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comparison BAMqc.xml @ 2:f98435398c1d

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author cshl-bsr
date Tue, 29 Mar 2016 15:26:13 -0400
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1:b4ff32b63fcd 2:f98435398c1d
1 <tool id="cshl_BAMqc" name="ezBAMQC" version="0.6.7" >
2
3 <description>
4 performs QC on BAM files for gene abundances and sample correlation
5 </description>
6
7 <requirements>
8 <requirement type="package">BAMqc</requirement>
9 <requirement type="package">samtools</requirement>
10 <requirement type="package">R</requirement>
11 </requirements>
12
13 <command interpreter="sh">
14
15 BAMqc.sh
16
17 -r '${refdb}'
18
19 -f '${attrID}'
20
21 -R '${rRNAdb}'
22
23 -s '$stranded'
24
25 -o "$output"
26
27 #set $core = len($files)
28
29 -p $core
30
31 #if str($cond_adv_options.adv_options) == 'yes':
32 -q '$cond_adv_options.mapq'
33 #end if
34
35 #for $file in $files
36 '$file.input'
37 '$file.input.tag'
38 #end for
39
40 </command>
41
42 <inputs>
43 <repeat name="files" title="BAM files" min="1">
44 <param format="bam" name="input" type="data" label="Files for QC" />
45 </repeat>
46
47 <param name="refdb" type="select" label="Reference gene model (GTF)">
48 <options from_data_table="gene_GTF_database" />
49 </param>
50
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.">
52 <sanitizer>
53 <valid initial="none">
54 <add value="ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz01234567890_-." />
55 </valid>
56 </sanitizer>
57 </param>
58
59 <param name="rRNAdb" type="select" label="Ribosomal RNA locations (BED)">
60 <options from_data_table="rRNA_BED_database" />
61 </param>
62
63 <param name="stranded" type="select" label="Strandedness">
64 <option value="yes">Yes - Read from stranded library</option>
65 <option value="no">No - Reads from unstranded library</option>
66 <option value="reverse">Reverse - reverse-stranded library (e.g. NSR)</option>
67 </param>
68
69 <conditional name="cond_adv_options">
70 <param name="adv_options" type="select" label="Set advanced options">
71 <option value="no" selected="true">No</option>
72 <option value="yes">Yes</option>
73 </param>
74
75 <when value="yes">
76 <param name="mapq" type="integer" value="30" label="Minimum mapping quality for an alignment to be called uniquely mapped" />
77 </when>
78
79 <when value="no" />
80 </conditional>
81
82 </inputs>
83
84 <outputs>
85 <data format="html" name="output" label="BAM QC on $on_tag_string" />
86 <data format="txt" name="log" from_work_dir="bamqc.log" label="ezBAMQC log output" hidden="True" />
87 </outputs>
88
89 <help>
90
91 **What it does**
92
93 This tool takes the mapping results from RNA-Seq libraries (BAM), and performs rapid gene abundance quantification. If multiple files are provided, it will calculate and display correlation between each sample.
94
95 -----
96
97 The Galaxy wrapper for this tool is written by the `Cold Spring Harbor Laboratory`_ `Bioinformatics Shared Resources`_.
98
99 ezBAMQC_ is written by the `Molly Hammell Laboratory`_ and the `Bioinformatics Shared Resources`_ at CSHL_.
100
101 .. _CSHL: `Cold Spring Harbor Laboratory`_
102 .. _ezBAMQC: http://hammelllab.labsites.cshl.edu/software#ezBAMQC
103 .. _`Molly Hammell Laboratory`: http://hammelllab.labsites.cshl.edu/
104 .. _`Cold Spring Harbor Laboratory`: http://www.cshl.edu/
105 .. _`Bioinformatics Shared Resources`: http://bioinfo.cshl.edu/index.html
106
107 </help>
108 </tool>
109