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1 <tool name="Paired Read Mate Fixer" id="rgPicFixMate" version="1.56.0">
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2 <description>for paired data</description>
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3 <command interpreter="python">
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4 picard_wrapper.py -i "${input_file}" -o "${out_file}" --tmpdir "${__new_file_path__}" -n "${out_prefix}"
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5 --output-format "${outputFormat}" -j "\$JAVA_JAR_PATH/FixMateInformation.jar" --sortorder "${sortOrder}"
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6 </command>
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7 <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements>
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8 <inputs>
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9 <param format="bam,sam" name="input_file" type="data" label="SAM/BAM dataset to fix"
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10 help="If empty, upload or import a SAM/BAM dataset."/>
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11 <param name="sortOrder" type="select" help="If in doubt, leave as default and read Picard/Samtools documentation"
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12 label="Sort order">
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13 <option value="coordinate" selected ="true">Coordinate sort</option>
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14 <option value="queryname">Query name sort</option>
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15 <option value="unsorted">Unsorted - docs not clear if this means unchanged or not</option>
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16 </param>
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17 <param name="out_prefix" value="Fix Mate" type="text"
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18 label="Title for the output file" help="Use this remind you what the job was for." size="80" />
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19 <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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20 </inputs>
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21 <outputs>
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22 <data format="bam" name="out_file" label="${tool.name} on ${on_string}: ${outputFormat} with fixed mates">
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23 <change_format>
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24 <when input="outputFormat" value="sam" format="sam" />
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25 </change_format>
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26 </data>
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27 </outputs>
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28 <tests>
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29 <test>
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30 <param name="input_file" value="picard_input_sorted_pair.sam" />
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31 <param name="sortOrder" value="coordinate" />
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32 <param name="outputFormat" value="True" />
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33 <param name="out_prefix" value="Test FixMate" />
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34 <output name="out_file" file="picard_output_fixmate_sorted_pair.bam" ftype="bam" />
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35 </test>
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36 <test>
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37 <param name="input_file" value="picard_input_sorted_pair.sam" />
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38 <param name="sortOrder" value="coordinate" />
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39 <param name="outputFormat" value="False" />
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40 <param name="out_prefix" value="Test FixMate" />
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41 <output name="out_file" file="picard_output_fixmate_sorted_pair.sam" ftype="sam" />
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42 </test>
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43 </tests>
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44 <help>
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45
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46
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47 .. class:: infomark
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48
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49 **Purpose**
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50
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51 Ensure that all mate-pair information is in sync between each read and it's mate pair.
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52
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53 **Picard documentation**
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54
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55 This is a Galaxy wrapper for FixMateInformation, a part of the external package Picard-tools_.
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56
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57 .. _Picard-tools: http://www.google.com/search?q=picard+samtools
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58
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59 .. class:: warningmark
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60
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61 **Useful for paired data only**
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62
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63 Likely won't do anything helpful for single end sequence data
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64 Currently, Galaxy doesn't distinguish paired from single ended SAM/BAM so make sure
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65 the data you choose are valid (paired end) SAM or BAM data - unless you trust this
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66 tool not to harm your data.
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67
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68 -----
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69
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70 .. class:: infomark
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71
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72 **Syntax**
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73
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74 - **Input** - a paired read sam/bam format aligned short read data in your current history
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75 - **Sort order** - can be used to adjust the ordering of reads
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76 - **Title** - the title to use for all output files from this job - use it for high level metadata
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77 - **Output Format** - either SAM or compressed as BAM
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78
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79 -----
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80
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81 .. class:: infomark
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82
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83 **Inputs, outputs, and parameters**
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84
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85 .. csv-table::
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86
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87 :header-rows: 1
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88
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89 Option,Description
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90 "INPUT=File","The input file to fix. This option may be specified 0 or more times."
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91 "OUTPUT=File","The output file to write to"
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92 "SORT_ORDER=SortOrder","Optional sort order if the OUTPUT file should be sorted differently than the INPUT file. Default value: null. Possible values: {unsorted, queryname, coordinate}"
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93 "CREATE_MD5_FILE=Boolean","Whether to create an MD5 digest for any BAM files created. Default value: false"
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94
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95 .. class:: warningmark
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96
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97 **Warning on SAM/BAM quality**
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98
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99 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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100 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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101 to be the only way to deal with SAM/BAM that cannot be parsed.
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102
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103
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104 </help>
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105 </tool>
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106
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107
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