Mercurial > repos > iuc > stacks_clonefilter
comparison stacks_clonefilter.xml @ 0:a8a0cd05d47d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
author | iuc |
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date | Sun, 21 May 2017 18:54:11 -0400 |
parents | |
children | a0a51078cb61 |
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-1:000000000000 | 0:a8a0cd05d47d |
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1 <tool id="stacks_clonefilter" name="Stacks: clone filter" version="@WRAPPER_VERSION@.0"> | |
2 <description>Identify PCR clones</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements"/> | |
7 <expand macro="stdio"/> | |
8 <command><![CDATA[ | |
9 | |
10 #if $data_type.dt_select == "single" | |
11 | |
12 #if $data_type.fname.is_of_type('fastqsanger') | |
13 #set $ext = ".fq" | |
14 #set inputype = "fastq" | |
15 #else | |
16 #set $ext = ".fq.gz" | |
17 #set inputype = "gzfastq" | |
18 #end if | |
19 | |
20 ln -s '$data_type.fname' R1$ext && | |
21 #else | |
22 | |
23 #if $data_type.fwd.is_of_type('fastqsanger') | |
24 #set $ext = ".fq" | |
25 #set inputype = "fastq" | |
26 #else | |
27 #set $ext = ".fq.gz" | |
28 #set inputype = "gzfastq" | |
29 #end if | |
30 | |
31 ln -s '$data_type.fwd' R1$ext && | |
32 ln -s '$data_type.rev' R2$ext && | |
33 #end if | |
34 | |
35 | |
36 mkdir clone_outputs | |
37 | |
38 && | |
39 | |
40 clone_filter | |
41 #if $data_type.dt_select == 'single': | |
42 -f R1$ext | |
43 | |
44 #else | |
45 -1 R1$ext | |
46 -2 R2$ext | |
47 #end if | |
48 | |
49 -i $inputype | |
50 | |
51 -o clone_outputs | |
52 | |
53 | |
54 #if $oligo_len_1 | |
55 --oligo_len_1 $oligo_len_1 | |
56 $data_type.barcode_encoding | |
57 #end if | |
58 #if $oligo_len_2 | |
59 --oligo_len_2 $oligo_len_2 | |
60 #end if | |
61 | |
62 -y gzfastq | |
63 | |
64 ]]></command> | |
65 <inputs> | |
66 <conditional name="data_type"> | |
67 <param name="dt_select" type="select" label="Single or Paired-end"> | |
68 <option value="single">Single</option> | |
69 <option value="pair">Pair</option> | |
70 </param> | |
71 <when value="single"> | |
72 <param name="fname" type="data" format="fastqsanger,fastqsanger.gz" label="FASTQ" /> | |
73 <param name="barcode_encoding" type="select" label="Barcode location"> | |
74 <expand macro="barcode_encoding_single" /> | |
75 </param> | |
76 | |
77 </when> | |
78 <when value="pair"> | |
79 <param name="fwd" type="data" format="fastqsanger,fastqsanger.gz" label="Forward FASTQ" /> | |
80 <param name="rev" type="data" format="fastqsanger,fastqsanger.gz" label="Reverse FASTQ" /> | |
81 <param name="barcode_encoding_pair" type="select" label="Barcode location"> | |
82 <expand macro="barcode_encoding_single" /> | |
83 </param> | |
84 </when> | |
85 </conditional> | |
86 <param name="oligo_len_1" optional="true" type="integer" label="length of the single-end oligo sequence in data set"/> | |
87 <param name="oligo_len_2" optional="true" type="integer" label="length of the paired-end oligo sequence in data set"/> | |
88 | |
89 </inputs> | |
90 <outputs> | |
91 <data format="fastqsangergz" name="clean" from_work_dir="clone_outputs/R1.fq.gz"> | |
92 <filter>data_type['dt_select'] == 'single'</filter> | |
93 </data> | |
94 | |
95 <data format="fastqsangergz" name="clean_fwd" from_work_dir="clone_outputs/R1.1.fq.gz"> | |
96 <filter>data_type['dt_select'] == 'pair'</filter> | |
97 </data> | |
98 <data format="fastqsangergz" name="clean_rev" from_work_dir="clone_outputs/R2.2.fq.gz"> | |
99 <filter>data_type['dt_select'] == 'pair'</filter> | |
100 </data> | |
101 </outputs> | |
102 <tests> | |
103 <test> | |
104 <conditional name="data_type"> | |
105 <param name="dt_select" value="single" /> | |
106 <param name="fname" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" /> | |
107 </conditional> | |
108 <param name="oligo_len_1" value="6" /> | |
109 <output name="clean" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.single.gz"/> | |
110 </test> | |
111 <test> | |
112 <conditional name="data_type"> | |
113 <param name="dt_select" value="single" /> | |
114 <param name="fname" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" /> | |
115 </conditional> | |
116 <output name="clean" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz"/> | |
117 </test> | |
118 <test> | |
119 <conditional name="data_type"> | |
120 <param name="dt_select" value="pair" /> | |
121 <param name="fwd" ftype="fastqsanger" value="clonefilter/R1_0001.1.fq.gz" /> | |
122 <param name="rev" ftype="fastqsanger" value="clonefilter/R2_0001.2.fq.gz" /> | |
123 </conditional> | |
124 <output name="clean_fwd" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz"/> | |
125 <output name="clean_rev" compare="sim_size" file="clonefilter/Removed2_0001.2.2.fq.gz"/> | |
126 </test> | |
127 <test> | |
128 <conditional name="data_type"> | |
129 <param name="dt_select" value="pair" /> | |
130 <param name="fwd" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" /> | |
131 <param name="rev" ftype="fastqsanger.gz" value="clonefilter/R2_0001.2.fq.gz" /> | |
132 </conditional> | |
133 <output name="clean_fwd" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz"/> | |
134 <output name="clean_rev" compare="sim_size" file="clonefilter/Removed2_0001.2.2.fq.gz"/> | |
135 </test> | |
136 </tests> | |
137 <help> | |
138 <![CDATA[ | |
139 .. class:: infomark | |
140 | |
141 | |
142 The clone_filter program is designed to identify PCR clones. | |
143 | |
144 @STACKS_INFOS@ | |
145 ]]> | |
146 </help> | |
147 <expand macro="citation" /> | |
148 </tool> |