Mercurial > repos > devteam > fastqc
comparison rgFastQC.xml @ 1:8fae48caaf06 draft
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author | devteam |
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date | Tue, 11 Nov 2014 12:46:27 -0500 |
parents | e28c965eeed4 |
children | d2cf2c0c8a11 |
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0:e28c965eeed4 | 1:8fae48caaf06 |
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1 <tool name="FastQC:Read QC" id="fastqc" version="0.52"> | 1 <tool name="FastQC:Read QC" id="fastqc" version="0.62"> |
2 <description>reports using FastQC</description> | 2 <description>reports using FastQC</description> |
3 <command interpreter="python"> | 3 <command interpreter="python"> |
4 rgFastQC.py -i "$input_file" -d "$html_file.files_path" -o "$html_file" -n "$out_prefix" -f "$input_file.ext" -j "$input_file.name" -e "\$JAVA_JAR_PATH/fastqc" | 4 rgFastQC.py -i "$input_file" -d "$html_file.files_path" -o "$html_file" -t "$text_file" -n "$out_prefix" -f "$input_file.ext" -j "$input_file.name" -e "\$FASTQC_JAR_PATH/fastqc" |
5 #if $contaminants.dataset and str($contaminants) > '' | 5 #if $contaminants.dataset and str($contaminants) > '' |
6 -c "$contaminants" | 6 -c "$contaminants" |
7 #end if | 7 #end if |
8 #if $limits.dataset and str($limits) > '' | |
9 -l "$limits" | |
10 #end if | |
8 </command> | 11 </command> |
9 <requirements> | 12 <requirements> |
10 <requirement type="package" version="0.10.1">FastQC</requirement> | 13 <requirement type="package" version="0.11.2">FastQC</requirement> |
11 </requirements> | 14 </requirements> |
12 <inputs> | 15 <inputs> |
13 <param format="fastqsanger,fastq,bam,sam" name="input_file" type="data" label="Short read data from your current history" /> | 16 <param format="fastqsanger,fastq,bam,sam" name="input_file" type="data" label="Short read data from your current history" /> |
14 <param name="out_prefix" value="FastQC" type="text" label="Title for the output file - to remind you what the job was for" size="80" | 17 <param name="out_prefix" value="FastQC" type="text" label="Title for the output file - to remind you what the job was for" size="80" |
15 help="Letters and numbers only please - other characters will be removed"> | 18 help="Letters and numbers only please - other characters will be removed"> |
16 <sanitizer invalid_char=""> | 19 <sanitizer invalid_char=""> |
17 <valid initial="string.letters,string.digits"/> | 20 <valid initial="string.letters,string.digits"/> |
18 </sanitizer> | 21 </sanitizer> |
19 </param> | 22 </param> |
20 <param name="contaminants" type="data" format="tabular" optional="true" label="Contaminant list" | 23 <param name="contaminants" type="data" format="tabular" optional="true" label="Contaminant list" |
21 help="tab delimited file with 2 columns: name and sequence. For example: Illumina Small RNA RT Primer CAAGCAGAAGACGGCATACGA"/> | 24 help="tab delimited file with 2 columns: name and sequence. For example: Illumina Small RNA RT Primer CAAGCAGAAGACGGCATACGA"/> |
25 <param name="limits" type="data" format="txt" optional="true" label="Submodule and Limit specifing file" | |
26 help="a file that specifies which submodules are to be executed (default=all) and also specifies the thresholds for the each submodules warning parameter" /> | |
22 </inputs> | 27 </inputs> |
23 <outputs> | 28 <outputs> |
24 <data format="html" name="html_file" label="${out_prefix}_${input_file.name}.html" /> | 29 <data format="html" name="html_file" label="${out_prefix}_${input_file.name}_Webpage.html" /> |
30 <data format="txt" name="text_file" label="${out_prefix}_${input_file.name}_RawData.txt" /> | |
25 </outputs> | 31 </outputs> |
26 <tests> | 32 <tests> |
27 <test> | 33 <test> |
28 <param name="input_file" value="1000gsample.fastq" /> | 34 <param name="input_file" value="1000gsample.fastq" /> |
29 <param name="out_prefix" value="fastqc_out" /> | 35 <param name="out_prefix" value="fastqc_out" /> |
30 <param name="contaminants" value="fastqc_contaminants.txt" ftype="tabular" /> | 36 <param name="contaminants" value="fastqc_contaminants.txt" ftype="tabular" /> |
31 <output name="html_file" file="fastqc_report.html" ftype="html" lines_diff="100"/> | 37 <output name="html_file" file="fastqc_report.html" ftype="html" lines_diff="100"/> |
38 <output name="text_file" file="fastqc_data.txt" ftype="txt" lines_diff="100"/> | |
39 </test> | |
40 <test> | |
41 <param name="input_file" value="1000gsample.fastq" /> | |
42 <param name="out_prefix" value="fastqc_out" /> | |
43 <param name="limits" value="fastqc_customlimits.txt" ftype="txt" /> | |
44 <output name="html_file" file="fastqc_report2.html" ftype="html" lines_diff="100"/> | |
45 <output name="text_file" file="fastqc_data2.txt" ftype="txt" lines_diff="100"/> | |
32 </test> | 46 </test> |
33 </tests> | 47 </tests> |
34 <help> | 48 <help> |
35 | 49 |
36 .. class:: infomark | 50 .. class:: infomark |
63 Kindly acknowledge it as well as this tool if you use it. | 77 Kindly acknowledge it as well as this tool if you use it. |
64 FastQC incorporates the Picard-tools_ libraries for sam/bam processing. | 78 FastQC incorporates the Picard-tools_ libraries for sam/bam processing. |
65 | 79 |
66 The contaminants file parameter was borrowed from the independently developed | 80 The contaminants file parameter was borrowed from the independently developed |
67 fastqcwrapper contributed to the Galaxy Community Tool Shed by J. Johnson. | 81 fastqcwrapper contributed to the Galaxy Community Tool Shed by J. Johnson. |
82 Adaption to version 0.11.2 by T. McGowan. | |
68 | 83 |
69 ----- | 84 ----- |
70 | 85 |
71 .. class:: infomark | 86 .. class:: infomark |
72 | 87 |
75 FastQC_ is the best place to look for documentation - it's very good. | 90 FastQC_ is the best place to look for documentation - it's very good. |
76 A summary follows below for those in a tearing hurry. | 91 A summary follows below for those in a tearing hurry. |
77 | 92 |
78 This wrapper will accept a Galaxy fastq, sam or bam as the input read file to check. | 93 This wrapper will accept a Galaxy fastq, sam or bam as the input read file to check. |
79 It will also take an optional file containing a list of contaminants information, in the form of | 94 It will also take an optional file containing a list of contaminants information, in the form of |
80 a tab-delimited file with 2 columns, name and sequence. | 95 a tab-delimited file with 2 columns, name and sequence. As another option the tool takes a custom |
96 limits.txt file that allows setting the warning thresholds for the different modules and also specifies | |
97 which modules to include in the output. | |
81 | 98 |
82 The tool produces a single HTML output file that contains all of the results, including the following: | 99 The tool produces a basic text and a HTML output file that contain all of the results, including the following: |
83 | 100 |
84 - Basic Statistics | 101 - Basic Statistics |
85 - Per base sequence quality | 102 - Per base sequence quality |
86 - Per sequence quality scores | 103 - Per sequence quality scores |
87 - Per base sequence content | 104 - Per base sequence content |