Mercurial > repos > iuc > umi_tools_extract

annotate macros.xml @ 12:d5ff68d2d5ff draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit 5d3fc4232e0e036ac1ed9e2c36adc41d6af4987f"
author iuc
date Tue, 10 Sep 2019 14:28:00 -0400
parents a472e995d157
children 27ac32a22ad2
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
79436b3019e9 planemo upload commit c8e46ecad0b1473097517e582ed6c43eb0635b36
iuc
parents:
diff changeset
1 <?xml version="1.0"?>
79436b3019e9 planemo upload commit c8e46ecad0b1473097517e582ed6c43eb0635b36
iuc
parents:
diff changeset
2 <macros>
11
a472e995d157 "planemo upload commit 28e58376e1d70e38276873a7d5e2ab44db88c2c0"
iuc
parents: 4
diff changeset
3 <macro name="barcode_sanitizer" >
a472e995d157 "planemo upload commit 28e58376e1d70e38276873a7d5e2ab44db88c2c0"
iuc
parents: 4
diff changeset
4 <sanitizer invalid_char="">
a472e995d157 "planemo upload commit 28e58376e1d70e38276873a7d5e2ab44db88c2c0"
iuc
parents: 4
diff changeset
5 <valid initial="string.letters,string.digits">
a472e995d157 "planemo upload commit 28e58376e1d70e38276873a7d5e2ab44db88c2c0"
iuc
parents: 4
diff changeset
6 <add value="&#42;" /><!-- asterisk -->
a472e995d157 "planemo upload commit 28e58376e1d70e38276873a7d5e2ab44db88c2c0"
iuc
parents: 4
diff changeset
7 <add value="&#44;" /><!-- comma -->
a472e995d157 "planemo upload commit 28e58376e1d70e38276873a7d5e2ab44db88c2c0"
iuc
parents: 4
diff changeset
8 <add value="&#46;" /><!-- period -->
a472e995d157 "planemo upload commit 28e58376e1d70e38276873a7d5e2ab44db88c2c0"
iuc
parents: 4
diff changeset
9 <add value="&#60;" /><!-- less than -->
a472e995d157 "planemo upload commit 28e58376e1d70e38276873a7d5e2ab44db88c2c0"
iuc
parents: 4
diff changeset
10 <add value="&#61;" /><!-- equals sign -->
a472e995d157 "planemo upload commit 28e58376e1d70e38276873a7d5e2ab44db88c2c0"
iuc
parents: 4
diff changeset
11 <add value="&#62;" /><!-- greater than -->
a472e995d157 "planemo upload commit 28e58376e1d70e38276873a7d5e2ab44db88c2c0"
iuc
parents: 4
diff changeset
12 <add value="&#63;" /><!-- question mark -->
a472e995d157 "planemo upload commit 28e58376e1d70e38276873a7d5e2ab44db88c2c0"
iuc
parents: 4
diff changeset
13 <add value="&#95;" /><!-- underscore -->
12
d5ff68d2d5ff "planemo upload commit 5d3fc4232e0e036ac1ed9e2c36adc41d6af4987f"
iuc
parents: 11
diff changeset
14 <add value="&#40;" /><!-- left bracket -->
d5ff68d2d5ff "planemo upload commit 5d3fc4232e0e036ac1ed9e2c36adc41d6af4987f"
iuc
parents: 11
diff changeset
15 <add value="&#41;" /><!-- right bracket -->
d5ff68d2d5ff "planemo upload commit 5d3fc4232e0e036ac1ed9e2c36adc41d6af4987f"
iuc
parents: 11
diff changeset
16 <add value="&#91;"/> <!-- left square bracket -->
d5ff68d2d5ff "planemo upload commit 5d3fc4232e0e036ac1ed9e2c36adc41d6af4987f"
iuc
parents: 11
diff changeset
17 <add value="&#93;"/> <!-- right square bracket -->
11
a472e995d157 "planemo upload commit 28e58376e1d70e38276873a7d5e2ab44db88c2c0"
iuc
parents: 4
diff changeset
18 <add value="&#123;"/><!-- left brace -->
a472e995d157 "planemo upload commit 28e58376e1d70e38276873a7d5e2ab44db88c2c0"
iuc
parents: 4
diff changeset
19 <add value="&#125;"/><!-- right brace -->
12
d5ff68d2d5ff "planemo upload commit 5d3fc4232e0e036ac1ed9e2c36adc41d6af4987f"
iuc
parents: 11
diff changeset
20 <add value="&#94;"/> <!-- caret -->
d5ff68d2d5ff "planemo upload commit 5d3fc4232e0e036ac1ed9e2c36adc41d6af4987f"
iuc
parents: 11
diff changeset
21 <add value="-"/>
d5ff68d2d5ff "planemo upload commit 5d3fc4232e0e036ac1ed9e2c36adc41d6af4987f"
iuc
parents: 11
diff changeset
22 <add value="!"/>
11
a472e995d157 "planemo upload commit 28e58376e1d70e38276873a7d5e2ab44db88c2c0"
iuc
parents: 4
diff changeset
23 </valid>
a472e995d157 "planemo upload commit 28e58376e1d70e38276873a7d5e2ab44db88c2c0"
iuc
parents: 4
diff changeset
24 </sanitizer>
a472e995d157 "planemo upload commit 28e58376e1d70e38276873a7d5e2ab44db88c2c0"
iuc
parents: 4
diff changeset
25 </macro>
4
e73a22ff585c planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
iuc
parents: 2
diff changeset
26 <macro name="barcode2_conditional" >
e73a22ff585c planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
iuc
parents: 2
diff changeset
27 <conditional name="barcode">
e73a22ff585c planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
iuc
parents: 2
diff changeset
28 <param name="barcode_select" argument="--split-barcode" type="select" label="Barcode on both reads?">
e73a22ff585c planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
iuc
parents: 2
diff changeset
29 <option value="first_read_only">Barcode on first read only</option>
e73a22ff585c planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
iuc
parents: 2
diff changeset
30 <option value="both_reads">Barcode on both reads</option>
e73a22ff585c planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
iuc
parents: 2
diff changeset
31 </param>
e73a22ff585c planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
iuc
parents: 2
diff changeset
32 <when value="first_read_only"/>
e73a22ff585c planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
iuc
parents: 2
diff changeset
33 <when value="both_reads">
e73a22ff585c planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
iuc
parents: 2
diff changeset
34 <param name="bc_pattern2" argument="--bc-pattern2" type="text" value="" label="Barcode pattern for second read"
e73a22ff585c planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
iuc
parents: 2
diff changeset
35 help="Use this option to specify the format of the UMI/barcode for
e73a22ff585c planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
iuc
parents: 2
diff changeset
36 the second read pair if required." >
11
a472e995d157 "planemo upload commit 28e58376e1d70e38276873a7d5e2ab44db88c2c0"
iuc
parents: 4
diff changeset
37 <expand macro="barcode_sanitizer" />
4
e73a22ff585c planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
iuc
parents: 2
diff changeset
38 </param>
e73a22ff585c planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
iuc
parents: 2
diff changeset
39 </when>
e73a22ff585c planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
iuc
parents: 2
diff changeset
40 </conditional>
e73a22ff585c planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
iuc
parents: 2
diff changeset
41 </macro>
e73a22ff585c planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
iuc
parents: 2
diff changeset
42 <xml name="input_types">
e73a22ff585c planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
iuc
parents: 2
diff changeset
43 <conditional name="input_type">
e73a22ff585c planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
iuc
parents: 2
diff changeset
44 <param name="type" type="select" label="Library type">
e73a22ff585c planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
iuc
parents: 2
diff changeset
45 <option value="single">Single-end</option>
e73a22ff585c planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
iuc
parents: 2
diff changeset
46 <option value="paired">Paired-end</option>
e73a22ff585c planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
iuc
parents: 2
diff changeset
47 <option value="paired_collection">Paired-end Dataset Collection</option>
e73a22ff585c planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
iuc
parents: 2
diff changeset
48 </param>
e73a22ff585c planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
iuc
parents: 2
diff changeset
49 <when value="single">
e73a22ff585c planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
iuc
parents: 2
diff changeset
50 <param name="input_single" type="data" format="fastq,fastq.gz" label="Reads in FASTQ format" />
e73a22ff585c planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
iuc
parents: 2
diff changeset
51 </when>
e73a22ff585c planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
iuc
parents: 2
diff changeset
52 <when value="paired">
e73a22ff585c planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
iuc
parents: 2
diff changeset
53 <param name="input_read1" type="data" format="fastq,fastq.gz" label="Reads in FASTQ format" />
e73a22ff585c planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
iuc
parents: 2
diff changeset
54 <param name="input_read2" type="data" format="fastq,fastq.gz" label="Reads in FASTQ format" />
e73a22ff585c planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
iuc
parents: 2
diff changeset
55 <expand macro="barcode2_conditional" />
e73a22ff585c planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
iuc
parents: 2
diff changeset
56 </when>
e73a22ff585c planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
iuc
parents: 2
diff changeset
57 <when value="paired_collection">
e73a22ff585c planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
iuc
parents: 2
diff changeset
58 <param name="input_readpair" type="data_collection" collection_type="paired" format="fastq,fastq.gz" label="Reads in FASTQ format" />
e73a22ff585c planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
iuc
parents: 2
diff changeset
59 <expand macro="barcode2_conditional" />
e73a22ff585c planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
iuc
parents: 2
diff changeset
60 </when>
e73a22ff585c planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
iuc
parents: 2
diff changeset
61 </conditional>
e73a22ff585c planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
iuc
parents: 2
diff changeset
62 </xml>
1
79436b3019e9 planemo upload commit c8e46ecad0b1473097517e582ed6c43eb0635b36
iuc
parents:
diff changeset
63 <xml name="citations">
79436b3019e9 planemo upload commit c8e46ecad0b1473097517e582ed6c43eb0635b36
iuc
parents:
diff changeset
64 <citations>
79436b3019e9 planemo upload commit c8e46ecad0b1473097517e582ed6c43eb0635b36
iuc
parents:
diff changeset
65 <citation type="doi">10.1101/gr.209601.116</citation>
79436b3019e9 planemo upload commit c8e46ecad0b1473097517e582ed6c43eb0635b36
iuc
parents:
diff changeset
66 <citation type="bibtex">
79436b3019e9 planemo upload commit c8e46ecad0b1473097517e582ed6c43eb0635b36
iuc
parents:
diff changeset
67 @misc{githubUMI-tools,
79436b3019e9 planemo upload commit c8e46ecad0b1473097517e582ed6c43eb0635b36
iuc
parents:
diff changeset
68 title = {UMI-tools},
79436b3019e9 planemo upload commit c8e46ecad0b1473097517e582ed6c43eb0635b36
iuc
parents:
diff changeset
69 publisher = {GitHub},
79436b3019e9 planemo upload commit c8e46ecad0b1473097517e582ed6c43eb0635b36
iuc
parents:
diff changeset
70 journal = {GitHub repository},
79436b3019e9 planemo upload commit c8e46ecad0b1473097517e582ed6c43eb0635b36
iuc
parents:
diff changeset
71 url = {https://github.com/CGATOxford/UMI-tools},
79436b3019e9 planemo upload commit c8e46ecad0b1473097517e582ed6c43eb0635b36
iuc
parents:
diff changeset
72 }
79436b3019e9 planemo upload commit c8e46ecad0b1473097517e582ed6c43eb0635b36
iuc
parents:
diff changeset
73 </citation>
79436b3019e9 planemo upload commit c8e46ecad0b1473097517e582ed6c43eb0635b36
iuc
parents:
diff changeset
74 </citations>
79436b3019e9 planemo upload commit c8e46ecad0b1473097517e582ed6c43eb0635b36
iuc
parents:
diff changeset
75 </xml>
79436b3019e9 planemo upload commit c8e46ecad0b1473097517e582ed6c43eb0635b36
iuc
parents:
diff changeset
76 <xml name="requirements">
79436b3019e9 planemo upload commit c8e46ecad0b1473097517e582ed6c43eb0635b36
iuc
parents:
diff changeset
77 <requirements>
79436b3019e9 planemo upload commit c8e46ecad0b1473097517e582ed6c43eb0635b36
iuc
parents:
diff changeset
78 <requirement type="package" version="@VERSION@">umi_tools</requirement>
79436b3019e9 planemo upload commit c8e46ecad0b1473097517e582ed6c43eb0635b36
iuc
parents:
diff changeset
79 <yield />
79436b3019e9 planemo upload commit c8e46ecad0b1473097517e582ed6c43eb0635b36
iuc
parents:
diff changeset
80 </requirements>
79436b3019e9 planemo upload commit c8e46ecad0b1473097517e582ed6c43eb0635b36
iuc
parents:
diff changeset
81 </xml>
11
a472e995d157 "planemo upload commit 28e58376e1d70e38276873a7d5e2ab44db88c2c0"
iuc
parents: 4
diff changeset
82 <token name="@VERSION@">0.5.5</token>
4
e73a22ff585c planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
iuc
parents: 2
diff changeset
83 <token name="@COMMAND_LINK@"><![CDATA[
e73a22ff585c planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
iuc
parents: 2
diff changeset
84 #set $gz = False
e73a22ff585c planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
iuc
parents: 2
diff changeset
85 #if $input_type.type == 'single':
e73a22ff585c planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
iuc
parents: 2
diff changeset
86 #if $input_type.input_single.is_of_type("fastq.gz", "fastqsanger.gz"):
e73a22ff585c planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
iuc
parents: 2
diff changeset
87 ln -s '$input_type.input_single' input_single.gz &&
e73a22ff585c planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
iuc
parents: 2
diff changeset
88 #set $gz = True
e73a22ff585c planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
iuc
parents: 2
diff changeset
89 #else
e73a22ff585c planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
iuc
parents: 2
diff changeset
90 ln -s '$input_type.input_single' input_single.txt &&
e73a22ff585c planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
iuc
parents: 2
diff changeset
91 #end if
e73a22ff585c planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
iuc
parents: 2
diff changeset
92 #elif $input_type.type == 'paired':
e73a22ff585c planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
iuc
parents: 2
diff changeset
93 #if $input_type.input_read1.is_of_type("fastq.gz", "fastqsanger.gz"):
e73a22ff585c planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
iuc
parents: 2
diff changeset
94 ln -s '$input_type.input_read1' input_read1.gz &&
e73a22ff585c planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
iuc
parents: 2
diff changeset
95 ln -s '$input_type.input_read2' input_read2.gz &&
e73a22ff585c planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
iuc
parents: 2
diff changeset
96 #set $gz = True
e73a22ff585c planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
iuc
parents: 2
diff changeset
97 #else
e73a22ff585c planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
iuc
parents: 2
diff changeset
98 ln -s '$input_type.input_read1' input_read1.txt &&
e73a22ff585c planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
iuc
parents: 2
diff changeset
99 ln -s '$input_type.input_read2' input_read2.txt &&
e73a22ff585c planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
iuc
parents: 2
diff changeset
100 #end if
e73a22ff585c planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
iuc
parents: 2
diff changeset
101 #else ## paired_collection
e73a22ff585c planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
iuc
parents: 2
diff changeset
102 #if $input_type.input_readpair.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
e73a22ff585c planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
iuc
parents: 2
diff changeset
103 ln -s '$input_type.input_readpair.forward' input_read1.gz &&
e73a22ff585c planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
iuc
parents: 2
diff changeset
104 ln -s '$input_type.input_readpair.reverse' input_read2.gz &&
e73a22ff585c planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
iuc
parents: 2
diff changeset
105 #set $gz = True
e73a22ff585c planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
iuc
parents: 2
diff changeset
106 #else
e73a22ff585c planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
iuc
parents: 2
diff changeset
107 ln -s '$input_type.input_readpair.forward' input_read1.txt &&
e73a22ff585c planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
iuc
parents: 2
diff changeset
108 ln -s '$input_type.input_readpair.reverse' input_read2.txt &&
e73a22ff585c planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
iuc
parents: 2
diff changeset
109 #end if
e73a22ff585c planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
iuc
parents: 2
diff changeset
110 #end if
e73a22ff585c planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
iuc
parents: 2
diff changeset
111 ]]></token>
1
79436b3019e9 planemo upload commit c8e46ecad0b1473097517e582ed6c43eb0635b36
iuc
parents:
diff changeset
112 </macros>