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1 <tool name="Insertion size metrics" id="PicardInsertSize" version="1.56.0">
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2 <description>for PAIRED data</description>
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3 <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements>
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4 <command interpreter="python">
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5 picard_wrapper.py -i "$input_file" -n "$out_prefix" --tmpdir "${__new_file_path__}" --deviations "$deviations"
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6 --histwidth "$histWidth" --minpct "$minPct" --malevel "$malevel"
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7 -j "\$JAVA_JAR_PATH/CollectInsertSizeMetrics.jar" -d "$html_file.files_path" -t "$html_file"
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8 </command>
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9 <inputs>
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10 <param format="bam,sam" name="input_file" type="data" label="SAM/BAM dataset to generate statistics for"
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11 help="If empty, upload or import a SAM/BAM dataset."/>
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12 <param name="out_prefix" value="Insertion size metrics" type="text"
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13 label="Title for the output file" help="Use this remind you what the job was for" size="120" />
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14 <param name="deviations" value="10.0" type="float"
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15 label="Deviations" size="5"
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16 help="See Picard documentation: Generate mean, sd and plots by trimming the data down to MEDIAN + DEVIATIONS*MEDIAN_ABSOLUTE_DEVIATION" />
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17 <param name="histWidth" value="0" type="integer"
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18 label="Histogram width" size="5"
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19 help="Explicitly sets the histogram width option - leave 0 to ignore" />
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20 <param name="minPct" value="0.05" type="float"
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21 label="Minimum percentage" size="5"
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22 help="Discard any data categories (out of FR, TANDEM, RF) that have fewer than this percentage of overall reads" />
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23 <param name="malevel" value="0" type="select" multiple="true" label="Metric Accumulation Level"
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24 help="Level(s) at which metrics will be accumulated">
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25 <option value="ALL_READS" selected="true">All reads (default)</option>
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26 <option value="SAMPLE" default="true">Sample</option>
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27 <option value="LIBRARY" default="true">Library</option>
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28 <option value="READ_GROUP" default="true">Read group</option>
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29 </param>
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30 </inputs>
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31 <outputs>
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32 <data format="html" name="html_file" label="InsertSize_${out_prefix}.html"/>
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33 </outputs>
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34 <tests>
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35 <test>
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36 <param name="input_file" value="picard_input_tiny.sam" />
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37 <param name="out_prefix" value="Insertion size metrics" />
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38 <param name="deviations" value="10.0" />
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39 <param name="histWidth" value="0" />
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40 <param name="minPct" value="0.01" />
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41 <param name="malevel" value="ALL_READS" />
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42 <output name="html_file" file="picard_output_insertsize_tinysam.html" ftype="html" compare="contains" lines_diff="40" />
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43 </test>
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44 </tests>
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45 <help>
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46
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47
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48 .. class:: infomark
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49
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50 **Purpose**
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51
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52 Reads a SAM or BAM file and describes the distribution
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53 of insert size (excluding duplicates) with metrics and a histogram plot.
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54
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55 **Picard documentation**
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56
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57 This is a Galaxy wrapper for CollectInsertSizeMetrics, a part of the external package Picard-tools_.
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58
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59 .. _Picard-tools: http://www.google.com/search?q=picard+samtools
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60
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61 .. class:: warningmark
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62
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63 **Useful for paired data only**
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64
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65 This tool works for paired data only and can be expected to fail for single end data.
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66
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67 -----
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68
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69 .. class:: infomark
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70
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71 **Inputs, outputs, and parameters**
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72
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73 Picard documentation says (reformatted for Galaxy):
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74
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75 .. csv-table::
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76 :header-rows: 1
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77
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78 Option,Description
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79 "INPUT=File","SAM or BAM file Required."
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80 "OUTPUT=File","File to write insert size metrics to Required."
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81 "HISTOGRAM_FILE=File","File to write insert size histogram chart to Required."
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82 "TAIL_LIMIT=Integer","When calculating mean and stdev stop when the bins in the tail of the distribution contain fewer than mode/TAIL_LIMIT items. This also limits how much data goes into each data category of the histogram."
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83 "HISTOGRAM_WIDTH=Integer","Explicitly sets the histogram width, overriding the TAIL_LIMIT option. Also, when calculating mean and stdev, only bins LE HISTOGRAM_WIDTH will be included. "
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84 "MINIMUM_PCT=Float","When generating the histogram, discard any data categories (out of FR, TANDEM, RF) that have fewer than this percentage of overall reads. (Range: 0 to 1) Default value: 0.01."
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85 "STOP_AFTER=Integer","Stop after processing N reads, mainly for debugging. Default value: 0."
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86 "CREATE_MD5_FILE=Boolean","Whether to create an MD5 digest for any BAM files created. Default value: false."
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87
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88 .. class:: warningmark
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89
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90 **Warning on SAM/BAM quality**
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91
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92 Many SAM/BAM files produced externally and uploaded to Galaxy do not fully conform to SAM/BAM specifications. Galaxy deals with this by using the **LENIENT**
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93 flag when it runs Picard, which allows reads to be discarded if they're empty or don't map. This appears
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94 to be the only way to deal with SAM/BAM that cannot be parsed.
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95
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96 </help>
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97 </tool>
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