Mercurial > repos > gandres > vcftools_filter_stats_diversity

comparison VCFToolsSlidingWindow/vcfToolsSlidingWindow.xml @ 7:ca045c1d5fa5 draft

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planemo upload
author gandres
date Thu, 31 Mar 2016 10:41:59 -0400
parents ff9c990466be
children
comparison
equal deleted inserted replaced
6:1420a55ca72b 7:ca045c1d5fa5
1 <tool id="sniplay_vcftoolsslidingwindow" name="VCF tools SlidingWindow" version="1.2.0"> 1 <tool id="sniplay_vcftoolsslidingwindow" name="VCF tools SlidingWindow" version="1.3.0">
2 2
3 <!-- [REQUIRED] Tool description displayed after the tool name --> 3 <!-- [REQUIRED] Tool description displayed after the tool name -->
4 <description> Make diversity computation with sliding window </description> 4 <description> Make diversity computation with sliding window </description>
5 5
6 <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work --> 6 <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work -->
18 18
19 <!-- [REQUIRED] The command to execute --> 19 <!-- [REQUIRED] The command to execute -->
20 <command interpreter="bash"> 20 <command interpreter="bash">
21 vcfToolsSlidingWindow.sh ${filein} $window $filelog ${fileout_taj} ${fileout_tstv} ${fileout_windowed} ${fileout_snp} 21 vcfToolsSlidingWindow.sh ${filein} $window $filelog ${fileout_taj} ${fileout_tstv} ${fileout_windowed} ${fileout_snp}
22 #if $group : 22 #if $group :
23 $group ${fileout_fst} ${fileout_fst_marker} ${fileout_taj_combined} ${fileout_windowed_combined} 23 $group ${fileout_fst} ${fileout_fst_marker} ${fileout_taj_combined} ${fileout_windowed_combined} ${fileout_tstv_combined} ${fileout_snp_combined}
24 #else : 24 #else :
25 "none" 25 "none"
26 #end if 26 #end if
27 </command> 27 </command>
28 28
45 <filter>(group != None)</filter> 45 <filter>(group != None)</filter>
46 </data> 46 </data>
47 <data name="fileout_fst_marker" format="txt" label="${fileout_label}.fst.by_marker.genes.txt"> 47 <data name="fileout_fst_marker" format="txt" label="${fileout_label}.fst.by_marker.genes.txt">
48 <filter>(group != None)</filter> 48 <filter>(group != None)</filter>
49 </data> 49 </data>
50 <data name="fileout_windowed_combined" format="tabular" label="${fileout_label}.combined.pi.txt" > 50 <data name="fileout_windowed_combined" format="txt" label="${fileout_label}.combined.pi.txt" >
51 <filter>(group != None)</filter> 51 <filter>(group != None)</filter>
52 </data> 52 </data>
53 <data name="fileout_taj_combined" format="tabular" label="${fileout_label}.combined.dtajima.txt" > 53 <data name="fileout_taj_combined" format="txt" label="${fileout_label}.combined.dtajima.txt" >
54 <filter>(group != None)</filter>
55 </data>
56 <data name="fileout_tstv_combined" format="txt" label="${fileout_label}.combined.TsTv.txt" >
57 <filter>(group != None)</filter>
58 </data>
59 <data name="fileout_snp_combined" format="txt" label="${fileout_label}.combined.snpden.txt" >
54 <filter>(group != None)</filter> 60 <filter>(group != None)</filter>
55 </data> 61 </data>
56 </outputs> 62 </outputs>
57 63
58 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> 64 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
67 <output name="fileout_windowed" file="sliding-result2.windowed.pi" /> 73 <output name="fileout_windowed" file="sliding-result2.windowed.pi" />
68 <output name="fileout_fst" file="sliding-result2.fst.txt" /> 74 <output name="fileout_fst" file="sliding-result2.fst.txt" />
69 <output name="fileout_fst_marker" file="sliding-result2.fst.by_marker.genes.txt" /> 75 <output name="fileout_fst_marker" file="sliding-result2.fst.by_marker.genes.txt" />
70 <output name="fileout_taj_combined" file="sliding-result2.combined.dtajima.txt" /> 76 <output name="fileout_taj_combined" file="sliding-result2.combined.dtajima.txt" />
71 <output name="fileout_windowed_combined" file="sliding-result2.combined.pi.txt" /> 77 <output name="fileout_windowed_combined" file="sliding-result2.combined.pi.txt" />
78 <output name="fileout_tstv_combined" file="sliding-result2.combined.TsTv.txt" />
79 <output name="fileout_snp_combined" file="sliding-result2.combined.snpden.txt" />
72 </test> 80 </test>
73 <test> 81 <test>
74 <param name="filein" value="sample.vcf" /> 82 <param name="filein" value="sample.vcf" />
75 <output name="fileout_snp" file="sliding-result.snpden" /> 83 <output name="fileout_snp" file="sliding-result.snpden" />
76 <output name="fileout_taj" file="sliding-result.Tajima.D" /> 84 <output name="fileout_taj" file="sliding-result.Tajima.D" />