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1 <tool name="MeanQualityByCycle" id="picard_MeanQualityByCycle" version="1.106.0">
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2 <description>Calculates mean quality by cycle</description>
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3 <requirements><requirement type="package" version="1.106.0">picard</requirement></requirements>
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4 <command interpreter="python">
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5 picard_wrapper.py -i "${input_file}" -d "${html_file.files_path}" -t "${html_file}"
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6 -n "${out_prefix}" --tmpdir "${__new_file_path__}" --assumesorted ${ASSUME_SORTED}
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7 --pfreadsonly ${PF_READS_ONLY} --alignedreadsonly ${ALIGNED_READS_ONLY}
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8 -j "\$JAVA_JAR_PATH/MeanQualityByCycle.jar"
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9 </command>
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10
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11 <stdio>
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12 <exit_code range="0" level="warning" description="Tool finished correctly" />
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13 </stdio>
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14
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15 <inputs>
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16 <param format="sam,bam" name="input_file" type="data" label="Input SAM or BAM file. Required." help="" />
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17 <param checked="False" truevalue="true" falsevalue="false" name="ALIGNED_READS_ONLY" type="boolean" label="If set to true, calculate mean quality over aligned reads only." help="" />
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18 <param checked="False" truevalue="true" falsevalue="false" name="PF_READS_ONLY" type="boolean" label="If set to true calculate mean quality over PF reads only." help="" />
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19 <param checked="True" truevalue="true" falsevalue="false" name="ASSUME_SORTED" type="boolean" label="If true (default), then the sort order in the header file will be ignored." />
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20 <param name="out_prefix" value="Mean quality by cycle" type="text"
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21 label="Title for the output file" help="Use this remind you what the job was for." size="80" />
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22 </inputs>
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23 <outputs>
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24 <data format="html" name="html_file" label="${out_prefix}.html"/>
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25 </outputs>
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26 <tests>
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27 <test>
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28 <!-- Here is a command line that works:
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29 java -jar ...
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30 -->
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31 <!--
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32 <param name="inputFile" value="XXCHANGEMEE-input" />
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33 <output name="outFile" file="XXCHANGEMEE-correct-output" lines_diff="2" ftype="XXCHANGEMEE" />
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34 -->
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35 </test>
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36 </tests>
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37 <help>
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38 Picard documentation says:
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39
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40
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41 MeanQualityByCycle
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42
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43 Usage: program [options...]
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44
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45 Option Description
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46 CHART_OUTPUT=File A file (with .pdf extension) to write the chart to. Required.
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47 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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48 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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49 INPUT=File Input SAM or BAM file. Required.
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50 OUTPUT=File File to write the output to. Required.
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51 REFERENCE_SEQUENCE=File Reference sequence fasta Default value: null. // Actually, this does not seem to be used anywhere in the tool -- so we removed it
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52 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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53 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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54
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55
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56 </help>
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57 </tool>
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