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planemo upload for repository https://github.com/phac-nml/galaxy_tools commit d5b7cb71616c0ac20e02ff8cb8c147b9d4a31691
author nml
date Wed, 11 Oct 2017 16:22:08 -0400
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1 <tool id="FastQC_Summary" name="FastQC Summary" version="1.2">
2 <description>Provide a one line summary of a FastQC report(s)</description>
3 <requirements>
4 <requirement type="package" version="1.6.924">perl-bioperl</requirement>
5 <requirement type="package" version="2.49">perl-getopt-long</requirement>
6 </requirements>
7 <command detect_errors="exit_code"><![CDATA[
8
9 perl $__tool_directory__/fastqc_stats.pl
10
11
12 #if $single_or_mate.library_type == "single"
13 --fastq_se $single_or_mate.fastq_file --g_rawdata_se $rawdata_file
14 --sample "$single_or_mate.fastq_file.name"
15 #elif $single_or_mate.library_type == "paired"
16 --fastq_pe_1 $single_or_mate.forward_fastq --fastq_pe_2 $single_or_mate.reverse_fastq --g_rawdata_pe_1 $single_or_mate.forward_rawdata --g_rawdata_pe_2 $single_or_mate.reverse_rawdata
17 --sample "$single_or_mate.forward_fastq.name"
18 #else
19 --fastq_pe_1 $single_or_mate.fastq_collection.forward --fastq_pe_2 $single_or_mate.fastq_collection.reverse --g_rawdata_pe_1 $single_or_mate.fastqc_collection.forward --g_rawdata_pe_2 $single_or_mate.fastqc_collection.reverse
20 --sample "$single_or_mate.fastq_collection.name"
21 #end if
22
23
24
25 #if $ref_or_num.select == "reference"
26 --ref $ref_or_num.ref_file
27 #else
28 --num_bps $ref_or_num.bp_num
29 #end if
30 -o $out_file
31
32 ]]></command>
33 <inputs>
34 <conditional name="single_or_mate">
35 <param name="library_type" type="select" label="Is this library single or paired-end?">
36 <option value="single">Single-end</option>
37 <option value="paired">Paired-end</option>
38 <option value="collection">Collection Paired-end Fastqs</option>
39 </param>
40 <when value="single">
41 <param name="fastq_file" type="data" format="fastqsanger,fastq" label="Single end FASTQ"/>
42 <param name="rawdata_file" type="data" format="txt" label="FastQC RawData"/>
43 </when>
44 <when value="paired">
45 <param name="forward_fastq" type="data" format="fastqsanger,fastq" label="Forward FASTQ"/>
46 <param name="reverse_fastq" type="data" format="fastqsanger,fastq" label="Reverse FASTQ"/>
47 <param name="forward_rawdata" type="data" format="txt" label="FASTQC forward RawData"/>
48 <param name="reverse_rawdata" type="data" format="txt" label="FASTQC reverse RawData"/>
49 </when>
50 <when value="collection">
51 <param name="fastq_collection" type="data_collection" label="Paired-end Fastq collection" help="" optional="false" format="txt" collection_type="paired" />
52 <param name="fastqc_collection" type="data_collection" label="Paired-end FastQC collection" help="" optional="false" format="txt" collection_type="paired" />
53 </when>
54 </conditional>
55 <conditional name="ref_or_num">
56 <param name="select" type="select" label="Reference file or number of base pairs?">
57 <option value="reference">Reference file</option>
58 <option value="num_pairs">Number of base pairs</option>
59 </param>
60 <when value="reference">
61 <param name="ref_file" type="data" format='fasta' help="To determine raw genome coverage." label="Reference file"/>
62 </when>
63 <when value="num_pairs">
64 <param name="bp_num" type="integer" value="" label="Number of base pairs"/>
65 </when>
66 </conditional>
67 </inputs>
68 <outputs>
69 <data format="tabular" name="out_file" label="Output csv file"/>
70 </outputs>
71 <tests>
72 <test>
73 <param name="fastq_file" value="forward.fastq"/>
74 <param name="rawdata_file" value="forward.txt"/>
75 <param name="ref_file" value="reference_1K.fa"/>
76 <output name="out_file" value="output_single.tsv"/>
77 </test>
78 <test>
79 <param name="library_type" value="paired"/>
80 <param name="forward_fastq" value="forward.fastq"/>
81 <param name="reverse_fastq" value="reverse.fastq"/>
82 <param name="forward_rawdata" value="forward.txt"/>
83 <param name="reverse_rawdata" value="reverse.txt"/>
84 <param name="ref_file" value="reference_1K.fa"/>
85 <output name="out_file" value="output_pe.tsv"/>
86 </test>
87 </tests>
88 <help>
89
90 What it does
91 ============
92 This script provides a one line summary of the FastQC report.
93
94 Inputs
95 ======
96 - **Is this library single or paired end?**: Choose Single-end or Paired-end. This option will display the correct number of input fields depending on the option selected
97 - **Fastq input**: - Fastqc file
98 - **FastQC rawData input**: - This is the txt file produced by the FastQC tool
99 - **Sample Name**: Sample name that will appear in the output file
100 - **Reference file or number of base pairs?**: Choose between providing a reference file or providing a number of basepairs to determine the raw genome coverage.
101
102 Outputs
103 =======
104 - **Output csv file**: Summarizes the FastQC report in a csv format
105 </help>
106 </tool>