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comparison umi-tools_extract.xml @ 4:e73a22ff585c draft

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planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
author iuc
date Mon, 16 Apr 2018 16:38:40 -0400
parents 79436b3019e9
children f77bc14eba31
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3:475ee31c61d9 4:e73a22ff585c
1 <tool id="umi_tools_extract" name="UMI-tools extract" version="@VERSION@.0"> 1 <tool id="umi_tools_extract" name="UMI-tools extract" version="@VERSION@.1">
2 <description>Extract UMI from fastq files</description> 2 <description>Extract UMI from fastq files</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 #set $gz = False 8 @COMMAND_LINK@
9 #if $input_type.type == 'single': 9
10 #if $input_type.input_single.is_of_type("fastq.gz", "fastqsanger.gz"): 10 umi_tools extract
11 ln -s '$input_type.input_single' input_single.gz &&
12 #set $gz = True
13 #end if
14 #else
15 #if $input_type.input_read1.is_of_type("fastq.gz", "fastqsanger.gz"):
16 ln -s '$input_type.input_read1' input_read1.gz &&
17 ln -s '$input_type.input_read2' input_read2.gz &&
18 #set $gz = True
19 #end if
20 #end if
21 umi_tools extract
22 --bc-pattern='$bc_pattern' 11 --bc-pattern='$bc_pattern'
23 #if $input_type.type == 'single': 12 #if $input_type.type == 'single':
24 #if $gz: 13 #if $gz:
25 --stdin=input_single.gz 14 --stdin=input_single.gz
26 --stdout out.gz 15 --stdout out.gz
38 --stdin='$input_type.input_read1' 27 --stdin='$input_type.input_read1'
39 --read2-in='$input_type.input_read2' 28 --read2-in='$input_type.input_read2'
40 --stdout '$out1' 29 --stdout '$out1'
41 --read2-out='$out2' 30 --read2-out='$out2'
42 #end if 31 #end if
43 #if $input_type.barcode.split == "1": 32 #if $input_type.barcode.barcode_select == "both_reads":
44 --split-barcode 33 --split-barcode
45 --bc-pattern2='$input_type.barcode.bc_pattern2' 34 --bc-pattern2='$input_type.barcode.bc_pattern2'
46 #end if 35 #end if
47 #end if 36 #end if
48 #if not $prime3: 37 #if not $prime3:
65 && mv out2.gz '$out2' 54 && mv out2.gz '$out2'
66 #end if 55 #end if
67 #end if 56 #end if
68 ]]></command> 57 ]]></command>
69 <inputs> 58 <inputs>
70 <conditional name="input_type"> 59 <expand macro="input_types" />
71 <param name="type" type="select" label="Library type">
72 <option value="single">Single-end</option>
73 <option value="paired">Paired-end</option>
74 </param>
75 <when value="single">
76 <param name="input_single" type="data" format="fastq,fastq.gz" label="Reads in FASTQ format" />
77 </when>
78 <when value="paired">
79 <param name="input_read1" type="data" format="fastq,fastq.gz" label="Reads in FASTQ format" />
80 <param name="input_read2" type="data" format="fastq,fastq.gz" label="Reads in FASTQ format" />
81 <conditional name="barcode">
82 <param name="split" argument="--split-barcode" type="select" label="Barcode on both reads?">
83 <option value="0">Barcode on first read only</option>
84 <option value="1">Barcode on both reads</option>
85 </param>
86 <when value="0">
87 </when>
88 <when value="1">
89 <param name="bc_pattern2" argument="--bc-pattern2" type="text" value="" label="Barcode pattern for second read"
90 help="Use this option to specify the format of the UMI/barcode for
91 the second read pair if required.">
92 </param>
93 </when>
94 </conditional>
95 </when>
96 </conditional>
97 <param name="bc_pattern" argument="--bc-pattern" type="text" label="Barcode pattern for first read" 60 <param name="bc_pattern" argument="--bc-pattern" type="text" label="Barcode pattern for first read"
98 help="Use this option to specify the format of the UMI/barcode. Use Ns to 61 help="Use this option to specify the format of the UMI/barcode. Use Ns to
99 represent the random positions and Xs to indicate the bc positions. 62 represent the random positions and Xs to indicate the bc positions.
100 Bases with Ns will be extracted and added to the read name. Remaining 63 Bases with Ns will be extracted and added to the read name. Remaining
101 bases, marked with an X will be reattached to the read."> 64 bases, marked with an X will be reattached to the read.">
130 <outputs> 93 <outputs>
131 <data name="out" format_source="input_single"> 94 <data name="out" format_source="input_single">
132 <filter>input_type['type'] == "single"</filter> 95 <filter>input_type['type'] == "single"</filter>
133 </data> 96 </data>
134 <data name="out1" format_source="input_read1"> 97 <data name="out1" format_source="input_read1">
135 <filter>input_type['type'] == "paired"</filter> 98 <filter>input_type['type'] !== "single"</filter>
136 </data> 99 </data>
137 <data name="out2" format_source="input_read2"> 100 <data name="out2" format_source="input_read2">
138 <filter>input_type['type'] == "paired"</filter> 101 <filter>input_type['type'] !== "single"</filter>
139 </data> 102 </data>
140 <data name="out_log" format="txt"> 103 <data name="out_log" format="txt">
141 <filter>print_log == True</filter> 104 <filter>print_log == True</filter>
142 </data> 105 </data>
143 </outputs> 106 </outputs>
160 <param name="bc_pattern" value="NNNXXX" /> 123 <param name="bc_pattern" value="NNNXXX" />
161 <output name="out1" file="out_R1.fastq.gz" decompress="true" lines_diff="2" /> 124 <output name="out1" file="out_R1.fastq.gz" decompress="true" lines_diff="2" />
162 <output name="out2" file="out_R2.fastq.gz" decompress="true" lines_diff="2" /> 125 <output name="out2" file="out_R2.fastq.gz" decompress="true" lines_diff="2" />
163 <output name="out_log" file="out_paired.log" lines_diff="16"/> 126 <output name="out_log" file="out_paired.log" lines_diff="16"/>
164 </test> 127 </test>
128 <test>
129 <param name="type" value="paired_collection" />
130 <param name="input_readpair" >
131 <collection type="paired">
132 <element name="forward" ftype="fastq.gz" value="t_R1.fastq.gz" />
133 <element name="reverse" ftype="fastq.gz" value="t_R2.fastq.gz" />
134 </collection>
135 </param>
136 <param name="bc_pattern" value="NNNXXX" />
137 <output name="out1" file="out_R1.fastq.gz" decompress="true" lines_diff="2" />
138 <output name="out2" file="out_R2.fastq.gz" decompress="true" lines_diff="2" />
139 <output name="out_log" file="out_paired.log" lines_diff="16"/>
140 </test>
165 </tests> 141 </tests>
166 <help><![CDATA[ 142 <help><![CDATA[
167 143
168 144
169 UMI-tools extract.py - Extract UMI from fastq 145 UMI-tools extract.py - Extract UMI from fastq