Mercurial > repos > iuc > nugen_nudup

annotate nugen_nudup.xml @ 2:57a00c4e43ec draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup commit c3b2bf5ee64db2e334711d6f012190f9f7b4ea28
author iuc
date Fri, 03 Mar 2017 19:35:28 -0500
parents 24693e595caf
children 2bad02c1cb0d
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57a00c4e43ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup commit c3b2bf5ee64db2e334711d6f012190f9f7b4ea28
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1 <tool id="nugen_nudup" name="NuDUP" version="2.3.2" profile="17.01">
1
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2 <description>
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3 mark/remove PCR duplicates based on molecular tags
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4 </description>
0
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5 <requirements>
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6 <requirement type="package" version="2.3.2">nudup</requirement>
0
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7 </requirements>
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8 <stdio>
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9 <exit_code range="1:" />
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10 </stdio>
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11 <version_command>nudup.py --version</version_command>
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12 <command><![CDATA[
1
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13 ln -f -s '$input' 'input.bam' &&
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14 ln -f -s '$input.metadata.bam_index' 'input.bai' &&
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15 mkdir 'tmp' &&
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16 #if $umi_fastq.is_of_type('fastq.gz','fastqsanger.gz'):
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17 #set umi_file = 'umi.fastq.gz'
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18 #else:
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19 #set umi_file = 'umi.fastq'
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20 #end if
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21 ln -f -s '$umi_fastq' '$umi_file' &&
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22 nudup.py
2
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23 -T 'tmp'
1
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24 $paired_end
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25 -f '$umi_file'
0
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26 --start $start
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27 --length $length
1
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28 $rmdup_only
0
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29 'input.bam'
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30 ]]>
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31 </command>
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32 <inputs>
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33 <param type="data" name="input" label="Input SAM/BAM file"
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34 format="sam,bam" help="Input SAM/BAM containing only unique
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35 alignments" />
1
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36 <param type="data" name="umi_fastq"
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37 label="Fastq file containing molecular tag sequence"
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38 format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" help="FASTQ
0
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39 file containing the molecular tag sequence for each read name in
0ad51e73587e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup commit 9f2d2e8d94050274a4eaae7fa1e48887fed657d4
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40 the corresponding SAM/BAM file" />
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41 <param type="boolean" argument="--paired-end"
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42 label="Paired-end deduping" name="paired_end"
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43 truevalue="--paired-end" falsevalue=""
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44 checked="false"
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45 help="use paired end deduping with template. SAM/BAM alignment
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46 must contain paired end reads. Degenerate read pairs
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47 (alignments for one read of pair) will be discarded." />
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48 <param type="integer" argument="--start" label="Tag sequence start
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49 position from 3' end" value="6" help="position in index read where
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50 molecular tag sequence begins. This should be a 1-based value that
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51 counts in from the 3' END of the read." />
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52 <param type="integer" argument="--length" label="Tag sequence length"
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53 value="6" help="length of molecular tag sequence" />
1
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54 <param type="boolean" argument="--rmdup-only" name="rmdup_only"
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55 label="Only output BAM with duplicates removed"
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56 truevalue="--rmdup-only" falsevalue="" checked="false"
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57 help="Do not ouput BAM with duplicates marked. Default is to ouput
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58 both marked duplicates and removed duplicates BAM files." />
0
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59 </inputs>
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60 <outputs>
1
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61 <data format="bam" name="markdup" metadata_source="input"
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62 label="${tool.name} on ${on_string}: MarkDup"
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63 from_work_dir="prefix.sorted.markdup.bam">
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64 <filter>not rmdup_only</filter>
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65 </data>
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66 <data format="bam" name="dedup" metadata_source="input"
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67 label="${tool.name} on ${on_string}: DeDup"
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68 from_work_dir="prefix.sorted.dedup.bam" />
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69 <data format="txt" name="log"
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70 label="${tool.name} on ${on_string}: Log"
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71 from_work_dir="prefix_dup_log.txt" />
0
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72 </outputs>
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73 <tests>
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74 <test>
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75 <param name="input" value="nudup_test_1.bam" ftype="bam" />
1
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76 <param name="umi_fastq" value="nudup_umis.fastq"
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77 ftype="fastqsanger" />
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78 <param name="start" value="8" />
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79 <param name="length" value="8" />
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80 <output name="markdup" file="nudup_markdup_1.bam" ftype="bam" />
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81 <output name="dedup" file="nudup_dedup_1.bam" ftype="bam" />
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82 <output name="log" file="nudup_log_1.txt" ftype="txt" />
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83 </test>
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84 <test>
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85 <param name="input" value="nudup_test_1.bam" ftype="bam" />
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86 <param name="umi_fastq" value="nudup_umis.fastq.gz"
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87 ftype="fastqsanger.gz" />
0
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88 <param name="start" value="8" />
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89 <param name="length" value="8" />
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90 <output name="markdup" file="nudup_markdup_1.bam" ftype="bam" />
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91 <output name="dedup" file="nudup_dedup_1.bam" ftype="bam" />
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92 <output name="log" file="nudup_log_1.txt" ftype="txt" />
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93 </test>
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94 </tests>
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95 <help><![CDATA[
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96 Marks/removes PCR introduced duplicate molecules based on the molecular tagging
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97 technology used in NuGEN products.
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98
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99 For SINGLE END reads, duplicates are marked if they fulfill the following
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100 criteria: a) start at the same genomic coordinate b) have the same strand
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101 orientation c) have the same molecular tag sequence. The read with the
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102 highest mapping quality is kept as the non-duplicate read.
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103
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104 For PAIRED END reads, duplicates are marked if they fulfill the following
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105 criteria: a) start at the same genomic coordinate b) have the same template
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106 length c) have the same molecular tag sequence. The read pair with the highest
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107 mapping quality is kept as the non-duplicate read.
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108
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109 Author: Anand Patel
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110
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111 Contact: NuGEN Technologies Inc., techserv@nugen.com
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112
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113 ::
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114
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115 Input:
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116 IN.sam|IN.bam input sorted/unsorted SAM/BAM containing only unique
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117 alignments (sorted required for case 2 detailed above)
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118
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119 Options:
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120 -2, --paired-end use paired end deduping with template. SAM/BAM
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121 alignment must contain paired end reads. Degenerate
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122 read pairs (alignments for one read of pair) will be
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123 discarded.
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124 -f INDEX.fq|READ.fq FASTQ file containing the molecular tag sequence for
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125 each read name in the corresponding SAM/BAM file
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126 (required only for CASE 1 detailed above)
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127 -o OUT_PREFIX, --out OUT_PREFIX
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128 prefix of output file paths for sorted BAMs (default
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129 will create prefix.sorted.markdup.bam,
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130 prefix.sorted.dedup.bam, prefix_dup_log.txt)
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131 -s START, --start START
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132 position in index read where molecular tag sequence
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133 begins. This should be a 1-based value that counts in
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134 from the 3' END of the read. (default = 6)
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135 -l LENGTH, --length LENGTH
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136 length of molecular tag sequence (default = 6)
1
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137 -T TEMP_DIR directory for reading and writing to temporary files
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138 and named pipes (default: /tmp)
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139 --old-samtools required for compatibility with samtools sort style in
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140 samtools versions <=0.1.19
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141 --rmdup-only required for only outputting duplicates removed file
0
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142 -v, --version show program's version number and exit
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143 -h, --help show this help message and exit
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144 ]]></help>
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145 <citations>
1
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146 <citation type="bibtex">@misc{Patel2017,
0
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147 author = {Patel, Anand},
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148 title = {NuDUP},
2
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149 version = {2.3.2},
1
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150 year = {2017},
0
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151 publisher = {GitHub},
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152 journal = {GitHub repository},
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153 howpublished = {\url{https://github.com/nugentechnologies/nudup}},
2
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154 commit = {7a126eb5a4ccc2bacb426c7cf58b351962798093}
0
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155 }
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156 </citation>
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157 </citations>
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158 </tool>