Mercurial > repos > devteam > picard
annotate picard_CollectAlignmentSummaryMetrics.xml @ 4:2589e6207cb4 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
author | devteam |
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date | Tue, 13 Oct 2015 12:27:49 -0400 |
parents | 52fdfc45590a |
children | 08f69add4d06 |
rev | line source |
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4
2589e6207cb4
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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1 <tool name="Collect Alignment Summary Metrics" id="picard_CASM" version="@TOOL_VERSION@.1"> |
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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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2 <description>writes a file containing summary alignment metrics</description> |
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3 <macros> |
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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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4 <import>picard_macros.xml</import> |
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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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5 </macros> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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6 <expand macro="requirements" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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7 <stdio> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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8 <exit_code range="1:" level="fatal"/> |
2589e6207cb4
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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9 </stdio> |
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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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10 <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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11 @java_options@ |
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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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12 ##set up input files |
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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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13 |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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14 #set $reference_fasta_filename = "localref.fa" |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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15 |
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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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16 #if str( $reference_source.reference_source_selector ) == "history": |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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17 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" && |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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18 #else: |
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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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19 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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20 #end if |
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2589e6207cb4
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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21 |
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52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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22 java -jar \$JAVA_JAR_PATH/picard.jar |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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23 CollectAlignmentSummaryMetrics |
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24 INPUT="${inputFile}" |
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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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25 OUTPUT="${outFile}" |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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26 MAX_INSERT_SIZE=${maxinsert} |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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27 #for $sequence in $adapters: |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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28 ADAPTER_SEQUENCE="${sequence.adapter}" |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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29 #end for |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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30 #for $level in str($metric_accumulation_level).split(','): |
2589e6207cb4
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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31 METRIC_ACCUMULATION_LEVEL="${level}" |
2589e6207cb4
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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32 #end for |
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52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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33 IS_BISULFITE_SEQUENCED="${bisulphite}" |
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2589e6207cb4
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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34 |
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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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35 REFERENCE_SEQUENCE="${reference_fasta_filename}" |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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36 |
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52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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37 ASSUME_SORTED="${assume_sorted}" |
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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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38 |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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39 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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40 QUIET=true |
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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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41 VERBOSITY=ERROR |
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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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42 |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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43 </command> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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44 <inputs> |
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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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45 <param format="sam,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 <conditional name="reference_source"> |
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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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47 <param name="reference_source_selector" type="select" label="Load reference genome from"> |
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48 <option value="cached">Local cache</option> |
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49 <option value="history">History</option> |
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50 </param> |
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51 <when value="cached"> |
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52 <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE"> |
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53 <options from_data_table="all_fasta"> |
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54 </options> |
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55 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> |
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56 </param> |
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57 </when> |
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58 <when value="history"> |
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59 <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence" help="REFERENCE_SEQUENCE; You can upload a FASTA sequence to the history and use it as reference" /> |
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60 </when> |
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61 </conditional> |
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62 <param name="metric_accumulation_level" type="select" label="The level(s) at which to accumulate metrics" multiple="true" help="METRIC_ACCUMULATION_LEVEL"> |
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63 <option value="ALL_READS" selected="True">All reads</option> |
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64 <option value="SAMPLE">Sample</option> |
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65 <option value="LIBRARY">Library</option> |
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66 <option value="READ_GROUP">Read group</option> |
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67 </param> |
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68 <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED"/> |
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69 <param name="bisulphite" type="boolean" label="Input file contains Bisulphite sequenced reads" checked="false" falsevalue="false" truevalue="true" help="IS_BISULFITE_SEQUENCED"/> |
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70 <repeat name="adapters" title="Adapter" min="0" help="You can provide multiple adaptor sequences"> |
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71 <param name="adapter" type="text" label="Use this adaptor sequence" help="ADAPTER_SEQUENCE"/> |
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72 </repeat> |
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73 <param name="maxinsert" value="100000" type="integer" label="Larger paired end reads and inter-chromosomal pairs considered chimeric" help="MAX_INSERT_SIZE"/> |
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74 <expand macro="VS" /> |
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75 |
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76 </inputs> |
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77 <outputs> |
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78 <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary stats"/> |
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79 </outputs> |
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80 <tests> |
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81 <test> |
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82 <param name="bisulphite" value="false" /> |
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83 <param name="sorted" value="true" /> |
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84 <param name="adaptors" value="" /> |
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85 <param name="maxinsert" value="100000" /> |
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86 <param name="reference_source_selector" value="history" /> |
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87 <param name="ref_file" value="picard_CASM_ref.fa" /> |
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88 <param name="inputFile" value="picard_CASM.bam" ftype="bam" /> |
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89 <output name="outFile" file="picard_CASM_test1.tab" ftype="tabular" lines_diff="4"/> |
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90 </test> |
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91 </tests> |
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92 <help> |
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93 |
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94 .. class:: infomark |
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95 |
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96 **Purpose** |
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97 |
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98 Reads a SAM or BAM file and writes a file containing summary alignment metrics. |
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99 |
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100 @dataset_collections@ |
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101 |
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102 @description@ |
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103 |
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104 MAX_INSERT_SIZE=Integer Paired end reads above this insert size will be considered chimeric along with |
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105 inter-chromosomal pairs. Default value: 100000. |
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106 |
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107 ADAPTER_SEQUENCE=String List of adapter sequences to use when processing the alignment metrics This option may |
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108 be specified 0 or more times. |
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109 |
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110 METRIC_ACCUMULATION_LEVEL=MetricAccumulationLevel |
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111 LEVEL=MetricAccumulationLevel The level(s) at which to accumulate metrics. Possible values: {ALL_READS, SAMPLE, |
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112 LIBRARY, READ_GROUP} This option may be specified 0 or more times. |
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113 |
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114 IS_BISULFITE_SEQUENCED=Boolean |
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115 BS=Boolean Whether the SAM or BAM file consists of bisulfite sequenced reads. |
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116 |
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117 |
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118 REFERENCE_SEQUENCE=File |
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119 R=File Reference sequence fasta Default value: null. |
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120 |
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121 ASSUME_SORTED=Boolean |
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122 AS=Boolean If true (default), then the sort order in the header file will be ignored. |
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123 |
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124 @more_info@ |
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125 |
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126 </help> |
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127 </tool> |
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128 |
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129 |