Mercurial > repos > devteam > picard
annotate picard_ValidateSamFile.xml @ 33:3f254c5ced1d draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
author | iuc |
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date | Sun, 03 Mar 2024 16:06:11 +0000 |
parents | f9242e01365a |
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rev | line source |
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3f254c5ced1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents:
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changeset
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1 <tool name="ValidateSamFile" id="picard_ValidateSamFile" 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
parents:
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2 <description>assess validity of SAM/BAM dataset</description> |
3f254c5ced1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents:
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3 <macros> |
3f254c5ced1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents:
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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
iuc
parents:
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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
iuc
parents:
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6 </macros> |
3f254c5ced1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents:
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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
iuc
parents:
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8 <stdio> |
3f254c5ced1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents:
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9 <exit_code range="1:" level="warning"/> |
3f254c5ced1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents:
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changeset
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10 </stdio> |
3f254c5ced1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents:
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11 <command><![CDATA[ |
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05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
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12 |
5 | 13 ##set the maximum number of open file to hard maximum or 4096 if on a mac (mac gives 'unlimited' as output of `ulimit -Hn` command |
12
05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
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14 |
05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
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15 [ `ulimit -Hn` = unlimited ] && ulimit -Sn 4096 || ulimit -Sn `ulimit -Hn` |
05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents:
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16 |
05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
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17 && |
05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
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18 |
5 | 19 ##set up input files |
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7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
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20 @symlink_element_identifier@ |
5 | 21 #set $reference_fasta_filename = "localref.fa" |
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05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents:
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22 |
5 | 23 #if str( $reference_source.reference_source_selector ) == "history": |
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3f254c5ced1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents:
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24 ln -sf '${reference_source.ref_file}' '${reference_fasta_filename}' && |
5 | 25 #else: |
26 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) | |
27 #end if | |
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05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents:
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28 |
5 | 29 @java_options@ |
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05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents:
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30 |
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3f254c5ced1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents:
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31 picard ValidateSamFile |
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05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents:
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32 |
33
3f254c5ced1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents:
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33 --INPUT '$escaped_element_identifier' |
3f254c5ced1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents:
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34 --OUTPUT '${outFile}' |
3f254c5ced1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents:
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35 --MODE '${mode}' |
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05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents:
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36 |
5 | 37 #if str( $ignore ) != "None": |
38 #for $element in str( $ignore ).split(','): ## See trello card https://trello.com/c/9nW02Zhd | |
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3f254c5ced1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents:
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39 --IGNORE '${element}' |
5 | 40 #end for |
41 #end if | |
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05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents:
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42 |
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3f254c5ced1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents:
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43 --MAX_OUTPUT '${max_output}' |
3f254c5ced1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents:
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44 --REFERENCE_SEQUENCE '${reference_fasta_filename}' |
3f254c5ced1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents:
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45 --IGNORE_WARNINGS '${ignore_warnings}' |
3f254c5ced1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents:
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46 --IS_BISULFITE_SEQUENCED '${is_bisulfite_sequenced}' |
3f254c5ced1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents:
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47 --MAX_OPEN_TEMP_FILES `ulimit -Sn` |
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05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
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48 |
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3f254c5ced1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents:
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49 --VERBOSITY ERROR |
3f254c5ced1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
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50 --QUIET true |
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05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents:
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51 |
05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
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52 ]]></command> |
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3f254c5ced1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents:
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53 <inputs> |
3f254c5ced1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents:
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54 <param format="sam,bam" name="inputFile" type="data" label="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
iuc
parents:
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55 <conditional name="reference_source"> |
3f254c5ced1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents:
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56 <param name="reference_source_selector" type="select" label="Load reference genome from"> |
3f254c5ced1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents:
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57 <option value="cached">Local cache</option> |
3f254c5ced1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents:
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58 <option value="history">History</option> |
3f254c5ced1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents:
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59 </param> |
3f254c5ced1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents:
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60 <when value="cached"> |
3f254c5ced1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents:
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61 <param name="ref_file" type="select" label="Use dictionary from the list" help="Select genome from the list"> |
3f254c5ced1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents:
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62 <options from_data_table="picard_indexes"> |
3f254c5ced1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents:
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63 <filter type="sort_by" column="2"/> |
3f254c5ced1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents:
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64 <validator type="no_options" message="No indexes are available"/> |
3f254c5ced1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents:
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65 </options> |
3f254c5ced1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents:
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66 <validator type="no_options" message="A built-in dictionary is not available for the build associated with the selected input file"/> |
3f254c5ced1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents:
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67 </param> |
3f254c5ced1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents:
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68 </when> |
3f254c5ced1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents:
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69 <when value="history"> |
3f254c5ced1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents:
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70 <param name="ref_file" type="data" format="fasta" label="Use the following dataset to create dictionary" help="You can upload a FASTA sequence to the history from which Picard will automatically generate dictionary using CreateSequenceDictionary command"/> |
3f254c5ced1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
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71 </when> |
3f254c5ced1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
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72 </conditional> |
3f254c5ced1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents:
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73 <param name="mode" type="select" label="Select output mode" help="MODE"> |
3f254c5ced1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
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74 <option value="VERBOSE">Verbose</option> |
3f254c5ced1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
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75 <option value="SUMMARY">Summary</option> |
5 | 76 </param> |
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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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77 <param name="ignore" type="select" multiple="true" display="checkboxes" label="Select validation error types to ignore" help="IGNORE"> |
3f254c5ced1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
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78 <option value="INVALID_QUALITY_FORMAT">INVALID_QUALITY_FORMAT</option> |
3f254c5ced1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
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79 <option value="INVALID_FLAG_PROPER_PAIR">INVALID_FLAG_PROPER_PAIR</option> |
3f254c5ced1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
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80 <option value="INVALID_FLAG_MATE_UNMAPPED">INVALID_FLAG_MATE_UNMAPPED</option> |
3f254c5ced1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
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81 <option value="MISMATCH_FLAG_MATE_UNMAPPED">MISMATCH_FLAG_MATE_UNMAPPED</option> |
3f254c5ced1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents:
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82 <option value="INVALID_FLAG_MATE_NEG_STRAND">INVALID_FLAG_MATE_NEG_STRAND</option> |
3f254c5ced1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
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83 <option value="MISMATCH_FLAG_MATE_NEG_STRAND">MISMATCH_FLAG_MATE_NEG_STRAND</option> |
3f254c5ced1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents:
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84 <option value="INVALID_FLAG_FIRST_OF_PAIR">INVALID_FLAG_FIRST_OF_PAIR</option> |
3f254c5ced1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
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85 <option value="INVALID_FLAG_SECOND_OF_PAIR">INVALID_FLAG_SECOND_OF_PAIR</option> |
3f254c5ced1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
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86 <option value="PAIRED_READ_NOT_MARKED_AS_FIRST_OR_SECOND">PAIRED_READ_NOT_MARKED_AS_FIRST_OR_SECOND</option> |
3f254c5ced1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
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87 <option value="INVALID_FLAG_NOT_PRIM_ALIGNMENT">INVALID_FLAG_NOT_PRIM_ALIGNMENT</option> |
3f254c5ced1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
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88 <option value="INVALID_FLAG_SUPPLEMENTARY_ALIGNMENT">INVALID_FLAG_SUPPLEMENTARY_ALIGNMENT</option> |
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89 <option value="INVALID_FLAG_READ_UNMAPPED">INVALID_FLAG_READ_UNMAPPED</option> |
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90 <option value="INVALID_INSERT_SIZE">INVALID_INSERT_SIZE</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
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91 <option value="INVALID_MAPPING_QUALITY">INVALID_MAPPING_QUALITY</option> |
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92 <option value="INVALID_CIGAR">INVALID_CIGAR</option> |
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93 <option value="ADJACENT_INDEL_IN_CIGAR">ADJACENT_INDEL_IN_CIGAR</option> |
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94 <option value="INVALID_MATE_REF_INDEX">INVALID_MATE_REF_INDEX</option> |
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95 <option value="MISMATCH_MATE_REF_INDEX">MISMATCH_MATE_REF_INDEX</option> |
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96 <option value="INVALID_REFERENCE_INDEX">INVALID_REFERENCE_INDEX</option> |
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97 <option value="INVALID_ALIGNMENT_START">INVALID_ALIGNMENT_START</option> |
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98 <option value="MISMATCH_MATE_ALIGNMENT_START">MISMATCH_MATE_ALIGNMENT_START</option> |
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99 <option value="MATE_FIELD_MISMATCH">MATE_FIELD_MISMATCH</option> |
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100 <option value="INVALID_TAG_NM">INVALID_TAG_NM</option> |
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101 <option value="MISSING_TAG_NM">MISSING_TAG_NM</option> |
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102 <option value="MISSING_HEADER">MISSING_HEADER</option> |
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103 <option value="MISSING_SEQUENCE_DICTIONARY">MISSING_SEQUENCE_DICTIONARY</option> |
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104 <option value="MISSING_READ_GROUP">MISSING_READ_GROUP</option> |
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105 <option value="RECORD_OUT_OF_ORDER">RECORD_OUT_OF_ORDER</option> |
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106 <option value="READ_GROUP_NOT_FOUND">READ_GROUP_NOT_FOUND</option> |
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107 <option value="RECORD_MISSING_READ_GROUP">RECORD_MISSING_READ_GROUP</option> |
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108 <option value="INVALID_INDEXING_BIN">INVALID_INDEXING_BIN</option> |
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109 <option value="MISSING_VERSION_NUMBER">MISSING_VERSION_NUMBER</option> |
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110 <option value="INVALID_VERSION_NUMBER">INVALID_VERSION_NUMBER</option> |
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111 <option value="TRUNCATED_FILE">TRUNCATED_FILE</option> |
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112 <option value="MISMATCH_READ_LENGTH_AND_QUALS_LENGTH">MISMATCH_READ_LENGTH_AND_QUALS_LENGTH</option> |
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113 <option value="EMPTY_READ">EMPTY_READ</option> |
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114 <option value="CIGAR_MAPS_OFF_REFERENCE">CIGAR_MAPS_OFF_REFERENCE</option> |
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115 <option value="MISMATCH_READ_LENGTH_AND_E2_LENGTH">MISMATCH_READ_LENGTH_AND_E2_LENGTH</option> |
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116 <option value="MISMATCH_READ_LENGTH_AND_U2_LENGTH">MISMATCH_READ_LENGTH_AND_U2_LENGTH</option> |
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117 <option value="E2_BASE_EQUALS_PRIMARY_BASE">E2_BASE_EQUALS_PRIMARY_BASE</option> |
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118 <option value="BAM_FILE_MISSING_TERMINATOR_BLOCK">BAM_FILE_MISSING_TERMINATOR_BLOCK</option> |
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119 <option value="UNRECOGNIZED_HEADER_TYPE">UNRECOGNIZED_HEADER_TYPE</option> |
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120 <option value="POORLY_FORMATTED_HEADER_TAG">POORLY_FORMATTED_HEADER_TAG</option> |
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121 <option value="HEADER_TAG_MULTIPLY_DEFINED">HEADER_TAG_MULTIPLY_DEFINED</option> |
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122 <option value="HEADER_RECORD_MISSING_REQUIRED_TAG">HEADER_RECORD_MISSING_REQUIRED_TAG</option> |
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123 <option value="INVALID_DATE_STRING">INVALID_DATE_STRING</option> |
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124 <option value="TAG_VALUE_TOO_LARGE">TAG_VALUE_TOO_LARGE</option> |
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125 <option value="INVALID_INDEX_FILE_POINTER">INVALID_INDEX_FILE_POINTER</option> |
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126 <option value="INVALID_PREDICTED_MEDIAN_INSERT_SIZE">INVALID_PREDICTED_MEDIAN_INSERT_SIZE</option> |
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127 <option value="DUPLICATE_READ_GROUP_ID">DUPLICATE_READ_GROUP_ID</option> |
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128 <option value="MISSING_PLATFORM_VALUE">MISSING_PLATFORM_VALUE</option> |
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129 <option value="INVALID_PLATFORM_VALUE">INVALID_PLATFORM_VALUE</option> |
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130 <option value="DUPLICATE_PROGRAM_GROUP_ID">DUPLICATE_PROGRAM_GROUP_ID</option> |
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131 <option value="MATE_NOT_FOUND">MATE_NOT_FOUND</option> |
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132 <option value="MATES_ARE_SAME_END">MATES_ARE_SAME_END</option> |
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133 <option value="MISMATCH_MATE_CIGAR_STRING">MISMATCH_MATE_CIGAR_STRING</option> |
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134 <option value="MATE_CIGAR_STRING_INVALID_PRESENCE">MATE_CIGAR_STRING_INVALID_PRESENCE</option> |
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135 </param> |
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136 <param name="max_output" type="integer" value="100" label="The maximum number of lines output in verbose mode" help="MAX_OUTPUT; default=100"/> |
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137 <param name="ignore_warnings" type="boolean" label="If true, only report errors and ignore warnings" help="IGNORE_WARNINGS; default=False"/> |
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138 <param name="validate_index" type="boolean" checked="True" label="If true and input is a BAM file with an index file, also validates the index" help="VALIDATE_INDEX; default=True"/> |
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139 <param name="is_bisulfite_sequenced" type="boolean" label="Whether the SAM or BAM file consists of bisulfite sequenced reads" help="IS_BISULFITE_SEQUENCED; If so, C->T is not counted as an error in computing the value of the NM tag; default=False"/> |
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140 </inputs> |
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141 <outputs> |
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142 <data format="txt" name="outFile" label="${tool.name} on ${on_string}: BAM validation summary"/> |
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143 </outputs> |
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144 <tests> |
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145 <test> |
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146 <param name="inputFile" value="picard_ValidateSamFile.bam" ftype="bam"/> |
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147 <param name="reference_source_selector" value="history"/> |
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148 <param name="ref_file" value="picard_ValidateSamFile_ref.fa"/> |
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149 <param name="mode" value="VERBOSE"/> |
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150 <param name="ignore" value="INVALID_QUALITY_FORMAT,INVALID_FLAG_PROPER_PAIR"/> |
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151 <param name="max_output" value="100"/> |
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152 <param name="ignore_warnings" value="Fasle"/> |
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153 <param name="validate_index" value="True"/> |
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154 <param name="is_bisulfite_sequenced" value="False"/> |
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155 <output name="outFile" file="picard_ValidateSamFile_test1.txt" ftype="txt"/> |
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156 </test> |
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157 </tests> |
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158 <help> |
5 | 159 |
160 **Purpose** | |
161 | |
162 Reads a SAM/BAM dataset and report on its validity. | |
163 | |
164 @dataset_collections@ | |
165 | |
166 @description@ | |
167 | |
168 MODE=Mode | |
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169 M=Mode Mode of output Default value: VERBOSE. This option can be set to 'null' to clear the |
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170 default value. Possible values: {VERBOSE, SUMMARY} |
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171 |
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172 IGNORE=Type List of validation error types to ignore. Possible values: {INVALID_QUALITY_FORMAT, |
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173 INVALID_FLAG_PROPER_PAIR, INVALID_FLAG_MATE_UNMAPPED, MISMATCH_FLAG_MATE_UNMAPPED, |
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174 INVALID_FLAG_MATE_NEG_STRAND, MISMATCH_FLAG_MATE_NEG_STRAND, INVALID_FLAG_FIRST_OF_PAIR, |
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175 INVALID_FLAG_SECOND_OF_PAIR, PAIRED_READ_NOT_MARKED_AS_FIRST_OR_SECOND, |
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176 INVALID_FLAG_NOT_PRIM_ALIGNMENT, INVALID_FLAG_SUPPLEMENTARY_ALIGNMENT, |
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177 INVALID_FLAG_READ_UNMAPPED, INVALID_INSERT_SIZE, INVALID_MAPPING_QUALITY, INVALID_CIGAR, |
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178 ADJACENT_INDEL_IN_CIGAR, INVALID_MATE_REF_INDEX, MISMATCH_MATE_REF_INDEX, |
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179 INVALID_REFERENCE_INDEX, INVALID_ALIGNMENT_START, MISMATCH_MATE_ALIGNMENT_START, |
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180 MATE_FIELD_MISMATCH, INVALID_TAG_NM, MISSING_TAG_NM, MISSING_HEADER, |
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181 MISSING_SEQUENCE_DICTIONARY, MISSING_READ_GROUP, RECORD_OUT_OF_ORDER, |
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182 READ_GROUP_NOT_FOUND, RECORD_MISSING_READ_GROUP, INVALID_INDEXING_BIN, |
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183 MISSING_VERSION_NUMBER, INVALID_VERSION_NUMBER, TRUNCATED_FILE, |
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184 MISMATCH_READ_LENGTH_AND_QUALS_LENGTH, EMPTY_READ, CIGAR_MAPS_OFF_REFERENCE, |
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185 MISMATCH_READ_LENGTH_AND_E2_LENGTH, MISMATCH_READ_LENGTH_AND_U2_LENGTH, |
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186 E2_BASE_EQUALS_PRIMARY_BASE, BAM_FILE_MISSING_TERMINATOR_BLOCK, UNRECOGNIZED_HEADER_TYPE, |
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187 POORLY_FORMATTED_HEADER_TAG, HEADER_TAG_MULTIPLY_DEFINED, |
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188 HEADER_RECORD_MISSING_REQUIRED_TAG, INVALID_DATE_STRING, TAG_VALUE_TOO_LARGE, |
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189 INVALID_INDEX_FILE_POINTER, INVALID_PREDICTED_MEDIAN_INSERT_SIZE, |
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190 DUPLICATE_READ_GROUP_ID, MISSING_PLATFORM_VALUE, INVALID_PLATFORM_VALUE, |
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191 DUPLICATE_PROGRAM_GROUP_ID, MATE_NOT_FOUND, MATES_ARE_SAME_END, |
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192 MISMATCH_MATE_CIGAR_STRING, MATE_CIGAR_STRING_INVALID_PRESENCE} This option may be |
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193 specified 0 or more times. |
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194 |
5 | 195 MAX_OUTPUT=Integer |
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196 MO=Integer The maximum number of lines output in verbose mode Default value: 100. This option can |
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197 be set to 'null' to clear the default value. |
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198 |
5 | 199 REFERENCE_SEQUENCE=File |
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200 R=File Reference sequence file, the NM tag check will be skipped if this is missing Default |
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201 value: null. |
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202 |
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203 IGNORE_WARNINGS=Boolean If true, only report errors and ignore warnings. Default value: false. This option can |
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204 be set to 'null' to clear the default value. Possible values: {true, false} |
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205 |
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206 VALIDATE_INDEX=Boolean If true and input is a BAM file with an index file, also validates the index. Default |
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207 value: true. This option can be set to 'null' to clear the default value. Possible |
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208 values: {true, false} |
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209 |
5 | 210 IS_BISULFITE_SEQUENCED=Boolean |
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211 BISULFITE=Boolean Whether the SAM or BAM file consists of bisulfite sequenced reads. If so, C->T is not |
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212 counted as an error in computing the value of the NM tag. Default value: false. This |
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213 option can be set to 'null' to clear the default value. Possible values: {true, false} |
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214 |
5 | 215 @more_info@ |
216 | |
217 </help> | |
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218 <expand macro="citations"/> |
5 | 219 </tool> |