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1 <tool id="bam_to_sam" name="BAM-to-SAM" version="1.0.3">
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2 <requirements>
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3 <requirement type="package" version="0.1.18">samtools</requirement>
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4 </requirements>
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5 <description>converts BAM format to SAM format</description>
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6 <command interpreter="python">
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7 bam_to_sam.py
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8 --input1=$input1
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9 --output1=$output1
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10 $header
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11 </command>
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12 <inputs>
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13 <param name="input1" type="data" format="bam" label="BAM File to Convert" />
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14 <param name="header" type="boolean" truevalue="--header" falsevalue="" checked="False" label="Include header in output" />
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15 </inputs>
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16 <outputs>
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17 <data format="sam" name="output1" label="${tool.name} on ${on_string}: converted SAM" />
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18 </outputs>
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19 <tests>
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20 <test>
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21 <!--
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22 Bam-to-Sam command:
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23 samtools view -o bam_to_sam_out1.sam test-data/bam_to_sam_in1.bam
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24 bam_to_sam_in1.bam can be created from bam_to_sam_in1.sam
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25 -->
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26 <param name="input1" value="bam_to_sam_in1.bam" ftype="bam" />
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27 <param name="header" value="" />
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28 <output name="output1" file="bam_to_sam_out1.sam" sorted="True" />
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29 </test>
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30 <test>
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31 <!--
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32 Bam-to-Sam command:
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33 samtools view -o bam_to_sam_out2.sam test-data/bam_to_sam_in2.bam
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34 bam_to_sam_in2.bam can be created from bam_to_sam_in2.sam
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35 -->
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36 <param name="input1" value="bam_to_sam_in2.bam" ftype="bam" />
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37 <param name="header" value="" />
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38 <output name="output1" file="bam_to_sam_out2.sam" sorted="True" />
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39 </test>
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40 <test>
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41 <!--
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42 Bam-to-Sam command:
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43 samtools view -h -o bam_to_sam_out3.sam test-data/bam_to_sam_in1.bam
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44 bam_to_sam_in1.bam can be created from bam_to_sam_in1.sam
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45 -->
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46 <param name="input1" value="bam_to_sam_in1.bam" ftype="bam" />
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47 <param name="header" value="--header" />
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48 <output name="output1" file="bam_to_sam_out3.sam" sorted="True" lines_diff="6" /><!-- header param not working in func tests so won't produce correct 6-line header (fine in browser) -->
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49 </test>
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50 </tests>
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51 <help>
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52
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53 **What it does**
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54
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55 This tool uses the SAMTools_ toolkit to produce a SAM file from a BAM file.
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56
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57 .. _SAMTools: http://samtools.sourceforge.net/samtools.shtml
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58
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59 ------
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60
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61 **Citation**
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62
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63 For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. <http://www.ncbi.nlm.nih.gov/pubmed/19505943>`_
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64
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65 </help>
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66 </tool>
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