Mercurial > repos > devteam > picard
annotate picard_MarkDuplicates.xml @ 15:a5a13ea16d17 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ebd6c8453b49dd6a36e372eb1eb6e323bb7ad8a
author | iuc |
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date | Tue, 19 Jun 2018 11:28:30 -0400 |
parents | 486d7500da69 |
children | d837223d4ad2 |
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486d7500da69
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
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1 <tool name="MarkDuplicates" id="picard_MarkDuplicates" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> |
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52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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2 <description>examine aligned records in BAM datasets to locate duplicate molecules</description> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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3 <macros> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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4 <import>picard_macros.xml</import> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ebd6c8453b49dd6a36e372eb1eb6e323bb7ad8a
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5 <token name="@WRAPPER_VERSION@">1</token> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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6 </macros> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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7 <expand macro="requirements" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
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8 <command detect_errors="exit_code"><![CDATA[ |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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9 @java_options@ |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
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10 @symlink_element_identifier@ |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
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11 picard |
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52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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12 MarkDuplicates |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
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13 |
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41b8d087a2d2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 74ee0f0b594075fab7f707aaffb4a7f9dac35f2f
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14 INPUT='$escaped_element_identifier' |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit a55cff7dfc145ed17ec2ee9f6a70d51c6f9d74b6
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15 OUTPUT='${outFile}' |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
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16 |
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a459ead5ab75
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit a55cff7dfc145ed17ec2ee9f6a70d51c6f9d74b6
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17 METRICS_FILE='${metrics_file}' |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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18 #for $element in $comments: |
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a459ead5ab75
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit a55cff7dfc145ed17ec2ee9f6a70d51c6f9d74b6
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19 COMMENT='${element.comment}' |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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20 #end for |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
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21 |
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a459ead5ab75
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit a55cff7dfc145ed17ec2ee9f6a70d51c6f9d74b6
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22 REMOVE_DUPLICATES='${remove_duplicates}' |
a459ead5ab75
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit a55cff7dfc145ed17ec2ee9f6a70d51c6f9d74b6
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23 ASSUME_SORTED='${assume_sorted}' |
a459ead5ab75
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit a55cff7dfc145ed17ec2ee9f6a70d51c6f9d74b6
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24 |
a459ead5ab75
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit a55cff7dfc145ed17ec2ee9f6a70d51c6f9d74b6
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25 DUPLICATE_SCORING_STRATEGY='${duplicate_scoring_strategy}' |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
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26 |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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27 #import pipes |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 3ce5dea3af8f4816b4a83914b53402aa84e08fca
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28 #if $read_name_regex: |
c7dd8d7946b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 3ce5dea3af8f4816b4a83914b53402aa84e08fca
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29 READ_NAME_REGEX=${ pipes.quote( str( $read_name_regex ) ) } |
c7dd8d7946b8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 3ce5dea3af8f4816b4a83914b53402aa84e08fca
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30 #end if |
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a459ead5ab75
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit a55cff7dfc145ed17ec2ee9f6a70d51c6f9d74b6
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31 OPTICAL_DUPLICATE_PIXEL_DISTANCE='${optical_duplicate_pixel_distance}' |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
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32 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit a55cff7dfc145ed17ec2ee9f6a70d51c6f9d74b6
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33 # Optional arguments |
a459ead5ab75
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit a55cff7dfc145ed17ec2ee9f6a70d51c6f9d74b6
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34 #if $barcode_tag: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 3ce5dea3af8f4816b4a83914b53402aa84e08fca
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35 BARCODE_TAG='${barcode_tag}' |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit a55cff7dfc145ed17ec2ee9f6a70d51c6f9d74b6
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36 #end if |
a459ead5ab75
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit a55cff7dfc145ed17ec2ee9f6a70d51c6f9d74b6
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37 |
a459ead5ab75
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit a55cff7dfc145ed17ec2ee9f6a70d51c6f9d74b6
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38 VALIDATION_STRINGENCY='${validation_stringency}' |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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39 QUIET=true |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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40 VERBOSITY=ERROR |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ebd6c8453b49dd6a36e372eb1eb6e323bb7ad8a
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41 @TMPDIR_OPTION@ |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
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42 |
08f69add4d06
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
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43 ]]></command> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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44 <inputs> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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45 <param format="bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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46 <repeat name="comments" title="Comment" min="0" help="You can provide multiple comments"> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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47 <param name="comment" type="text" label="Add this comment to BAM dataset"/> |
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48 </repeat> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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49 <param name="remove_duplicates" type="boolean" label="If true do not write duplicates to the output file instead of writing them with appropriate flags set" help="REMOVE_DUPLICATES; default=False"/> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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50 <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED; default=True"/> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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51 |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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52 <param name="duplicate_scoring_strategy" type="select" label="The scoring strategy for choosing the non-duplicate among candidates" help="DUPLICATE_SCORING_STRATEGY; default=SUM_OF_BASE_QUALITIES"> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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53 <option value="SUM_OF_BASE_QUALITIES">SUM_OF_BASE_QUALITIES</option> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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54 <option value="TOTAL_MAPPED_REFERENCE_LENGTH">TOTAL_MAPPED_REFERENCE_LENGTH</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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55 </param> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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56 |
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57 <param name="read_name_regex" type="text" value="" label="Regular expression that can be used in unusual situations to parse non-standard read names in the incoming SAM/BAM dataset" help="READ_NAME_REGEX; Read names are parsed to extract three variables: tile/region, x coordinate and y coordinate. These values are used to estimate the rate of optical duplication in order to give a more accurate estimated library size. See help below for more info; default='' (uses : separation)"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
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58 |
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59 <sanitizer> |
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60 <valid initial="string.printable"> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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61 </valid> |
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62 </sanitizer> |
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63 </param> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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64 <param name="optical_duplicate_pixel_distance" type="integer" value="100" min="0" max="500" label="The maximum offset between two duplicte clusters in order to consider them optical duplicates" help="OPTICAL_DUPLICATE_PIXEL_DISTANCE; default=100"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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65 |
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66 <param name="barcode_tag" type="text" optional="True" label="Barcode Tag" help="Barcode SAM tag. This tag can be utilized when you have data from an assay that includes Unique Molecular Indices."/> |
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67 |
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68 <expand macro="VS" /> |
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69 |
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70 </inputs> |
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71 |
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72 <outputs> |
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73 <data format="txt" name="metrics_file" label="${tool.name} on ${on_string}: MarkDuplicate metrics"/> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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74 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: MarkDuplicates BAM output"/> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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75 </outputs> |
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76 |
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77 <tests> |
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78 <test> |
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79 <param name="inputFile" value="picard_MarkDuplicates.bam" ftype="bam"/> |
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80 <param name="comment" value="test-run"/> |
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81 <param name="assume_sorted" value="True"/> |
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82 <param name="remove_duplicates" value="True"/> |
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83 <param name="read_name_regex" value=".*[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*"/> |
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84 <param name="optical_duplicate_pixel_distance" value="100"/> |
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85 <param name="duplicate_scoring_strategy" value="SUM_OF_BASE_QUALITIES"/> |
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86 <param name="validation_stringency" value="LENIENT"/> |
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87 <output name="outFile" file="picard_MarkDuplicates_test1.bam" ftype="bam" lines_diff="4"/> |
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88 </test> |
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89 <test> |
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90 <param name="inputFile" value="picard_MarkDuplicates.bam" ftype="bam"/> |
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91 <param name="comment" value="test-run"/> |
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92 <param name="assume_sorted" value="True"/> |
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93 <param name="remove_duplicates" value="False"/> |
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94 <param name="read_name_regex" value=""/> |
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95 <param name="optical_duplicate_pixel_distance" value="100"/> |
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96 <param name="duplicate_scoring_strategy" value="SUM_OF_BASE_QUALITIES"/> |
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97 <param name="validation_stringency" value="LENIENT"/> |
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98 <output name="outFile" file="picard_MarkDuplicates_test2.bam" ftype="bam" lines_diff="4"/> |
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99 </test> |
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100 </tests> |
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101 |
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102 |
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103 <help> |
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104 |
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105 **Purpose** |
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106 |
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107 Examines aligned records in the supplied SAM or BAM dataset to locate duplicate molecules. All records are then written to the output file with the duplicate records flagged. |
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108 |
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109 @dataset_collections@ |
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110 |
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111 @description@ |
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112 |
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113 COMMENT=String |
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114 CO=String Comment(s) to include in the output file's header. This option may be specified 0 or |
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115 more times. |
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116 |
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117 REMOVE_DUPLICATES=Boolean If true do not write duplicates to the output file instead of writing them with |
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118 appropriate flags set. Default value: false. |
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119 |
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120 READ_NAME_REGEX=String This option is only needed if your read names do not follow a standard illumina convention |
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121 of colon separation but do contain tile, x, and y coordinates (unusual). |
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122 A regular expression that can be used to parse read names in the incoming SAM file. Read |
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123 names are parsed to extract three variables: tile/region, x coordinate and y coordinate. |
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124 These values are used to estimate the rate of optical duplication in order to give a more |
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125 accurate estimated library size. Set this option to null to disable optical duplicate |
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126 detection. The regular expression should contain three capture groups for the three |
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127 variables, in order. It must match the entire read name. Note that if the default regex |
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128 is specified, a regex match is not actually done, but instead the read name is split on |
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129 colon character. For 5 element names, the 3rd, 4th and 5th elements are assumed to be |
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130 tile, x and y values. For 7 element names (CASAVA 1.8), the 5th, 6th, and 7th elements |
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131 are assumed to be tile, x and y values. Default value: '' |
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132 |
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133 |
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134 DUPLICATE_SCORING_STRATEGY=ScoringStrategy |
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135 DS=ScoringStrategy The scoring strategy for choosing the non-duplicate among candidates. Default value: |
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136 SUM_OF_BASE_QUALITIES. Possible values: {SUM_OF_BASE_QUALITIES, TOTAL_MAPPED_REFERENCE_LENGTH} |
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137 |
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138 OPTICAL_DUPLICATE_PIXEL_DISTANCE=Integer |
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139 The maximum offset between two duplicate clusters in order to consider them optical |
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140 duplicates. This should be set to 100 for (circa 2011+) read names and typical flowcells. |
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141 Structured flow cells (NovaSeq, HiSeq 4000, X) should use ~2500. |
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142 For older conventions, distances could be to some fairly small number (e.g. 5-10 pixels) |
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143 Default value: 100. |
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144 |
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145 BARCODE_TAG=String Barcode SAM tag (ex. BC for 10X Genomics) Default value: null. |
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146 |
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147 @more_info@ |
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148 |
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149 </help> |
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150 <expand macro="citations" /> |
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151 </tool> |