Mercurial > repos > iuc > varscan_mpileup

comparison macros.xml @ 1:0bc800d67a0e draft

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planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
author iuc
date Sun, 15 Jul 2018 09:19:37 -0400
parents 1e667badbe87
children d062703d6f13
comparison
equal deleted inserted replaced
0:1e667badbe87 1:0bc800d67a0e
20 <xml name="citations"> 20 <xml name="citations">
21 <citations> 21 <citations>
22 <citation type="doi">10.1101/gr.129684.111</citation> 22 <citation type="doi">10.1101/gr.129684.111</citation>
23 </citations> 23 </citations>
24 </xml> 24 </xml>
25
26 <xml name="input_pileups">
27 <conditional name="pileup">
28 <param name="pileup_select" type="select" label="How do you want to provide your pileup files?" help="">
29 <option value="separated">As separated normal and tumor files</option>
30 <option value="combined">Normal and Tumor combined in one file</option>
31 </param>
32 <when value="separated">
33 <param name="normal_pileup" format="pileup" type="data" label="Samtools pileup dataset for Normal" help=""/>
34 <param name="tumor_pileup" format="pileup" type="data" label="Samtools pileup dataset for Tumor" help=""/>
35 </when>
36 <when value="combined">
37 <param name="combined_pileup" format="pileup" type="data" label="Samtools pileup dataset which has combined Normal and Tumor samples" help=""/>
38 </when>
39 </conditional>
40 </xml>
41
42 <token name="@INPUT_PILEUPS@">
43 #if $pileup.pileup_select == 'separated'
44 '${pileup.normal_pileup}'
45 '${pileup.tumor_pileup}'
46 galaxy_out
47 #else:
48 '${pileup.combined_pileup}'
49 galaxy_out
50 --mpileup 1
51 #end if
52
53 </token>
25 54
26 <xml name="min_coverage"> 55 <xml name="min_coverage">
27 <param argument="--min-coverage" name="min_coverage" type="integer" value="8" min="1" max="200" 56 <param argument="--min-coverage" name="min_coverage" type="integer" value="8" min="1" max="200"
28 label="Minimum read depth" help="Minimum depth at a position to make a call"/> 57 label="Minimum read depth" help="Minimum depth at a position to make a call"/>
29 </xml> 58 </xml>