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comparison nugen_nudup.xml @ 1:24693e595caf draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup commit 772d7fb670aaa4ad131909bf2aef5d7dd016e621
author iuc
date Sat, 25 Feb 2017 01:38:55 -0500
parents 0ad51e73587e
children 57a00c4e43ec
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0:0ad51e73587e 1:24693e595caf
1 <tool id="nugen_nudup" name="NuDUP" version="2.2_post2016104"> 1 <tool id="nugen_nudup" name="NuDUP" version="2.3.1" profile="17.01">
2 <description>mark/remove PCR duplicates based on molecular tags</description> 2 <description>
3 mark/remove PCR duplicates based on molecular tags
4 </description>
3 <requirements> 5 <requirements>
4 <requirement type="package" version="2.2_post2016104">nudup</requirement> 6 <requirement type="package" version="2.3.1">nudup</requirement>
5 </requirements> 7 </requirements>
6 <stdio> 8 <stdio>
7 <exit_code range="1:" /> 9 <exit_code range="1:" />
8 </stdio> 10 </stdio>
9 <version_command>nudup.py --version</version_command> 11 <version_command>nudup.py --version</version_command>
10 <command><![CDATA[ 12 <command><![CDATA[
11 ln -f -s '$input' 'input.bam' && 13 ln -f -s '$input' 'input.bam' &&
12 ln -f -s '$input.metadata.bam_index' 'input.bai' && 14 ln -f -s '$input.metadata.bam_index' 'input.bai' &&
13 nudup.py $paired_end 15 mkdir 'tmp' &&
14 -f '$umi_fastq' 16 #if $umi_fastq.is_of_type('fastq.gz','fastqsanger.gz'):
17 #set umi_file = 'umi.fastq.gz'
18 #else:
19 #set umi_file = 'umi.fastq'
20 #end if
21 ln -f -s '$umi_fastq' '$umi_file' &&
22 nudup.py
23 -T \$PWD'/tmp'
24 $paired_end
25 -f '$umi_file'
15 --start $start 26 --start $start
16 --length $length 27 --length $length
28 $rmdup_only
17 'input.bam' 29 'input.bam'
18 ]]> 30 ]]>
19 </command> 31 </command>
20 <inputs> 32 <inputs>
21 <param type="data" name="input" label="Input SAM/BAM file" 33 <param type="data" name="input" label="Input SAM/BAM file"
22 format="sam,bam" help="Input SAM/BAM containing only unique 34 format="sam,bam" help="Input SAM/BAM containing only unique
23 alignments" /> 35 alignments" />
24 <param type="data" name="umi_fastq" label="Fastq file containing 36 <param type="data" name="umi_fastq"
25 molecular tag sequence" format="fastq,fastqsanger" help="FASTQ 37 label="Fastq file containing molecular tag sequence"
38 format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" help="FASTQ
26 file containing the molecular tag sequence for each read name in 39 file containing the molecular tag sequence for each read name in
27 the corresponding SAM/BAM file" /> 40 the corresponding SAM/BAM file" />
28 <param type="boolean" argument="--paired-end" 41 <param type="boolean" argument="--paired-end"
29 label="Paired-end deduping" name="paired_end" 42 label="Paired-end deduping" name="paired_end"
30 truevalue="--paired-end" falsevalue="" 43 truevalue="--paired-end" falsevalue=""
36 position from 3' end" value="6" help="position in index read where 49 position from 3' end" value="6" help="position in index read where
37 molecular tag sequence begins. This should be a 1-based value that 50 molecular tag sequence begins. This should be a 1-based value that
38 counts in from the 3' END of the read." /> 51 counts in from the 3' END of the read." />
39 <param type="integer" argument="--length" label="Tag sequence length" 52 <param type="integer" argument="--length" label="Tag sequence length"
40 value="6" help="length of molecular tag sequence" /> 53 value="6" help="length of molecular tag sequence" />
54 <param type="boolean" argument="--rmdup-only" name="rmdup_only"
55 label="Only output BAM with duplicates removed"
56 truevalue="--rmdup-only" falsevalue="" checked="false"
57 help="Do not ouput BAM with duplicates marked. Default is to ouput
58 both marked duplicates and removed duplicates BAM files." />
41 </inputs> 59 </inputs>
42 <outputs> 60 <outputs>
43 <data format="bam" name="markdup" from_work_dir="prefix.sorted.markdup.bam" /> 61 <data format="bam" name="markdup" metadata_source="input"
44 <data format="bam" name="dedup" from_work_dir="prefix.sorted.dedup.bam" /> 62 label="${tool.name} on ${on_string}: MarkDup"
45 <data format="txt" name="log" from_work_dir="prefix_dup_log.txt" /> 63 from_work_dir="prefix.sorted.markdup.bam">
64 <filter>not rmdup_only</filter>
65 </data>
66 <data format="bam" name="dedup" metadata_source="input"
67 label="${tool.name} on ${on_string}: DeDup"
68 from_work_dir="prefix.sorted.dedup.bam" />
69 <data format="txt" name="log"
70 label="${tool.name} on ${on_string}: Log"
71 from_work_dir="prefix_dup_log.txt" />
46 </outputs> 72 </outputs>
47 <tests> 73 <tests>
48 <test> 74 <test>
49 <param name="input" value="nudup_test_1.bam" ftype="bam" /> 75 <param name="input" value="nudup_test_1.bam" ftype="bam" />
50 <param name="umi_fastq" value="nudup_umis.fastq" ftype="fastqsanger" /> 76 <param name="umi_fastq" value="nudup_umis.fastq"
77 ftype="fastqsanger" />
78 <param name="start" value="8" />
79 <param name="length" value="8" />
80 <output name="markdup" file="nudup_markdup_1.bam" ftype="bam" />
81 <output name="dedup" file="nudup_dedup_1.bam" ftype="bam" />
82 <output name="log" file="nudup_log_1.txt" ftype="txt" />
83 </test>
84 <test>
85 <param name="input" value="nudup_test_1.bam" ftype="bam" />
86 <param name="umi_fastq" value="nudup_umis.fastq.gz"
87 ftype="fastqsanger.gz" />
51 <param name="start" value="8" /> 88 <param name="start" value="8" />
52 <param name="length" value="8" /> 89 <param name="length" value="8" />
53 <output name="markdup" file="nudup_markdup_1.bam" ftype="bam" /> 90 <output name="markdup" file="nudup_markdup_1.bam" ftype="bam" />
54 <output name="dedup" file="nudup_dedup_1.bam" ftype="bam" /> 91 <output name="dedup" file="nudup_dedup_1.bam" ftype="bam" />
55 <output name="log" file="nudup_log_1.txt" ftype="txt" /> 92 <output name="log" file="nudup_log_1.txt" ftype="txt" />
95 position in index read where molecular tag sequence 132 position in index read where molecular tag sequence
96 begins. This should be a 1-based value that counts in 133 begins. This should be a 1-based value that counts in
97 from the 3' END of the read. (default = 6) 134 from the 3' END of the read. (default = 6)
98 -l LENGTH, --length LENGTH 135 -l LENGTH, --length LENGTH
99 length of molecular tag sequence (default = 6) 136 length of molecular tag sequence (default = 6)
137 -T TEMP_DIR directory for reading and writing to temporary files
138 and named pipes (default: /tmp)
139 --old-samtools required for compatibility with samtools sort style in
140 samtools versions <=0.1.19
141 --rmdup-only required for only outputting duplicates removed file
100 -v, --version show program's version number and exit 142 -v, --version show program's version number and exit
101 -h, --help show this help message and exit 143 -h, --help show this help message and exit
102 ]]></help> 144 ]]></help>
103 <citations> 145 <citations>
104 <citation type="bibtex">@misc{Patel2016, 146 <citation type="bibtex">@misc{Patel2017,
105 author = {Patel, Anand}, 147 author = {Patel, Anand},
106 title = {NuDUP}, 148 title = {NuDUP},
107 year = {2016}, 149 year = {2017},
108 publisher = {GitHub}, 150 publisher = {GitHub},
109 journal = {GitHub repository}, 151 journal = {GitHub repository},
110 howpublished = {\url{https://github.com/nugentechnologies/nudup}}, 152 howpublished = {\url{https://github.com/nugentechnologies/nudup}},
111 commit = {740d9fe439dd8917605a56483a8796b377eb24c6} 153 commit = {7451de86680d24f19638ed6ac88f6504f0817753}
112 } 154 }
113 </citation> 155 </citation>
114 </citations> 156 </citations>
115 </tool> 157 </tool>