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1 <tool name="MeanQualityByCycle" id="picard_MeanQualityByCycle" version="1.106.0">
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2 <description>Calculates mean quality</description>
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3 <requirements><requirement type="package" version="1.106.0">picard</requirement></requirements>
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4 <command interpreter="bash">
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5 <!-- generic_outformat_wrapper.sh MeanQualityByCycle $outFile $outputFormat
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6 CHART_OUTPUT=File A file (with .pdf extension) to write the chart to. Required.
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7
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8 #if str( $ALIGNED_READS_ONLY ):
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9 ALIGNED_READS_ONLY="${ALIGNED_READS_ONLY}"
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10 #end if
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11 #if str( $PF_READS_ONLY ):
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12 PF_READS_ONLY="${PF_READS_ONLY}"
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13 #end if
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14 #if str( $INPUT ):
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15 INPUT="${INPUT}"
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16 #end if
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17 #if str( $OUTPUT ):
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18 OUTPUT="${OUTPUT}"
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19 #end if
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20 #if str( $REFERENCE_SEQUENCE ):
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21 REFERENCE_SEQUENCE="${REFERENCE_SEQUENCE}"
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22 #end if
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23 #if str( $ASSUME_SORTED ):
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24 ASSUME_SORTED="${ASSUME_SORTED}"
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25 #end if
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26 #if str( $STOP_AFTER ):
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27 STOP_AFTER="${STOP_AFTER}"
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28 #end if
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29
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30 VALIDATION_STRINGENCY=LENIENT
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31 QUIET=True
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32 TMP_DIR="${__new_file_path__}" -->
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33 </command>
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34
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35 <stdio>
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36 <exit_code range="0" level="warning" description="Tool finished correctly" />
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37 </stdio>
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38
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39 <inputs>
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40 <!--
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41 <param format="XXCHANGEMEEE" name="ALIGNED_READS_ONLY" type="boolean" label="If set to true, calculate mean quality over aligned reads only. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}" help="" />
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42 <param format="XXCHANGEMEEE" name="PF_READS_ONLY" type="boolean" label="If set to true calculate mean quality over PF reads only. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}" help="" />
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43 <param format="XXCHANGEMEEE" name="INPUT" type="data" label="Input SAM or BAM file. Required." help="" />
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44 <param format="XXCHANGEMEEE" name="OUTPUT" type="data" label="File to write the output to. Required." help="" />
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45 <param format="XXCHANGEMEEE" name="REFERENCE_SEQUENCE" type="data" label="Reference sequence fasta Default value: null." help="" />
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46 <param format="XXCHANGEMEEE" name="ASSUME_SORTED" type="boolean" label="If true (default), then the sort order in the header file will be ignored. Default value: true. This option can be set to 'null' to clear the default value. Possible values: {true, false}" help="" />
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47 <param format="XXCHANGEMEEE" name="STOP_AFTER" type="string" label="Stop after processing N reads, mainly for debugging. Default value: 0. This option can be set to 'null' to clear the default value." help="" />
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48 -->
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49 </inputs>
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50 <outputs>
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51 <!--
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52 <data name="outFile" format="XXCHANGEMEEE">
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53
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54 </data>
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55 -->
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56 </outputs>
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57 <tests>
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58 <test>
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59 <!-- Here is a command line that works:
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60 java -jar ...
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61 -->
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62 <!--
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63 <param name="inputFile" value="XXCHANGEMEE-input" />
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64 <output name="outFile" file="XXCHANGEMEE-correct-output" lines_diff="2" ftype="XXCHANGEMEE" />
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65 -->
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66 </test>
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67 </tests>
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68 <help>
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69 Picard documentation says:
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70
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71
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72 MeanQualityByCycle
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73
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74 Usage: program [options...]
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75
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76 Option Description
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77 CHART_OUTPUT=File A file (with .pdf extension) to write the chart to. Required.
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78 ALIGNED_READS_ONLY=Boolean If set to true, calculate mean quality over aligned reads only. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}
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79 PF_READS_ONLY=Boolean If set to true calculate mean quality over PF reads only. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}
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80 INPUT=File Input SAM or BAM file. Required.
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81 OUTPUT=File File to write the output to. Required.
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82 REFERENCE_SEQUENCE=File Reference sequence fasta Default value: null.
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83 ASSUME_SORTED=Boolean If true (default), then the sort order in the header file will be ignored. Default value: true. This option can be set to 'null' to clear the default value. Possible values: {true, false}
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84 STOP_AFTER=Long Stop after processing N reads, mainly for debugging. Default value: 0. This option can be set to 'null' to clear the default value.
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85
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86
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87 </help>
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88 </tool>
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