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comparison fastqc_report.xml @ 16:1710b0e874f1 draft

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fix file name issue
author mingchen0919
date Sat, 21 Oct 2017 09:25:49 -0400
parents d1d20f341632
children 8635a4cee6dd
comparison
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15:d1d20f341632 16:1710b0e874f1
1 <tool id="fastqc_report" name="Fastqc report" version="2.0.0"> 1 <tool id="fastqc_report" name="Fastqc report" version="2.0.0">
2 <description> 2 <description>
3 Implements FastQC analysis and display results in R Markdown html. 3 Evaluate short reads with FastQC software on a single reads file or a paired of untrimmed and trimmed reads
4 files.
4 </description> 5 </description>
5 <requirements> 6 <requirements>
6 <requirement type="package" version="1.15.0.6-0">pandoc</requirement> 7 <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
7 <requirement type="package" version="1.14.1">bioconductor-deseq2</requirement> 8 <requirement type="package" version="1.14.1">bioconductor-deseq2</requirement>
8 <requirement type="package" version="1.20.0">r-getopt</requirement> 9 <requirement type="package" version="1.20.0">r-getopt</requirement>
27 <command> 28 <command>
28 <![CDATA[ 29 <![CDATA[
29 30
30 Rscript '${__tool_directory__}/fastqc_report_render.R' 31 Rscript '${__tool_directory__}/fastqc_report_render.R'
31 -e $echo 32 -e $echo
32 -r $reads 33 -r $reads_1
33 -n $reads.name 34 -n '$reads_1.name'
35 -R $reads_2
36 -N '$reads_2.name'
37 -c $contaminants
38 -l $limits
34 39
35 -o $report 40 -o $report
36 -d $report.files_path 41 -d $report.files_path
37 -s $sink_message 42 -s $sink_message
38 43
39 -p '${__tool_directory__}/fastqc_report.Rmd' 44 -p '${__tool_directory__}/fastqc_report.Rmd'
40 ]]> 45 ]]>
41 </command> 46 </command>
42 <inputs> 47 <inputs>
43 <param format="fastq,fastq.gz,fastq.bz2,bam,sam" name="reads" type="data" 48 <param format="fastq,fastq.gz,fastq.bz2,bam,sam" name="reads_1" type="data" optional="false"
44 label="Short reads data from history"/> 49 label="Short reads before trimming"
50 help="Short reads data from history. This could be reads before trimming."/>
51 <param format="fastq,fastq.gz,fastq.bz2,bam,sam" name="reads_2" type="data"
52 label="Short reads after trimming"
53 help="Short reads data from history. This could be reads after trimming."/>
54 <param name="contaminants" type="data" format="tabular" optional="true" label="Contaminant list"
55 help="Specifies a non-default file which contains the list of adapter sequences which will be explicitly
56 searched against the library. The file must contain sets of named adapters
57 in the form name[tab]sequence. Lines prefixed with a hash will be ignored."/>
58 <param name="limits" type="data" format="txt" optional="true" label="Submodule and Limit specifing file"
59 help="Specifies a non-default file which contains a set of criteria
60 which will be used to determine the warn/error limits for the
61 various modules. This file can also be used to selectively
62 remove some modules from the output all together. The format
63 needs to mirror the default limits.txt file found in the
64 Configuration folder."/>
45 <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" 65 <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false"
46 label="Display analysis code in report?"/> 66 label="Display analysis code in report?"/>
47 </inputs> 67 </inputs>
48 <outputs> 68 <outputs>
49 <data format="html" name="report" label="fastqc report"/> 69 <data format="html" name="report" label="fastqc report"/>