Mercurial > repos > chrisd > snipfinder

annotate variant_caller.xml @ 0:4b10ed36eb91 draft

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planemo upload for repository https://github.com/ChrisD11/snp_caller_dep commit 6abdb1a7169f828f14104fece8a69a81e92717f4
author chrisd
date Mon, 22 Feb 2016 19:43:25 -0500
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children d277ee3ce4e7
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4b10ed36eb91 planemo upload for repository https://github.com/ChrisD11/snp_caller_dep commit 6abdb1a7169f828f14104fece8a69a81e92717f4
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1 <tool id="variant_caller" name="Snip Finder identifies snips from single-end and paired-end data" version="0.1.0">
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2 <requirements>
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3 </requirements>
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4 <stdio>
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5 <exit_code range="1:" />
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6 </stdio>
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7 <command><![CDATA[
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8 $__tool_directory__/snp
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9 -amr_fp $input1
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10 #if $sam_type.mode == "single_end"
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11 -samse $sam_type.samse_input2
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12 $sam_type.best
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13 #else
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14 -sampe $sam_type.sampe_input2
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15 $sam_type.best
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16 #end if
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17 -out_fp $output1
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18 ]]></command>
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19 <inputs>
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20 <param type="data" name="input1" format="fasta" label="Specify fasta file"/>
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21 <conditional name="sam_type">
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22 <param name="mode" type="select" label="Specify sam file type">
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23 <option value="single_end"></option>
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24 <option value="paired_end"></option>
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25 </param>
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26 <when value="single_end">
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27 <param type="data" name="samse_input2" format="sam" label="Single-end SAM file"/>
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28 <param name="best" type="boolean" label="Filter on unique alignments"
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29 truevalue="-b" falsevalue="" />
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30 </when>
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31 <when value="paired_end">
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32 <param type="data" name="sampe_input2" format="sam" label="Paired-end SAM file"/>
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33 <param name="best" type="boolean" label="Filter on unique alignments"
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34 truevalue="-b" falsevalue="" />
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35 </when>
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36 </conditional>
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37 </inputs>
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38 <outputs>
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39 <data name="output1" format="tabular" />
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40 </outputs>
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41 <help><![CDATA[
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42
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43 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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44
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45 Program: SNP Caller
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46
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47 Contact: Chris Dean <cdean11@rams.colostate.edu>
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48
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49 Usage: snp [options]
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50
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51 Options:
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52
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53 -amr_fp amr database path
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54 -samse single-end sam file path
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55 -sampe paired-end sam file path
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56 -b filter on unique alignments
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57
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58
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59 ]]></help>
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60 </tool>