
parents 39ebc7633942
children 466cc910d640
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2:39ebc7633942 3:93fb82c0fc94
44 </outputs> 44 </outputs>
45 45
46 <tests> 46 <tests>
47 <!-- bams as list --> 47 <!-- bams as list -->
48 <test> 48 <test>
49 <param name="input_bam"> 49 <param name="input_bam" ftype="bam" value="refmap/PopA_01.bam,refmap/PopA_02.bam"/>
50 <collection type="list">
51 <element name="PopA_01" ftype="bam" value="refmap/PopA_01.bam" />
52 <element name="PopA_02" ftype="bam" value="refmap/PopA_01.bam" />
53 </collection>
54 </param>
55 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" /> 50 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" />
56 <param name="add_log" value="yes" /> 51 <param name="add_log" value="yes" />
57 <output ftype="txt" name="output_log"><assert_contents><has_text text="ref_map.pl is done." /></assert_contents></output> 52 <output ftype="txt" name="output_log"><assert_contents><has_text text="ref_map.pl is done." /></assert_contents></output>
58 <!-- TODO test for outputs --> 53 <!-- TODO test for outputs -->
59 </test> 54 </test>
60 <test> 55 <test>
61 <param name="input_bam" value="refmap/PopA_01.bam,refmap/PopA_02.bam"/> 56 <param name="input_bam" ftype="bam" value="refmap/PopA_01.bam,refmap/PopA_02.bam"/>
62 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" /> 57 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" />
63 <param name="paired_select" value="--unpaired"/> 58 <param name="paired_select" value="--unpaired"/>
64 <param name="model_options|var_alpha" value="0.1" /> 59 <param name="model_options|var_alpha" value="0.1" />
65 <param name="model_options|gt_alpha" value="0.1" /> 60 <param name="model_options|gt_alpha" value="0.1" />
66 <assert_command> 61 <assert_command>