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1 <tool name="Collect Alignment Summary Metrics" id="picard_CASM" version="1.126.0">
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2 <description>writes a file containing summary alignment metrics</description>
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3 <requirements>
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4 <requirement type="package" version="1.126.0">picard</requirement>
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5 </requirements>
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6
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7 <macros>
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8 <import>picard_macros.xml</import>
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9 </macros>
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10
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11 <command>
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12 @java_options@
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13 ##set up input files
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14
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15 #set $reference_fasta_filename = "localref.fa"
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16
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17 #if str( $reference_source.reference_source_selector ) == "history":
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18 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &&
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19 #else:
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20 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
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21 #end if
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22
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23 java -jar \$JAVA_JAR_PATH/picard.jar
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24 CollectAlignmentSummaryMetrics
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25 INPUT="${inputFile}"
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26 OUTPUT="${outFile}"
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27 MAX_INSERT_SIZE=${maxinsert}
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28 #for $sequence in $adapters:
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29 ADAPTER_SEQUENCE="${sequence.adapter}"
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30 #end for
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31 METRIC_ACCUMULATION_LEVEL="${metric_accumulation_level}"
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32 IS_BISULFITE_SEQUENCED="${bisulphite}"
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33
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34 REFERENCE_SEQUENCE="${reference_fasta_filename}"
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35
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36 ASSUME_SORTED="${assume_sorted}"
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37
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38 VALIDATION_STRINGENCY="${validation_stringency}"
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39 QUIET=true
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40 VERBOSITY=ERROR
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41
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42 </command>
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43 <inputs>
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44 <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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45 <conditional name="reference_source">
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46 <param name="reference_source_selector" type="select" label="Load reference genome from">
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47 <option value="cached">Local cache</option>
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48 <option value="history">History</option>
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49 </param>
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50 <when value="cached">
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51 <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE">
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52 <options from_data_table="all_fasta">
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53 </options>
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54 <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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55 </param>
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56 </when>
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57 <when value="history">
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58 <param name="ref_file" type="data" format="fasta" label="Use the folloing 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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59 </when>
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60 </conditional>
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61 <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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62 <option value="ALL_READS" selected="True">All reads</option>
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63 <option value="SAMPLE">Sample</option>
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64 <option value="LIBRARY">Library</option>
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65 <option value="READ_GROUP">Read group</option>
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66 </param>
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67 <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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68 <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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69 <repeat name="adapters" title="Adapter" min="0" help="You can provide multiple adaptor sequences">
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70 <param name="adapter" type="text" size="50" label="Use this adaptor sequence" help="ADAPTER_SEQUENCE"/>
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71 </repeat>
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72 <param name="maxinsert" value="100000" type="integer" label="Larger paired end reads and inter-chromosomal pairs considered chimeric" size="20" help="MAX_INSERT_SIZE"/>
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73
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74 <expand macro="VS" />
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75
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76 </inputs>
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77
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78 <outputs>
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79 <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary stats"/>
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80 </outputs>
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81
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82 <stdio>
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83 <exit_code range="1:" level="fatal"/>
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84 </stdio>
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85
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86
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87 <tests>
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88 <test>
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89 <param name="bisulphite" value="false" />
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90 <param name="sorted" value="true" />
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91 <param name="adaptors" value="" />
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92 <param name="maxinsert" value="100000" />
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93 <param name="reference_source_selector" value="history" />
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94 <param name="ref_file" value="picard_CASM_ref.fa" />
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95 <param name="inputFile" value="picard_CASM.bam" ftype="bam" />
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96 <output name="outFile" file="picard_CASM_test1.tab" ftype="tabular" lines_diff="4"/>
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97 </test>
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98 </tests>
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99
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100 <help>
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101
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102 .. class:: infomark
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103
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104 **Purpose**
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105
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106 Reads a SAM or BAM file and writes a file containing summary alignment metrics.
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107
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108 @dataset_collections@
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109
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110 @description@
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111
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112 MAX_INSERT_SIZE=Integer Paired end reads above this insert size will be considered chimeric along with
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113 inter-chromosomal pairs. Default value: 100000.
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114
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115 ADAPTER_SEQUENCE=String List of adapter sequences to use when processing the alignment metrics This option may
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116 be specified 0 or more times.
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117
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118 METRIC_ACCUMULATION_LEVEL=MetricAccumulationLevel
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119 LEVEL=MetricAccumulationLevel The level(s) at which to accumulate metrics. Possible values: {ALL_READS, SAMPLE,
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120 LIBRARY, READ_GROUP} This option may be specified 0 or more times.
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121
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122 IS_BISULFITE_SEQUENCED=Boolean
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123 BS=Boolean Whether the SAM or BAM file consists of bisulfite sequenced reads.
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124
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125
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126 REFERENCE_SEQUENCE=File
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127 R=File Reference sequence fasta Default value: null.
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128
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129 ASSUME_SORTED=Boolean
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130 AS=Boolean If true (default), then the sort order in the header file will be ignored.
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131
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132 @more_info@
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133
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134 </help>
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135 </tool>
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136
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137
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