Mercurial > repos > iuc > umi_tools_whitelist

comparison umi-tools_whitelist.xml @ 2:c1743022a8cd draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit e274ffd67bede657f4f5a2c6524023ff57f0db87
author iuc
date Thu, 29 Mar 2018 18:24:04 -0400
parents dac4e7dc837d
children 853f74e08009
comparison
equal deleted inserted replaced
1:dac4e7dc837d 2:c1743022a8cd
1 <tool id="umi_tools_whitelist" name="UMI-tools whitelist" version="@VERSION@.0"> 1 <tool id="umi_tools_whitelist" name="UMI-tools whitelist" version="@VERSION@.1">
2 <description>Extract cell barcodes from FASTQ files</description> 2 <description>Extract cell barcodes from FASTQ files</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 <macro name="barcode2_conditional" >
6 <conditional name="barcode">
7 <param name="barcode_select" argument="--split-barcode" type="select" label="Barcode on both reads?">
8 <option value="first_read_only">Barcode on first read only</option>
9 <option value="both_reads">Barcode on both reads</option>
10 </param>
11 <when value="first_read_only"/>
12 <when value="both_reads">
13 <param name="bc_pattern2" argument="--bc-pattern2" type="text" value="" label="Barcode pattern for second read"
14 help="Use this option to specify the format of the UMI/barcode for
15 the second read pair if required.">
16 </param>
17 </when>
18 </conditional>
19 </macro>
5 </macros> 20 </macros>
6 <expand macro="requirements" /> 21 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[ 22 <command detect_errors="exit_code"><![CDATA[
8 #set $gz = False 23 #set $gz = False
9 #if $input_type.type == 'single': 24 #if $input_type.type == 'single':
10 #if $input_type.input_single.is_of_type("fastq.gz", "fastqsanger.gz"): 25 #if $input_type.input_single.is_of_type("fastq.gz", "fastqsanger.gz"):
11 ln -s '$input_type.input_single' input_single.gz && 26 ln -s '$input_type.input_single' input_single.gz &&
12 #set $gz = True 27 #set $gz = True
13 #end if 28 #end if
14 #else 29 #elif $input_type.type == 'paired':
15 #if $input_type.input_read1.is_of_type("fastq.gz", "fastqsanger.gz"): 30 #if $input_type.input_read1.is_of_type("fastq.gz", "fastqsanger.gz"):
16 ln -s '$input_type.input_read1' input_read1.gz && 31 ln -s '$input_type.input_read1' input_read1.gz &&
17 ln -s '$input_type.input_read2' input_read2.gz && 32 ln -s '$input_type.input_read2' input_read2.gz &&
33 #set $gz = True
34 #end if
35 #else ## paired_collection
36 #if $input_type.input_readpair.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
37 ln -s '$input_type.input_readpair.forward' input_read1.gz &&
38 ln -s '$input_type.input_readpair.reverse' input_read2.gz &&
18 #set $gz = True 39 #set $gz = True
19 #end if 40 #end if
20 #end if 41 #end if
21 umi_tools whitelist 42 umi_tools whitelist
22 --bc-pattern='$bc_pattern' 43 --bc-pattern='$bc_pattern'
25 #if $gz: 46 #if $gz:
26 --stdin=input_single.gz 47 --stdin=input_single.gz
27 #else 48 #else
28 --stdin='$input_type.input_single' 49 --stdin='$input_type.input_single'
29 #end if 50 #end if
30 #else: 51 #else: ## equally valid for both 'paired' and 'paired_collection'
31 #if $gz: 52 #if $gz:
32 --stdin=input_read1.gz 53 --stdin=input_read1.gz
33 --read2-in=input_read2.gz 54 --read2-in=input_read2.gz
34 #else: 55 #else:
35 --stdin='$input_type.input_read1' 56 --stdin='$input_type.input_read1'
55 76
56 #if $log: 77 #if $log:
57 --log='$out_log' 78 --log='$out_log'
58 #end if 79 #end if
59 80
60 --log2stderr 81 --log2stderr
61 82
62 > '$out_whitelist' && 83 > '$out_whitelist' &&
63 84
64 mkdir '${ out_html_report.files_path }' && 85 mkdir '${ out_html_report.files_path }' &&
65 cp OUT_*.png '${ out_html_report.files_path }' && 86 cp OUT_*.png '${ out_html_report.files_path }' &&
77 <inputs> 98 <inputs>
78 <conditional name="input_type"> 99 <conditional name="input_type">
79 <param name="type" type="select" label="Library type"> 100 <param name="type" type="select" label="Library type">
80 <option value="single">Single-end</option> 101 <option value="single">Single-end</option>
81 <option value="paired">Paired-end</option> 102 <option value="paired">Paired-end</option>
103 <option value="paired_collection">Paired-end Dataset Collection</option>
82 </param> 104 </param>
83 <when value="single"> 105 <when value="single">
84 <param name="input_single" type="data" format="fastq,fastq.gz" label="Reads in FASTQ format" /> 106 <param name="input_single" type="data" format="fastq,fastq.gz" label="Reads in FASTQ format" />
85 </when> 107 </when>
86 <when value="paired"> 108 <when value="paired">
87 <param name="input_read1" type="data" format="fastq,fastq.gz" label="Reads in FASTQ format" /> 109 <param name="input_read1" type="data" format="fastq,fastq.gz" label="Reads in FASTQ format" />
88 <param name="input_read2" type="data" format="fastq,fastq.gz" label="Reads in FASTQ format" /> 110 <param name="input_read2" type="data" format="fastq,fastq.gz" label="Reads in FASTQ format" />
89 <conditional name="barcode"> 111 <expand macro="barcode2_conditional" />
90 <param name="barcode_select" argument="--split-barcode" type="select" label="Barcode on both reads?"> 112 </when>
91 <option value="first_read_only">Barcode on first read only</option> 113 <when value="paired_collection">
92 <option value="both_reads">Barcode on both reads</option> 114 <param name="input_readpair" type="data_collection" collection_type="paired" format="fastq,fastq.gz" label="Reads in FASTQ format" />
93 </param> 115 <expand macro="barcode2_conditional" />
94 <when value="first_read_only"/>
95 <when value="both_reads">
96 <param name="bc_pattern2" argument="--bc-pattern2" type="text" value="" label="Barcode pattern for second read"
97 help="Use this option to specify the format of the UMI/barcode for
98 the second read pair if required.">
99 </param>
100 </when>
101 </conditional>
102 </when> 116 </when>
103 </conditional> 117 </conditional>
104 <param name="bc_pattern" argument="--bc-pattern" type="text" label="Barcode pattern for first read" 118 <param name="bc_pattern" argument="--bc-pattern" type="text" label="Barcode pattern for first read"
105 help="Use this option to specify the format of the UMI/barcode. Use Ns to 119 help="Use this option to specify the format of the UMI/barcode. Use Ns to
106 represent the random positions and Xs to indicate the bc positions. 120 represent the random positions and Xs to indicate the bc positions.
169 <output name="out_whitelist" file="out_wl_paired.txt" /> 183 <output name="out_whitelist" file="out_wl_paired.txt" />
170 <output name="out_log" file="out_wl_paired.log" lines_diff="40" /> 184 <output name="out_log" file="out_wl_paired.log" lines_diff="40" />
171 <output name="out_html_report" file="out_wl_paired.html" /> 185 <output name="out_html_report" file="out_wl_paired.html" />
172 <output name="out_thresh" file="out_wl_paired.tresh.tab" /> 186 <output name="out_thresh" file="out_wl_paired.tresh.tab" />
173 </test> 187 </test>
188 <test expect_num_outputs="4"> <!-- As previous, identical outputs but paired collection input -->
189 <param name="type" value="paired_collection" />
190 <param name="input_readpair" >
191 <collection type="paired">
192 <element name="forward" ftype="fastq.gz" value="t_R1.fastq.gz" />
193 <element name="reverse" ftype="fastq.gz" value="t_R2.fastq.gz" />
194 </collection>
195 </param>
196 <param name="barcode_select" value="both_reads" />
197 <param name="bc_pattern" value="CCCNNNNNNNNXXXXX" />
198 <param name="bc_pattern2" value="CCCCCCCCNNNNNNNN" />
199 <param name="method" value="reads" />
200 <param name="prime3" value="false" />
201 <param name="use_cell_opts" value="advanced" />
202 <param name="expect_cells" value="5" />
203 <param name="error_correct_thresh" value="3" />
204 <param name="log" value="true" />
205 <output name="out_whitelist" file="out_wl_paired.txt" />
206 <output name="out_log" file="out_wl_paired.log" lines_diff="40" />
207 <output name="out_html_report" file="out_wl_paired.html" />
208 <output name="out_thresh" file="out_wl_paired.tresh.tab" />
209 </test>
174 </tests> 210 </tests>
175 <help><![CDATA[ 211 <help><![CDATA[
176 212
177 213
178 UMI-tools whitelist - Extract barcodes from fastq 214 UMI-tools whitelist - Extract barcodes from fastq