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author jjohnson
date Thu, 19 Oct 2017 10:05:54 -0400
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1 <?xml version="1.0"?>
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2 <tool id="defuse_bamfastq" name="Defuse BamFastq" version="@DEFUSE_VERSION@.1">
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3 <description>converts a bam file to fastq files.</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <requirements>
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8 <expand macro="defuse_requirement" />
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9 </requirements>
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10 <command>bamfastq
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11 #if $pair == True :
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12 $pair
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13 #end if
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14 #if $multiple == True :
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15 $multiple
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16 #end if
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17 #if $rename == True :
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18 $rename
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19 #end if
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20 -b $bamfile
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21 -1 $fastq1
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22 -2 $fastq2
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23 </command>
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24 <inputs>
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25 <param name="bamfile" type="data" format="bam" label="Bam file"/>
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26 <param name="pair" type="boolean" truevalue="-p" falsevalue="" checked="true" label="Name contains pair info as /1 /2."/>
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27 <param name="multiple" type="boolean" truevalue="-m" falsevalue="" checked="true" label="Bam contains multiple mappings per read."/>
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28 <param name="rename" type="boolean" truevalue="-r" falsevalue="" checked="true" label="Rename with integer IDs."/>
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29 </inputs>
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30 <stdio>
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31 <exit_code range="1:" level="fatal" description="Error" />
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32 </stdio>
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33 <outputs>
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34 <data format="fastqsanger" name="fastq1" label="fastq1" />
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35 <data format="fastqsanger" name="fastq2" label="fastq2" />
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36 </outputs>
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37 <tests>
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38 <test>
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39 <param name="bamfile" ftype="bam" value="tophat_out2h.bam" />
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40 <param name="pair" value="True" />
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41 <param name="multiple" value="True" />
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42 <param name="rename" value="True" />
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43 <output name="fastq1">
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44 <assert_contents>
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45 <has_text text="@test_mRNA_36_146_27/1" />
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46 <not_has_text text="@test_mRNA_36_146_27/2" />
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47 <not_has_text text="test_mRNA_150_290_0" />
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48 </assert_contents>
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49 </output>
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50 <output name="fastq2">
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51 <assert_contents>
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52 <has_text text="@test_mRNA_36_146_27/2" />
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53 <not_has_text text="@test_mRNA_36_146_27/1" />
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54 <not_has_text text="test_mRNA_150_290_0" />
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55 </assert_contents>
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56 </output>
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57 </test>
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58 </tests>
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59 <help>
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60 bamfastq converts a bam file input into a pair of fastq files that can be used as input to deFuse.
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61 </help>
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62 <expand macro="citations"/>
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63 </tool>