Mercurial > repos > chrisd > snipfinder

annotate variant_caller.xml @ 3:61b6570a752e draft

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planemo upload for repository https://github.com/ChrisD11/snp_caller_dep commit 5f7fc159c80a8548b1edba582e5fe84064f09281
author chrisd
date Mon, 22 Feb 2016 21:08:37 -0500
parents bc3b8b21e62b
children b40e1a5130db
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1 <tool id="variant_caller" name="Snip Finder" version="0.1.0">
0
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2 <requirements>
2
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3 <requirement type="package" version="0.1">snp</requirement>
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4 </requirements>
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5 <stdio>
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6 <exit_code range="1:" />
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7 </stdio>
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8 <command><![CDATA[
1
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9 snp
0
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10 -amr_fp $input1
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11 #if $sam_type.mode == "single_end"
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12 -samse $sam_type.samse_input2
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13 $sam_type.best
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14 #else
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15 -sampe $sam_type.sampe_input2
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16 $sam_type.best
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17 #end if
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18 -out_fp $output1
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19 ]]></command>
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20 <inputs>
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21 <param type="data" name="input1" format="fasta" label="Specify fasta file"/>
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22 <conditional name="sam_type">
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23 <param name="mode" type="select" label="Specify sam file type">
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24 <option value="single_end"></option>
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25 <option value="paired_end"></option>
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26 </param>
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27 <when value="single_end">
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28 <param type="data" name="samse_input2" format="sam" label="Single-end SAM file"/>
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29 <param name="best" type="boolean" label="Filter on unique alignments"
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30 truevalue="-b" falsevalue="" />
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31 </when>
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32 <when value="paired_end">
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33 <param type="data" name="sampe_input2" format="sam" label="Paired-end SAM file"/>
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34 <param name="best" type="boolean" label="Filter on unique alignments"
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35 truevalue="-b" falsevalue="" />
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36 </when>
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37 </conditional>
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38 </inputs>
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39 <outputs>
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40 <data name="output1" format="tabular" />
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41 </outputs>
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42 <help><![CDATA[
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43
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44 This program parses a SAM file and looks for single nucleotide polymorphisms (SNPs). In single-end mode, only alignments with bit four not set are considered. In paired-end mode, only reads that mapped in a proper pair are considered. When filtering on unique alignments, only alignments with the XT:A:U field are considered.
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45
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46 Program: SNP Caller
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47
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48 Contact: Chris Dean <cdean11@rams.colostate.edu>
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49
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50 Usage: snp [options]
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51
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52 Options:
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53
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54 -amr_fp amr database path
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55 -samse single-end sam file path
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56 -sampe paired-end sam file path
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57 -b filter on unique alignments
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58
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59
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60 ]]></help>
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61 </tool>