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comparison vcfrandomsample.xml @ 1:03030ecd1961 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfrandomsample commit 0b9b6512272b82637c2f1e831367e89aed77ae79
author devteam
date Thu, 15 Sep 2016 16:05:17 -0400
parents ad12ba1db0e4
children 939834d8de40
comparison
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0:ad12ba1db0e4 1:03030ecd1961
1 <tool id="vcfrandomsample" name="VCFrandomSample:" version="0.0.3"> 1 <tool id="vcfrandomsample" name="VCFrandomSample:" version="@WRAPPER_VERSION@.0">
2 <description>Randomly sample sites from VCF dataset</description> 2 <description>Randomly sample sites from VCF dataset</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"></expand> 6 <expand macro="requirements"/>
7 <expand macro="stdio" /> 7 <expand macro="stdio" />
8 <command> 8 <command>
9 9 vcfrandomsample
10 #if $adv_options.adv_options_selector == True: 10 #if $adv_options.adv_options_selector == "use_adv_controls":
11 vcfrandomsample -s "${adv_options.scale_by}" -p ${random_seed} -r ${rate} "${vcf_input}" > "${out_file1}" 11 -s "${adv_options.scale_by}"
12 #else: 12 #end if
13 vcfrandomsample -p ${random_seed} -r ${rate} "${vcf_input}" > "${out_file1}" 13 -p ${random_seed}
14 #end if 14 -r ${rate}
15 </command> 15 "${vcf_input}" > "${out_file1}"
16 <inputs> 16 </command>
17 <param format="vcf" name="vcf_input" type="data" label="Select random sites from"/> 17 <inputs>
18 <param name="rate" type="float" value="0.1" label="base sampling probability per locus" help="-r, --rate"/> 18 <param format="vcf" name="vcf_input" type="data" label="Select random sites from"/>
19 <param name="random_seed" type="integer" value="17823618326" label="use this random seed" help="-p, --random-seed; use this to make results reproducible" /> 19 <param name="rate" type="float" value="0.1" label="base sampling probability per locus" help="-r, --rate"/>
20 <conditional name="adv_options"> 20 <param name="random_seed" type="integer" value="17823618326" label="use this random seed"
21 <param name="adv_options_selector" type="boolean" truevalue="use_adv_controls" label="Advanced controls" help="Allows you to specify options that are not listed above"/> 21 help="-p, --random-seed; use this to make results reproducible" />
22 <when value="use_adv_controls"> 22 <conditional name="adv_options">
23 <param name="scale_by" type="text" value="AF" label="scale sampling likelihood by this INFO field" help="-s, --scale-by; this only works for Float info fields such as AF" /> 23 <param name="adv_options_selector" type="select" label="Advanced controls" help="Allows you to specify options that are not listed above">
24 </when> 24 <option value="no">Don't use advanced options</option>
25 </conditional> 25 <option value="use_adv_controls">Use advanced options</option>
26 </inputs> 26 </param>
27 <outputs> 27 <when value="" />
28 <data format="vcf" name="out_file1" /> 28 <when value="use_adv_controls">
29 </outputs> 29 <param name="scale_by" type="text" value="AF" label="scale sampling likelihood by this INFO field" help="-s, --scale-by; this only works for Float info fields such as AF" />
30 <tests> 30 </when>
31 <test> 31 </conditional>
32 <param name="vcf_input" value="vcflib.vcf"/> 32 </inputs>
33 <param name="rate" value="0.2" /> 33 <outputs>
34 <param name="random_seed" value="1" /> 34 <data format="vcf" name="out_file1" />
35 <param name="adv_options_selector" value="False" /> 35 </outputs>
36 <output name="out_file1" file="vcfrandomsample-test1.vcf" lines_diff="2" /> 36 <tests>
37 </test> 37 <test>
38 <param name="vcf_input" value="vcflib.vcf"/>
39 <param name="rate" value="0.2" />
40 <param name="random_seed" value="1" />
41 <param name="adv_options_selector" value="no" />
42 <output name="out_file1" file="vcfrandomsample-test1.vcf" lines_diff="2" />
43 </test>
38 </tests> 44 </tests>
39 <help> 45 <help>
40 46
41 Randomly sample sites from an input VCF dataset. Scale the sampling probability by the field specified by --scale-by (see advanced controls). This may be 47 Randomly sample sites from an input VCF dataset. Scale the sampling probability by the field specified by --scale-by (see advanced controls). This may be
42 used to provide uniform sampling across allele frequencies, for instance (AF field in this case). 48 used to provide uniform sampling across allele frequencies, for instance (AF field in this case).
43 49
44 Options::
45
46 -r, --rate RATE base sampling probability per locus
47 -s, --scale-by KEY scale sampling likelihood by this Float info field
48 -p, --random-seed N use this random seed
49
50 ---- 50 ----
51 51
52 Vcfrandomsample @IS_PART_OF_VCFLIB@ 52 Vcfrandomsample @IS_PART_OF_VCFLIB@
53 </help> 53 </help>
54 <expand macro="citations" /> 54 <expand macro="citations" />
55 </tool> 55 </tool>