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comparison htseq_count.xml @ 3:1545e24c9ba7 draft

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add r-dt
author mingchen0919
date Wed, 07 Mar 2018 01:10:13 -0500
parents db9da9716914
children 0fdb0d5f53ce
comparison
equal deleted inserted replaced
2:db9da9716914 3:1545e24c9ba7
1 <tool id="aurora_htseq" name="Aurora htseq" version="1.0.0"> 1 <tool id="aurora_htseq" name="Aurora htseq" version="1.0.0">
2 <description>Counting reads in features.</description> 2 <description>Counting reads in features.</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.15.0.6-0">pandoc</requirement> 4 <requirement type="package" version="1.15.0.6-0">pandoc</requirement><requirement type="package" version="1.20.0">r-getopt</requirement><requirement type="package" version="1.6">r-rmarkdown</requirement><requirement type="package" version="0.9.1">htseq</requirement><requirement type="package" version="0.2">r-dt</requirement></requirements>
5 <requirement type="package" version="1.20.0">r-getopt</requirement> 5 <stdio>
6 <requirement type="package" version="1.6">r-rmarkdown</requirement> 6 <regex match="XXX" source="stderr" level="warning" description="Check the warnings_and_errors.txt file for more details."/></stdio>
7 <requirement type="package" version="0.9.1">htseq</requirement> 7 <command><![CDATA[Rscript '${__tool_directory__}/htseq_count_render.R'
8 </requirements>
9 <stdio>
10 <regex match="XXX" source="stderr" level="warning"
11 description="Check the warnings_and_errors.txt file for more details."/>
12 </stdio>
13 <command><![CDATA[Rscript '${__tool_directory__}/htseq_count_render.R'
14 8
15 -e $echo 9 -e $echo
16 -o $report 10 -o $report
17 -d $report.files_path 11 -d $report.files_path
18 -s $sink_message 12 -s $sink_message
19 -t '${__tool_directory__}' 13 -t '${__tool_directory__}'
20 14
21 -A '$alignment_files' 15 -A '$alignment_files'
22 -B '$sample_names' 16 -B '$sample_names'
23 -G $gff 17 -G $gff
24 -f $format 18 -f $format
25 -r $order 19 -r $order
26 -S $stranded 20 -S $stranded
27 -a $minaqual 21 -a $minaqual
28 -T $feature_type 22 -T $feature_type
29 -i $idattr 23 -i $idattr
30 -m $mode 24 -m $mode
31 -c $count]]></command> 25 -c $count]]></command>
32 <inputs> 26 <inputs>
33 <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" 27 <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?"/><param type="data" name="alignment_files" label="Alignment file (SAM/BAM)" optional="False" format="sam,bam" multiple="True"/><param type="text" name="sample_names" label="Sample names" help="sample names for each input SAM/BAM file. Use comma to separate multiple names, for example, sample_1, sample_2, sample_3. The number of sample names should be the same as the number of input SAM/BAM files." optional="False" size="5x25"/><param type="select" name="format" argument="-f" label="Input data format" optional="False" multiple="False"><option value="sam" selected="false">SAM</option><option value="bam" selected="true">BAM</option></param><param type="data" name="gff" label="GFF file" optional="False" format="gff, gff3"/><param type="select" name="order" argument="-r" label="Order" help="Use this option to indicate how the input data has been sorted. The default is name.&#13;&#10;&#13;&#10;" optional="False" multiple="False"><option value="name" selected="false">Name</option><option value="pos" selected="false">Position</option></param><param type="select" name="stranded" argument="-s" label="Stranded" optional="False" multiple="False"><option value="yes" selected="true">Yes</option><option value="no" selected="false">No</option><option value="reverse" selected="false">Reverse</option></param><param type="integer" name="minaqual" argument="-a" label="Alignment quality " help="Skip all reads with alignment quality lower than the given minimum value (default: 10)" optional="False" value="10" min="0"/><param type="text" name="feature_type" argument="-t" label="Feature type" help="Feature type (3rd column in GFF file) to be used, all features of other type are ignored (default, suitable for RNA-Seq analysis using an Ensembl GTF file: exon)" optional="False" value="exon"/><param type="text" name="idattr" argument="-i" label="ID attribute" help="GFF attribute to be used as feature ID. Several GFF lines with the same feature ID will be considered as parts of the same feature. The feature ID is used to identity the counts in the output table. The default, suitable for RNA-Seq analysis using an Ensembl GTF file, is gene_id." optional="False" value="gene_id"/><param type="select" name="mode" argument="-m" label="Mode" help="Mode to handle reads overlapping more than one feature. Possible values for &lt;mode&gt; are union, intersection-strict and intersection-nonempty (default: union)" optional="False" multiple="False"><option value="union" selected="true">Union</option><option value="intersection-strict" selected="false">Intersection (strict)</option><option value="intersection-nonempty" selected="false">Intersection (nonempty)</option></param></inputs>
34 label="Display analysis code in report?"/> 28 <outputs>
35 <param type="data" name="alignment_files" label="Alignment file (SAM/BAM)" optional="False" format="sam,bam" 29 <data name="report" format="html" label="Aurora htseq on ${on_string}" hidden="false"/><data format="txt" name="sink_message" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt"/><data name="count" format="txt" label="Aurora htseq-count on ${on_string}" hidden="false"/></outputs>
36 multiple="True"/> 30 <citations>
37 <param type="text" name="sample_names" label="Sample names"
38 help="sample names for each input SAM/BAM file. Use comma to separate multiple names, for example, sample_1, sample_2, sample_3. The number of sample names should be the same as the number of input SAM/BAM files."
39 optional="False" size="5x25"/>
40 <param type="select" name="format" argument="-f" label="Input data format" optional="False" multiple="False">
41 <option value="sam" selected="false">SAM</option>
42 <option value="bam" selected="false">BAM</option>
43 </param>
44 <param type="data" name="gff" label="GFF file" optional="False" format="gff, gff3"/>
45 <param type="select" name="order" argument="-r" label="Order"
46 help="Use this option to indicate how the input data has been sorted. The default is name.&#13;&#10;&#13;&#10;"
47 optional="False" multiple="False">
48 <option value="name" selected="false">Name</option>
49 <option value="pos" selected="false">Position</option>
50 </param>
51 <param type="select" name="stranded" argument="-s" label="Stranded" optional="False" multiple="False">
52 <option value="yes" selected="true">Yes</option>
53 <option value="no" selected="false">No</option>
54 <option value="reverse" selected="false">Reverse</option>
55 </param>
56 <param type="integer" name="minaqual" argument="-a" label="Alignment quality "
57 help="Skip all reads with alignment quality lower than the given minimum value (default: 10)"
58 optional="False" value="10" min="0"/>
59 <param type="text" name="feature_type" argument="-t" label="Feature type"
60 help="Feature type (3rd column in GFF file) to be used, all features of other type are ignored (default, suitable for RNA-Seq analysis using an Ensembl GTF file: exon)"
61 optional="False" value="exon"/>
62 <param type="text" name="idattr" argument="-i" label="ID attribute"
63 help="GFF attribute to be used as feature ID. Several GFF lines with the same feature ID will be considered as parts of the same feature. The feature ID is used to identity the counts in the output table. The default, suitable for RNA-Seq analysis using an Ensembl GTF file, is gene_id."
64 optional="False" value="gene_id"/>
65 <param type="select" name="mode" argument="-m" label="Mode"
66 help="Mode to handle reads overlapping more than one feature. Possible values for &lt;mode&gt; are union, intersection-strict and intersection-nonempty (default: union)"
67 optional="False" multiple="False">
68 <option value="union" selected="true">Union</option>
69 <option value="intersection-strict" selected="false">Intersection (strict)</option>
70 <option value="intersection-nonempty" selected="false">Intersection (nonempty)</option>
71 </param>
72 </inputs>
73 <outputs>
74 <data name="report" format="html" label="Aurora htseq on ${on_string}" hidden="false"/>
75 <data format="txt" name="sink_message" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt"/>
76 <data name="count" format="txt" label="Aurora htseq-count on ${on_string}" hidden="false"/>
77 </outputs>
78 <citations>
79 <citation type="bibtex"><![CDATA[ 31 <citation type="bibtex"><![CDATA[
80 @article{allaire2016rmarkdown, 32 @article{allaire2016rmarkdown,
81 title={rmarkdown: Dynamic Documents for R, 2016}, 33 title={rmarkdown: Dynamic Documents for R, 2016},
82 author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff 34 author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff
83 and Wickham, Hadley and Atkins, Aron and Hyndman, Rob}, 35 and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
84 journal={R package version 0.9}, 36 journal={R package version 0.9},
85 volume={6}, 37 volume={6},
86 year={2016} 38 year={2016}
87 } 39 }
88 ]]></citation> 40 ]]></citation><citation type="bibtex"><![CDATA[
89 <citation type="bibtex"><![CDATA[
90 @book{xie2015dynamic, 41 @book{xie2015dynamic,
91 title={Dynamic Documents with R and knitr}, 42 title={Dynamic Documents with R and knitr},
92 author={Xie, Yihui}, 43 author={Xie, Yihui},
93 volume={29}, 44 volume={29},
94 year={2015}, 45 year={2015},
95 publisher={CRC Press} 46 publisher={CRC Press}
96 } 47 }
97 ]]></citation> 48 ]]></citation><citation type="bibtex"><![CDATA[@article{anders2015htseq,
98 <citation type="bibtex"><![CDATA[@article{anders2015htseq,
99 title={HTSeq—a Python framework to work with high-throughput sequencing data}, 49 title={HTSeq—a Python framework to work with high-throughput sequencing data},
100 author={Anders, Simon and Pyl, Paul Theodor and Huber, Wolfgang}, 50 author={Anders, Simon and Pyl, Paul Theodor and Huber, Wolfgang},
101 journal={Bioinformatics}, 51 journal={Bioinformatics},
102 volume={31}, 52 volume={31},
103 number={2}, 53 number={2},
104 pages={166--169}, 54 pages={166--169},
105 year={2015}, 55 year={2015},
106 publisher={Oxford University Press} 56 publisher={Oxford University Press}
107 }]]></citation> 57 }]]></citation></citations>
108 </citations>
109 </tool> 58 </tool>