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comparison stacks_clonefilter.xml @ 0:a8a0cd05d47d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
author iuc
date Sun, 21 May 2017 18:54:11 -0400
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children a0a51078cb61
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-1:000000000000 0:a8a0cd05d47d
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>