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comparison ezBAMQC.xml @ 17:161866cee2a2

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wrapper rename
author youngkim
date Wed, 30 Mar 2016 13:28:47 -0400
parents BAMqc.xml@736260d32237
children caed0168f704
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16:736260d32237 17:161866cee2a2
1 <tool id="cshl_BAMqc" name="ezBAMQC" version="0.6.7" >
2
3 <description>
4 perform QC on BAM files of NGS dataset
5 </description>
6
7 <requirements>
8 <requirement type="package">ezBAMQC</requirement>
9 <requirement type="package">R</requirement>
10 </requirements>
11
12 <command interpreter="sh">
13
14 ezBAMQC.sh
15
16 -r '${refdb}'
17
18 -f '${attrID}'
19
20 -R '${rRNAdb}'
21
22 -s '$stranded'
23
24 -o "$output"
25
26 #set $core = len($files)
27
28 -p $core
29
30 #if str($cond_adv_options.adv_options) == 'yes':
31 -q '$cond_adv_options.mapq'
32 #end if
33
34 #for $file in $files
35 '$file.input'
36 '$file.input.tag'
37 #end for
38
39 </command>
40
41 <inputs>
42 <repeat name="files" title="BAM files" min="1">
43 <param format="bam" name="input" type="data" label="Files for QC" />
44 </repeat>
45
46 <param name="refdb" type="select" label="Reference gene model (GTF)">
47 <options from_data_table="gene_GTF_database" />
48 </param>
49
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.">
51 <sanitizer>
52 <valid initial="none">
53 <add value="ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz01234567890_-." />
54 </valid>
55 </sanitizer>
56 </param>
57
58 <param name="rRNAdb" type="select" label="Ribosomal RNA locations (BED)">
59 <options from_data_table="rRNA_BED_database" />
60 </param>
61
62 <param name="stranded" type="select" label="Strandedness">
63 <option value="yes">Yes - Read from stranded library</option>
64 <option value="no">No - Reads from unstranded library</option>
65 <option value="reverse">Reverse - reverse-stranded library (e.g. NSR)</option>
66 </param>
67
68 <conditional name="cond_adv_options">
69 <param name="adv_options" type="select" label="Set advanced options">
70 <option value="no" selected="true">No</option>
71 <option value="yes">Yes</option>
72 </param>
73
74 <when value="yes">
75 <param name="mapq" type="integer" value="30" label="Minimum mapping quality for an alignment to be called uniquely mapped" />
76 </when>
77
78 <when value="no" />
79 </conditional>
80
81 </inputs>
82
83 <outputs>
84 <data format="html" name="output" label="BAM QC on $on_tag_string" />
85 <data format="txt" name="log" from_work_dir="bamqc.log" label="ezBAMQC log output" hidden="True" />
86 </outputs>
87
88 <help>
89
90 **What it does**
91
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.
93
94 -----
95
96 The Galaxy wrapper for this tool is written by the `Cold Spring Harbor Laboratory`_ `Bioinformatics Shared Resources`_.
97
98 ezBAMQC_ is written by the `Molly Hammell Laboratory`_ and the `Bioinformatics Shared Resources`_ at CSHL_.
99
100 .. _CSHL: `Cold Spring Harbor Laboratory`_
101 .. _ezBAMQC: http://hammelllab.labsites.cshl.edu/software#ezBAMQC
102 .. _`Molly Hammell Laboratory`: http://hammelllab.labsites.cshl.edu/
103 .. _`Cold Spring Harbor Laboratory`: http://www.cshl.edu/
104 .. _`Bioinformatics Shared Resources`: http://bioinfo.cshl.edu/index.html
105
106 </help>
107 </tool>
108