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1 <tool name="Picard SAM Format Converter" id="picard_SFC" version="0.1.0">
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2 <requirements><requirement type="package">picard</requirement></requirements>
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3 <command interpreter="python">
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4 picard_wrapper.py
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5 --input="$inputFile"
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6 --output-format=$outputFormat
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7 --output=$outFile
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8 -j "\$JAVA_JAR_PATH/SamFormatConverter.jar"
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9 </command>
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10 <inputs>
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11 <param format="bam,sam" name="inputFile" type="data" label="SAM/BAM"
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12 help="If empty, upload or import a SAM/BAM dataset." />
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13 <param name="outputFormat" type="boolean" checked="True" truevalue="bam" falsevalue="sam" label="Output bam instead of sam" help="Uncheck for sam output"/>
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14 </inputs>
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15 <outputs>
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16 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: ${outputFormat} with read groups replaced">
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17 <change_format>
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18 <when input="outputFormat" value="sam" format="sam" />
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19 </change_format>
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20 </data>
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21 </outputs>
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22 <tests>
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23 <test>
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24 <!-- Command for replacing read groups in bam:
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25 java -jar SamFormatConverter.jar VALIDATION_STRINGENCY=LENIENT I=test-data/picard_SFC_input1.sam O=picard_SFC_output1.sam·
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26 -->
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27 <param name="inputFile" value="picard_ARRG_input1.bam" />
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28 <param name="outputFormat" value="False" />
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29 <output name="outFile" file="picard_ARRG_output1.sam" ftype="sam" />
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30 </test>
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31 <test>
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32 <!-- Command for replacing read groups in sam:
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33 java -jar AddOrReplaceReadGroups.jar VALIDATION_STRINGENCY=LENIENT I=test-data/picard_ARRG_input1.sam O=picard_ARRG_output2.sam RGLB=LIB RGPL=IL RGPU=PL
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34 picard_ARRG_input1.bam can be created from picard_ARRG_input1.sam
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35 -->
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36 <param name="inputFile" value="picard_ARRG_input1.sam" />
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37 <output name="outFile" file="picard_ARRG_output2.sam" ftype="sam" />
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38 </test>
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39 </tests>
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40 <help>
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41
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42 .. class:: infomark
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43
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44 **Purpose**
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45
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46 Convert a BAM file to a SAM file, or BAM to SAM.
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47
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48 This is a Galaxy wrapper for SamFormatConverter, a part of the external package Picard-tools_.
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49
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50 .. _Picard-tools: http://www.google.com/search?q=picard+samtools
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51
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52 ------
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53
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54 .. class:: infomark
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55
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56 **Inputs, outputs, and parameters**
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57
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58 Either a sam file or a bam file must be supplied. If a bam file is used, it must
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59 be coordinate-sorted. Galaxy currently coordinate-sorts all bam files.
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60
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61 The output file is either bam (the default) or sam, according to user selection,
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62 and contains the same information as the input file except for the appropraite
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63 additional (or modified) read group tags. Bam is recommended since it is smaller.
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64
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65 **Warning on SAM/BAM quality**
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66
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67 Many SAM/BAM files produced externally and uploaded to Galaxy do not fully conform to SAM/BAM specifications. Galaxy deals with this by using the **LENIENT**
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68 flag when it runs Picard, which allows reads to be discarded if they're empty or don't map. This appears
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69 to be the only way to deal with SAM/BAM that cannot be parsed.
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70
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71
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72 </help>
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73 </tool>
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74
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