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1 <tool id="muse_call" name="muse call" version="1.0.rc">
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2 <description>First step of somatic point mutation caller for tumor-normal paired samples in next-generation sequencing data.</description>
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3 <requirements>
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4 <requirement type="package" version="1.0.rc" >muse</requirement>
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5 <requirement type="package" version="1.7">samtools</requirement>
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6 </requirements>
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1
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7 <macros>
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8 <import>muse_macros.xml</import>
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9 </macros>
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10 <command> <![CDATA[
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11 ##creation of the bam indexes and execution of the MuSE call command with all the advanced options
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12
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13 samtools index $input2 2> log && samtools index $input3 2>log &&
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14
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15 MuSE call -O variant_call
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16 #if $reference_source.reference_source_selector == "history"
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17 -f $reference_source.reference
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18 #end if
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19 #if $reference_source.reference_source_selector == "cached"
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20 -f $reference_source.ref_file.fields.path
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21 #end if
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22
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23 $input2 $input3
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24
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25 #if $region
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26 -r $region
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27 #end if
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28 #if $positions
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29 -l $positions
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30 #end if]]>
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31 </command>
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32 <inputs>
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33 <expand macro="reference_loc"/>
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34 <param format="bam" name="input2" type="data" label="tumor bam" help="tumor sample bamfile"/>
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35 <param format="bam" name="input3" type="data" label="normal bam" help="normal sample bamfile"/>
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36 <param name="region" type="text" optional="true" label="region" help="(chr:pos-pos)"/>
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37 <param format="txt,bed" name="positions" type="data" optional="true" label="list of regions" help="file txt or BED (chr:pos-pos or BED),with one region per line" />
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38 </inputs>
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39 <outputs>
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40 <data format="txt" name="output" from_work_dir="variant_call.MuSE.txt" label="${tool.name} on ${on_string}"/>
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41 </outputs>
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42 <tests>
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43 <test>
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44 <param name="input1" value="test_fasta.fa" ftype="fasta"/>
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45 <param name="input2" value="Muse_test_tumoral.bam"/>
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46 <param name="input3" value="Muse_test_normal.bam"/>
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47 <output name="output" file="results.txt" lines_diff="8"/>
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48 </test>
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49 </tests>
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50 <help>
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51 **MuSE call**, takes as input the indexed reference genome FASTA file and the BAM file from normal and tumoral sample.
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52 The BAM files require aligning all the sequence reads against the reference genome using the Burrows-Wheeler alignment tool (BWA),
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53 with either the backtrack or the maximal exact matches (MEM) algorithm. In addition,
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54 the BAM files need to be processed by following the Genome Analysis Toolkit (GATK) Best Practices that include:
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55 Marking duplicates,realigning the paired tumor-normal BAMs jointly recalibrating base quality scores.
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56 More information at MuSE: http://bioinformatics.mdanderson.org/main/MuSE
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57
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58 Galaxy wrapper for MuSE call implements all options available through the command line. Supported options are described below.
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59
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60 Usage: MuSE call [options] tumor.bam matched_normal.bam
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61 Options:
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62 -f FILE faidx indexed reference sequence file
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63 -r STR single region (chr:pos-pos) where somatic
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64 mutations are called
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65 -l FILE list of regions (chr:pos-pos or BED), one
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66 region per line
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67 -O STR output file name (suffix '.MuSE.txt' is
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68 automatically added)
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69 </help>
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70 <citations>
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71 <citation type="doi">10.1186/s13059-016-1029-6</citation>
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72 </citations>
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73 </tool>
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