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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">samtools</requirement>
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10 <requirement type="package">R</requirement>
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11 </requirements>
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12
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13 <command interpreter="sh">
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14
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15 ezBAMQC.sh
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16
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17 -r '${refdb}'
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18
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19 -f '${attrID}'
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20
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21 -R '${rRNAdb}'
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22
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23 -s '$stranded'
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24
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25 -o "$output"
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26
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27 #set $core = len($files)
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28
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29 -p $core
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30
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31 #if str($cond_adv_options.adv_options) == 'yes':
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32 -q '$cond_adv_options.mapq'
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33 #end if
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34
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35 #for $file in $files
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36 '$file.input'
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37 '$file.input.tag'
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38 #end for
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39
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40 </command>
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41
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42 <inputs>
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43 <repeat name="files" title="BAM files" min="1">
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44 <param format="bam" name="input" type="data" label="Files for QC" />
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45 </repeat>
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46
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47 <param name="refdb" type="select" label="Reference gene model (GTF)">
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48 <options from_data_table="gene_GTF_database" />
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49 </param>
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50
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51 <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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52 <sanitizer>
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53 <valid initial="none">
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54 <add value="ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz01234567890_-." />
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55 </valid>
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56 </sanitizer>
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57 </param>
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58
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59 <param name="rRNAdb" type="select" label="Ribosomal RNA locations (BED)">
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60 <options from_data_table="rRNA_BED_database" />
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61 </param>
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62
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63 <param name="stranded" type="select" label="Strandedness">
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64 <option value="yes">Yes - Read from sense-stranded library</option>
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65 <option value="no">No - Reads from unstranded library</option>
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66 <option value="reverse">Reverse - reverse-stranded library (e.g. NSR)</option>
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67 </param>
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68
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69 <conditional name="cond_adv_options">
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70 <param name="adv_options" type="select" label="Set advanced options">
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71 <option value="no" selected="true">No</option>
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72 <option value="yes">Yes</option>
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73 </param>
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74
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75 <when value="yes">
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76 <param name="mapq" type="integer" value="30" label="Minimum mapping quality for an alignment to be called uniquely mapped" />
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77 </when>
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78
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79 <when value="no" />
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80 </conditional>
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81
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82 </inputs>
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83
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84 <outputs>
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85 <data format="html" name="output" label="BAM QC on $on_tag_string" />
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86 <data format="txt" name="log" from_work_dir="bamqc.log" label="ezBAMQC log output" hidden="True" />
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87 </outputs>
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88
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89 <help>
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90
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91 **What it does**
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92
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93 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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94
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95 -----
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96
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97 The Galaxy wrapper for this tool is written by the `Cold Spring Harbor Laboratory`_ `Bioinformatics Shared Resources`_.
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98
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99 ezBAMQC_ is written by the `Molly Hammell Laboratory`_ and the `Bioinformatics Shared Resources`_ at CSHL_.
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100
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101 .. _CSHL: `Cold Spring Harbor Laboratory`_
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102 .. _ezBAMQC: http://hammelllab.labsites.cshl.edu/software#ezBAMQC
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103 .. _`Molly Hammell Laboratory`: http://hammelllab.labsites.cshl.edu/
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104 .. _`Cold Spring Harbor Laboratory`: http://www.cshl.edu/
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105 .. _`Bioinformatics Shared Resources`: http://bioinfo.cshl.edu/index.html
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106
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107 </help>
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108 </tool>
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109
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