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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
author iuc
date Sun, 03 Mar 2024 16:06:11 +0000
parents f9242e01365a
children
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3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
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1 <tool name="FixMateInformation" id="picard_FixMateInformation" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@">
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
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2 <description>ensure that all mate-pair information is in sync between each read and it's mate pair</description>
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
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3 <macros>
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4 <import>picard_macros.xml</import>
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
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5 <token name="@WRAPPER_VERSION@">0</token>
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
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6 </macros>
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
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7 <expand macro="requirements"/>
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
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8 <command detect_errors="exit_code"><![CDATA[
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9 @java_options@
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3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
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10 picard FixMateInformation
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
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11 --INPUT '${inputFile}'
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
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12 --OUTPUT '${outFile}'
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13 --ASSUME_SORTED ${assume_sorted}
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
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14 --ADD_MATE_CIGAR ${add_mate_cigar}
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3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
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16 --SORT_ORDER coordinate
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17 --VALIDATION_STRINGENCY '${validation_stringency}'
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18 --QUIET true
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19 --VERBOSITY ERROR
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20
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21 ]]></command>
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22 <inputs>
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23 <param name="inputFile" multiple="True" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
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24 <param name="add_mate_cigar" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Adds the mate CIGAR tag (MC) if true, does not if false" help="ADD_MATE_CIGAR; default=True"/>
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
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25 <param name="assume_sorted" type="boolean" truevalue="True" falsevalue="False" label="Assume that the input file is QUERYNAME sorted" help="ASSUME_SORTED; default=False"/>
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
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26 <expand macro="VS"/>
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
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27 </inputs>
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
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28 <outputs>
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
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29 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: BAM with fixed mates"/>
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
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30 </outputs>
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
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31 <tests>
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
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32 <test>
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
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33 <param name="inputFile" value="picard_FixMateInformation.bam" ftype="bam"/>
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
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34 <param name="add_mate_cigar" value="True"/>
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
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35 <param name="assume_sorted" value="False"/>
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
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36 <param name="validation_stringency" value="LENIENT"/>
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
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37 <output name="outFile" file="picard_FixMateInformation_test1.bam" ftype="bam" lines_diff="4"/>
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
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38 </test>
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
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39 </tests>
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
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40 <help>
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41
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42 **Purpose**
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43
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44 Ensure that all mate-pair information is in sync between each read and it's mate pair. Reads marked with the secondary alignment flag are written to the output file unchanged.
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45
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46 ------
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47
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48 .. class:: warningmark
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49
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50 **Warning on using ASSUME_SORTED option**
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51
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52 Datasets imported into Galaxy are automatically coordinate sorted. So use this option (set it to True) only if you are sure that this is necessary. If you are not sure - a good rule of thumb
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53 is to assume that the BAM you are working with is coordinate sorted.
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54
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55 @dataset_collections@
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56
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57 @description@
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59 ASSUME_SORTED=Boolean
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60 AS=Boolean If true, assume that the input file is queryname sorted, even if the header says
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61 otherwise. Default value: false.
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63 ADD_MATE_CIGAR=Boolean
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64 MC=Boolean Adds the mate CIGAR tag (MC) if true, does not if false. Default value: true.
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65
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66 @more_info@
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68 </help>
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69 <expand macro="citations"/>
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70 </tool>