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comparison macros.xml @ 3:7d886fe41f56 draft

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planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
author iuc
date Mon, 16 Apr 2018 16:37:49 -0400
parents f73f13641bb6
children 3b8fecdf9058
comparison
equal deleted inserted replaced
2:4325a02ea7a3 3:7d886fe41f56
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <macros> 2 <macros>
3 <macro name="barcode2_conditional" >
4 <conditional name="barcode">
5 <param name="barcode_select" argument="--split-barcode" type="select" label="Barcode on both reads?">
6 <option value="first_read_only">Barcode on first read only</option>
7 <option value="both_reads">Barcode on both reads</option>
8 </param>
9 <when value="first_read_only"/>
10 <when value="both_reads">
11 <param name="bc_pattern2" argument="--bc-pattern2" type="text" value="" label="Barcode pattern for second read"
12 help="Use this option to specify the format of the UMI/barcode for
13 the second read pair if required." >
14 </param>
15 </when>
16 </conditional>
17 </macro>
18 <xml name="input_types">
19 <conditional name="input_type">
20 <param name="type" type="select" label="Library type">
21 <option value="single">Single-end</option>
22 <option value="paired">Paired-end</option>
23 <option value="paired_collection">Paired-end Dataset Collection</option>
24 </param>
25 <when value="single">
26 <param name="input_single" type="data" format="fastq,fastq.gz" label="Reads in FASTQ format" />
27 </when>
28 <when value="paired">
29 <param name="input_read1" type="data" format="fastq,fastq.gz" label="Reads in FASTQ format" />
30 <param name="input_read2" type="data" format="fastq,fastq.gz" label="Reads in FASTQ format" />
31 <expand macro="barcode2_conditional" />
32 </when>
33 <when value="paired_collection">
34 <param name="input_readpair" type="data_collection" collection_type="paired" format="fastq,fastq.gz" label="Reads in FASTQ format" />
35 <expand macro="barcode2_conditional" />
36 </when>
37 </conditional>
38 </xml>
3 <xml name="citations"> 39 <xml name="citations">
4 <citations> 40 <citations>
5 <citation type="doi">10.1101/gr.209601.116</citation> 41 <citation type="doi">10.1101/gr.209601.116</citation>
6 <citation type="bibtex"> 42 <citation type="bibtex">
7 @misc{githubUMI-tools, 43 @misc{githubUMI-tools,
18 <requirement type="package" version="@VERSION@">umi_tools</requirement> 54 <requirement type="package" version="@VERSION@">umi_tools</requirement>
19 <yield /> 55 <yield />
20 </requirements> 56 </requirements>
21 </xml> 57 </xml>
22 <token name="@VERSION@">0.5.3</token> 58 <token name="@VERSION@">0.5.3</token>
59 <token name="@COMMAND_LINK@"><![CDATA[
60 #set $gz = False
61 #if $input_type.type == 'single':
62 #if $input_type.input_single.is_of_type("fastq.gz", "fastqsanger.gz"):
63 ln -s '$input_type.input_single' input_single.gz &&
64 #set $gz = True
65 #else
66 ln -s '$input_type.input_single' input_single.txt &&
67 #end if
68 #elif $input_type.type == 'paired':
69 #if $input_type.input_read1.is_of_type("fastq.gz", "fastqsanger.gz"):
70 ln -s '$input_type.input_read1' input_read1.gz &&
71 ln -s '$input_type.input_read2' input_read2.gz &&
72 #set $gz = True
73 #else
74 ln -s '$input_type.input_read1' input_read1.txt &&
75 ln -s '$input_type.input_read2' input_read2.txt &&
76 #end if
77 #else ## paired_collection
78 #if $input_type.input_readpair.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
79 ln -s '$input_type.input_readpair.forward' input_read1.gz &&
80 ln -s '$input_type.input_readpair.reverse' input_read2.gz &&
81 #set $gz = True
82 #else
83 ln -s '$input_type.input_readpair.forward' input_read1.txt &&
84 ln -s '$input_type.input_readpair.reverse' input_read2.txt &&
85 #end if
86 #end if
87 ]]></token>
23 </macros> 88 </macros>