[2] | 1 | <tool id="rgPedSub1" name="Subset markers:"> |
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| 2 | <code file="rgPedSub_code.py"/> |
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| 3 | |
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| 4 | <description>region or rs list</description> |
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| 5 | |
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| 6 | <command interpreter="python"> |
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| 7 | rgPedSub.py $script_file |
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| 8 | </command> |
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| 9 | |
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| 10 | <inputs> |
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| 11 | <page> |
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| 12 | <param name="title" type="text" size="80" label="Title for output files" |
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| 13 | help="Descriptive title for new genotype/map files" value="Genotype_Subset" /> |
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| 14 | <param name="input1" type="data" format="lped" |
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| 15 | label="Current history lPed format data" optional="false" |
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| 16 | size="120" help="Choose a Linkage Ped format data from your current history" /> |
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| 17 | <param name='relfilter' label = "Filter out family relatedness" type="select" |
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| 18 | optional="false" size="132" |
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| 19 | help="Optionally remove related subjects if pedigree identifies founders and their offspring"> |
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| 20 | <option value="all" selected='true'>No filter on relatedness - all subjects passed through</option> |
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| 21 | <option value="fo" >Founders only (pedigree mother and father ID = "0")</option> |
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| 22 | <option value="oo" >Offspring only (one randomly chosen if >1 sibs in family)</option> |
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| 23 | </param> |
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| 24 | |
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| 25 | </page><page> |
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| 26 | <conditional name="m"> |
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| 27 | <param name="mtype" type="select" label="Markers in a genomic interval,or as an rs list?" refresh_on_change='true' |
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| 28 | help="Indicate the markers to be saved - as a list or as genomic region coordinates"> |
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| 29 | <option value="grslist" >Cut and paste a list of marker ids as rs numbers</option> |
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| 30 | <option value="gregion" selected='true'>Supply genomic coordinates for a region (as UCSC location)</option> |
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| 31 | </param> |
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| 32 | <when value="gregion"> |
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| 33 | <param name="region" type="text" label="Genomic refseq coordinates - chromosome:start-end" |
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| 34 | size="120" help="Region to be saved as chr9:119,506,000-119,518,000"/> |
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| 35 | <param name="rslist" type="hidden" value='' /> |
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| 36 | </when> |
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| 37 | <when value="grslist"> |
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| 38 | <param name="region" value="" type="hidden"/> |
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| 39 | <param name="rslist" type="text" area='true' size='15x20' label="marker id (rs) list" |
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| 40 | help="Cut and paste, or type a list of marker ids separated by spaces" /> |
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| 41 | </when> |
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| 42 | </conditional> |
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| 43 | </page> |
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| 44 | </inputs> |
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| 45 | |
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| 46 | <outputs> |
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| 47 | <data format="lped" name="output1" metadata_source="input1"/> |
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| 48 | </outputs> |
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| 49 | |
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| 50 | <configfiles> |
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| 51 | <configfile name="script_file"> |
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| 52 | title~~~~$title |
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| 53 | output1~~~~$output1 |
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| 54 | userId~~~~$userId |
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| 55 | outformat~~~~lped |
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| 56 | basename~~~~$input1.metadata.base_name |
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| 57 | inped~~~~$input1.extra_files_path/$input1.metadata.base_name |
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| 58 | outdir~~~~$output1.files_path |
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| 59 | relfilter~~~~$relfilter |
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| 60 | #if $m.mtype=='grslist' |
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| 61 | rslist~~~~$m.rslist |
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| 62 | region~~~~ |
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| 63 | #else |
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| 64 | rslist~~~~ |
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| 65 | region~~~~$m.region |
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| 66 | #end if |
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| 67 | </configfile> |
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| 68 | </configfiles> |
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| 69 | |
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| 70 | <tests> |
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| 71 | <test> |
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| 72 | <param name='input1' value='tinywga' ftype='lped' > |
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| 73 | <metadata name='base_name' value='tinywga' /> |
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| 74 | <composite_data value='tinywga.ped' /> |
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| 75 | <composite_data value='tinywga.map' /> |
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| 76 | <edit_attributes type='name' value='tinywga' /> |
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| 77 | </param> |
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| 78 | <param name='title' value='rgPedSubtest1' /> |
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| 79 | <param name="region" value="" /> |
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| 80 | <param name="rslist" value="rs2283802Xrs2267000Xrs16997606Xrs4820537Xrs3788347Xrs756632Xrs4820539Xrs2283804Xrs2267006Xrs4822363X" /> |
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| 81 | <param name="relfilter" value="all" /> |
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| 82 | <param name="mtype" value="grslist" /> |
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| 83 | <output name='output1' file='rgtestouts/rgPedSub/rgPedSubtest1.lped' ftype='lped' linesDiff='7'/> |
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| 84 | </test> |
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| 85 | </tests> |
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| 86 | |
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| 87 | <help> |
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| 88 | |
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| 89 | .. class:: infomark |
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| 90 | |
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| 91 | **Note** |
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| 92 | |
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| 93 | There are 2 forms to complete before the job is ready to be run |
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| 94 | |
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| 95 | **Page 1** |
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| 96 | |
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| 97 | give the job a mnemonic descriptive title and select the output format. |
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| 98 | |
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| 99 | Choose a file containing genotypes and a pedigree from your current history |
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| 100 | |
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| 101 | The input file must be in linkage ped format. |
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| 102 | |
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| 103 | If the data are not yet in your history, import from one of the system libraries or upload from your computer using the get data tool |
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| 104 | |
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| 105 | **Page 2** |
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| 106 | |
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| 107 | Define the markers to be used. You can supply a UCSC style location as chr:start_offset-end_offset |
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| 108 | |
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| 109 | or a list of marker ids - rs numbers. You can flip between marker input style by changing the select box. |
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| 110 | |
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| 111 | If you supply a list, the markers must all be from the same chromosome or region for sensible results. |
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| 112 | |
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| 113 | Run the job and the subset file will eventually appear in your history ready to be used with other tools. |
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| 114 | |
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| 115 | ----- |
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| 116 | |
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| 117 | **Syntax** |
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| 118 | |
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| 119 | - **Library Linkage Ped** is a linkage format pedigree file chosen from the system file Library |
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| 120 | - **History Linkage Ped** is a linkage format pedigree file chosen from your current Galaxy History |
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| 121 | - **Region** is the genomic region cut and paste from a UCSC browser location window |
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| 122 | - **Genome Build** is the version of the genome your markers are from - use hg18 for CAMP illumina data |
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| 123 | |
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| 124 | ----- |
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| 125 | |
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| 126 | .. class:: infomark |
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| 127 | |
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| 128 | **Summary** |
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| 129 | |
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| 130 | This tool is a special purpose tool to extract genotypes from genotype data in linkage |
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| 131 | pedigree format (separate map file) over a specified genomic region |
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| 132 | The region to be extracted can be described as UCSC browser location, or as a list of |
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| 133 | markers. |
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| 134 | |
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| 135 | It is possible to retain ALL markers by leaving the rslist and region empty if you just want to remove |
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| 136 | all offspring from a pedigree for example |
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| 137 | |
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| 138 | The extracted data will appear in your current history as a new lped data set |
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| 139 | |
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| 140 | Copyright, Ross Lazarus, March 2008 for the Rgenetics project |
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| 141 | Released under the LGPL. See http://www.gnu.org/licenses/lgpl.html for license terms. |
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| 142 | |
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| 143 | </help> |
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| 144 | </tool> |
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