Mercurial > repos > iuc > umi_tools_dedup

comparison macros.xml @ 8:746615d72e00 draft

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"planemo upload commit 28e58376e1d70e38276873a7d5e2ab44db88c2c0"
author iuc
date Tue, 27 Aug 2019 17:08:34 -0400
parents d336205854b8
children a289db9d3bbc
comparison
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7:c5178facf925 8:746615d72e00
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <macros> 2 <macros>
3 <macro name="barcode_sanitizer" >
4 <sanitizer invalid_char="">
5 <valid initial="string.letters,string.digits">
6 <add value="&#40;" /><!-- left bracket -->
7 <add value="&#41;" /><!-- right bracket -->
8 <add value="&#42;" /><!-- asterisk -->
9 <add value="&#44;" /><!-- comma -->
10 <add value="&#46;" /><!-- period -->
11 <add value="&#60;" /><!-- less than -->
12 <add value="&#61;" /><!-- equals sign -->
13 <add value="&#62;" /><!-- greater than -->
14 <add value="&#63;" /><!-- question mark -->
15 <add value="&#95;" /><!-- underscore -->
16 <add value="&#123;"/><!-- left brace -->
17 <add value="&#125;"/><!-- right brace -->
18 </valid>
19 </sanitizer>
20 </macro>
3 <macro name="barcode2_conditional" > 21 <macro name="barcode2_conditional" >
4 <conditional name="barcode"> 22 <conditional name="barcode">
5 <param name="barcode_select" argument="--split-barcode" type="select" label="Barcode on both reads?"> 23 <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> 24 <option value="first_read_only">Barcode on first read only</option>
7 <option value="both_reads">Barcode on both reads</option> 25 <option value="both_reads">Barcode on both reads</option>
9 <when value="first_read_only"/> 27 <when value="first_read_only"/>
10 <when value="both_reads"> 28 <when value="both_reads">
11 <param name="bc_pattern2" argument="--bc-pattern2" type="text" value="" label="Barcode pattern for second read" 29 <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 30 help="Use this option to specify the format of the UMI/barcode for
13 the second read pair if required." > 31 the second read pair if required." >
32 <expand macro="barcode_sanitizer" />
14 </param> 33 </param>
15 </when> 34 </when>
16 </conditional> 35 </conditional>
17 </macro> 36 </macro>
18 <xml name="input_types"> 37 <xml name="input_types">
53 <requirements> 72 <requirements>
54 <requirement type="package" version="@VERSION@">umi_tools</requirement> 73 <requirement type="package" version="@VERSION@">umi_tools</requirement>
55 <yield /> 74 <yield />
56 </requirements> 75 </requirements>
57 </xml> 76 </xml>
58 <token name="@VERSION@">0.5.3</token> 77 <token name="@VERSION@">0.5.5</token>
59 <token name="@COMMAND_LINK@"><![CDATA[ 78 <token name="@COMMAND_LINK@"><![CDATA[
60 #set $gz = False 79 #set $gz = False
61 #if $input_type.type == 'single': 80 #if $input_type.type == 'single':
62 #if $input_type.input_single.is_of_type("fastq.gz", "fastqsanger.gz"): 81 #if $input_type.input_single.is_of_type("fastq.gz", "fastqsanger.gz"):
63 ln -s '$input_type.input_single' input_single.gz && 82 ln -s '$input_type.input_single' input_single.gz &&