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annotate defuse_bamfastq.xml @ 22:68494d6aabeb

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Update datamanager and defuse.xml config file generation
author Jim Johnson <jj@umn.edu>
date Thu, 27 Jun 2013 13:11:50 -0500
parents 547d8db4673e
children 225750bf3770
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1 <?xml version="1.0"?>
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2 <tool id="defuse_bamfastq" name="Defuse BamFastq" version="0.6.1">
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3 <description>converts a bam file to fastq files.</description>
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4 <requirements>
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5 <requirement type="package" version="0.6.1">defuse</requirement>
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6 </requirements>
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7 <version_command>bamfastq --version</version_command>
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8 <command>bamfastq
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9 #if $pair == True :
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10 $pair
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11 #end if
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12 #if $multiple == True :
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13 $multiple
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14 #end if
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15 #if $rename == True :
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16 $rename
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17 #end if
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18 -b $bamfile
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19 -1 $fastq1
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20 -2 $fastq2
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21 </command>
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22 <inputs>
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23 <param name="bamfile" type="data" format="bam" label="Bam file"/>
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24 <param name="pair" type="boolean" truevalue="-p" falsevalue="" checked="true" label="Name contains pair info as /1 /2."/>
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25 <param name="multiple" type="boolean" truevalue="-m" falsevalue="" checked="true" label="Bam contains multiple mappings per read."/>
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26 <param name="rename" type="boolean" truevalue="-r" falsevalue="" checked="true" label="Rename with integer IDs."/>
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27 </inputs>
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28 <stdio>
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29 <exit_code range="1:" level="fatal" description="Error" />
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30 </stdio>
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31 <outputs>
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32 <data format="fastqsanger" name="fastq1" label="fastq1" />
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33 <data format="fastqsanger" name="fastq2" label="fastq2" />
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34 </outputs>
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35 <tests>
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36 <test>
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37 <param name="bamfile" ftype="bam" value="tophat_out2h.bam" />
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38 <param name="pair" value="True" />
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39 <param name="multiple" value="True" />
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40 <param name="rename" value="True" />
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41 <output name="fastq1">
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42 <assert_contents>
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43 <has_text text="@test_mRNA_36_146_27/1" />
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44 <not_has_text text="@test_mRNA_36_146_27/2" />
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45 <not_has_text text="test_mRNA_150_290_0" />
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46 </assert_contents>
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47 </output>
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48 <output name="fastq2">
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49 <assert_contents>
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50 <has_text text="@test_mRNA_36_146_27/2" />
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51 <not_has_text text="@test_mRNA_36_146_27/1" />
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52 <not_has_text text="test_mRNA_150_290_0" />
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53 </assert_contents>
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54 </output>
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55 </test>
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56 </tests>
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57 <help>
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58 bamfastq converts a bam file input into a pair of fastq files that can be used as input to deFuse.
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59 </help>
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60 </tool>