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1 <tool id="cshl_BAMqc" name="ezBAMQC" version="0.6.7" >
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3 <description>
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4 perform QC on BAM files of NGS dataset
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5 </description>
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6
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7 <requirements>
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8 <requirement type="package">ezBAMQC</requirement>
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9 <requirement type="package">R</requirement>
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10 </requirements>
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11
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12 <command interpreter="sh">
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13
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14 ezBAMQC.sh
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15
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16 -r '${refdb}'
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17
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18 -f '${attrID}'
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19
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20 -R '${rRNAdb}'
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21
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22 -s '$stranded'
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23
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24 -o "$output"
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25
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26 #set $core = len($files)
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27
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28 -p $core
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29
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30 #if str($cond_adv_options.adv_options) == 'yes':
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31 -q '$cond_adv_options.mapq'
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32 #end if
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33
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34 #for $file in $files
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35 '$file.input'
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36 '$file.input.tag'
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37 #end for
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38
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39 </command>
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40
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41 <inputs>
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42 <repeat name="files" title="BAM files" min="1">
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43 <param format="bam" name="input" type="data" label="Files for QC" />
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44 </repeat>
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45
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46 <param name="refdb" type="select" label="Reference gene model (GTF)">
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47 <options from_data_table="gene_GTF_database" />
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48 </param>
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49
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50 <param name="attrID" type="text" size="50" value="gene_id" label="Feature ID name" help="Summing reads based on gene (gene_id) or transcript (transcript_id.">
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51 <sanitizer>
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52 <valid initial="none">
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53 <add value="ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz01234567890_-." />
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54 </valid>
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55 </sanitizer>
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56 </param>
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57
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58 <param name="rRNAdb" type="select" label="Ribosomal RNA locations (BED)">
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59 <options from_data_table="rRNA_BED_database" />
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60 </param>
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61
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62 <param name="stranded" type="select" label="Strandedness">
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63 <option value="yes">Yes - Read from stranded library</option>
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64 <option value="no">No - Reads from unstranded library</option>
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65 <option value="reverse">Reverse - reverse-stranded library (e.g. NSR)</option>
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66 </param>
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67
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68 <conditional name="cond_adv_options">
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69 <param name="adv_options" type="select" label="Set advanced options">
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70 <option value="no" selected="true">No</option>
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71 <option value="yes">Yes</option>
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72 </param>
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73
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74 <when value="yes">
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75 <param name="mapq" type="integer" value="30" label="Minimum mapping quality for an alignment to be called uniquely mapped" />
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76 </when>
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77
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78 <when value="no" />
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79 </conditional>
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80
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81 </inputs>
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82
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83 <outputs>
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84 <data format="html" name="output" label="BAM QC on $on_tag_string" />
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85 <data format="txt" name="log" from_work_dir="bamqc.log" label="ezBAMQC log output" hidden="True" />
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86 </outputs>
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87
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88 <help>
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89
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90 **What it does**
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91
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92 This tool takes the mapping results from NGS libraries (BAM), and performs rapid quality assessment. If multiple files are provided, it will calculate and display correlation between each sample.
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93
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94 -----
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95
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96 The Galaxy wrapper for this tool is written by the `Cold Spring Harbor Laboratory`_ `Bioinformatics Shared Resources`_.
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97
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98 ezBAMQC_ is written by the `Molly Hammell Laboratory`_ and the `Bioinformatics Shared Resources`_ at CSHL_.
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99
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100 .. _CSHL: `Cold Spring Harbor Laboratory`_
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101 .. _ezBAMQC: http://hammelllab.labsites.cshl.edu/software#ezBAMQC
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102 .. _`Molly Hammell Laboratory`: http://hammelllab.labsites.cshl.edu/
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103 .. _`Cold Spring Harbor Laboratory`: http://www.cshl.edu/
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104 .. _`Bioinformatics Shared Resources`: http://bioinfo.cshl.edu/index.html
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105
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106 </help>
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107 </tool>
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108
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