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comparison stacks_assembleperead.xml @ 0:e3ca198820a8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
author iuc
date Tue, 14 Jun 2016 14:05:40 -0400
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children ee52d9cfaffc
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-1:000000000000 0:e3ca198820a8
1 <tool id="stacks_assembleperead" name="Stacks: assemble read pairs by locus" version="@WRAPPER_VERSION@.0">
2 <description>run the STACKS sort_read_pairs.pl and exec_velvet.pl wrappers</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
8 <command><![CDATA[
9
10 mkdir stacks_inputs reads stacks_outputs
11
12 &&
13
14 #for $input_file in $stacks_col:
15 #set $ext = ""
16 #if not str($input_file.name).endswith('.tsv'):
17 #set $ext = ".tsv"
18 #end if
19 ln -s "${input_file}" "stacks_inputs/${input_file.name}${ext}" &&
20 #end for
21
22 #for $input_file in $reads:
23 #set $name = str($input_file.name)
24 #if $name.endswith('.2.fq'):
25 ## sort_read_pairs is expecting strange fastq names...
26 #set $name = $name[:-5]+".fq_2"
27 #end if
28 ln -s "${input_file}" "reads/${name}" &&
29 #end for
30
31 sort_read_pairs.pl
32 -p stacks_inputs
33 -s 'reads'
34
35 #if $whitelist:
36 -w '$whitelist'
37 #end if
38
39 #if $threshold:
40 -r $threshold
41 #end if
42
43 -o stacks_outputs
44
45 #if $velvet.use_velvet:
46 ## remove possible empty files
47 && find stacks_outputs -type f -size 0 -delete
48
49 &&
50 mkdir assembled
51 &&
52 velvet_path=`which velveth` && velvet_path=`dirname "\$velvet_path"`
53 &&
54 exec_velvet.pl -s stacks_outputs -o assembled -c -M ${velvet.contig_length} -e "\$velvet_path"
55 #end if
56
57 ]]></command>
58 <inputs>
59 <param name="stacks_col" argument="-p" format="tabular,txt" type="data_collection" collection_type="list" label="Output from previous Stacks pipeline steps (e.g. denovo_map or refmap)" />
60 <param name="reads" argument="-s" format="fastqsanger" type="data" multiple="true" label="Files containing sequences" help="Files containing parent sequences from a mapping cross" />
61
62 <param name="whitelist" argument="-w" format="txt,tabular" type="data" optional="true" label="White list of catalog IDs to include" />
63 <param name="threshold" argument="-r" type="integer" value="" optional="true" label="Minimum number of reads by locus"/>
64
65 <conditional name="velvet">
66 <param name="use_velvet" type="boolean" checked="false" label="Perform assembly with Velvet" help="If not selected, the tool will only produce of collection of fasta files (one per locus) containing reads ready to assemble." />
67 <when value="false"></when>
68 <when value="true">
69 <param name="contig_length" type="integer" value="200" label="Minimum length for asssembled contigs"/>
70 </when>
71 </conditional>
72 </inputs>
73 <outputs>
74 <collection name="collated" type="list" label="Collated FASTA files per locus on ${on_string}">
75 <discover_datasets pattern="(?P&lt;name&gt;.+)\.fa(sta)?" ext="fasta" directory="stacks_outputs" />
76 </collection>
77
78 <data format="fasta" name="contigs" label="Assembled contigs on ${on_string}" from_work_dir="assembled/collated.fa">
79 <filter>velvet['use_velvet']</filter>
80 </data>
81 </outputs>
82
83 <tests>
84 <test>
85 <param name="stacks_col">
86 <collection type="list">
87 <element name="batch_1.catalog.alleles.tsv" ftype="tabular" value="genotypes/batch_1.catalog.alleles.tsv" />
88 <element name="batch_1.catalog.snps.tsv" ftype="tabular" value="genotypes/batch_1.catalog.snps.tsv" />
89 <element name="batch_1.catalog.tags.tsv" ftype="tabular" value="genotypes/batch_1.catalog.tags.tsv" />
90 <element name="PopA_01.alleles.tsv" ftype="tabular" value="genotypes/PopA_01.alleles.tsv" />
91 <element name="PopA_01.matches.tsv" ftype="tabular" value="genotypes/PopA_01.matches.tsv" />
92 <element name="PopA_01.snps.tsv" ftype="tabular" value="genotypes/PopA_01.snps.tsv" />
93 <element name="PopA_01.tags.tsv" ftype="tabular" value="genotypes/PopA_01.tags.tsv" />
94 <element name="PopA_02.alleles.tsv" ftype="tabular" value="genotypes/PopA_02.alleles.tsv" />
95 <element name="PopA_02.matches.tsv" ftype="tabular" value="genotypes/PopA_02.matches.tsv" />
96 <element name="PopA_02.snps.tsv" ftype="tabular" value="genotypes/PopA_02.snps.tsv" />
97 <element name="PopA_02.tags.tsv" ftype="tabular" value="genotypes/PopA_02.tags.tsv" />
98 </collection>
99 </param>
100 <param name="reads" value="demultiplexed/PopA_01.2.fq,demultiplexed/PopA_02.2.fq" ftype="fastqsanger" />
101
102 <output_collection name="collated">
103 <element name="1">
104 <assert_contents>
105 <has_text text="CCGATCAGCATCAGTAGTTTTCAACGAGCTGGCCCAATGGTGTATAACTATGTGGTAGAGAGAAACTGCTGCTATCACTCACGATATAAGCCCTCTGACG" />
106 </assert_contents>
107 </element>
108 </output_collection>
109 </test>
110 <test>
111 <param name="stacks_col">
112 <collection type="list">
113 <element name="batch_1.catalog.alleles.tsv" ftype="tabular" value="genotypes/batch_1.catalog.alleles.tsv" />
114 <element name="batch_1.catalog.snps.tsv" ftype="tabular" value="genotypes/batch_1.catalog.snps.tsv" />
115 <element name="batch_1.catalog.tags.tsv" ftype="tabular" value="genotypes/batch_1.catalog.tags.tsv" />
116 <element name="PopA_01.alleles.tsv" ftype="tabular" value="genotypes/PopA_01.alleles.tsv" />
117 <element name="PopA_01.matches.tsv" ftype="tabular" value="genotypes/PopA_01.matches.tsv" />
118 <element name="PopA_01.snps.tsv" ftype="tabular" value="genotypes/PopA_01.snps.tsv" />
119 <element name="PopA_01.tags.tsv" ftype="tabular" value="genotypes/PopA_01.tags.tsv" />
120 <element name="PopA_02.alleles.tsv" ftype="tabular" value="genotypes/PopA_02.alleles.tsv" />
121 <element name="PopA_02.matches.tsv" ftype="tabular" value="genotypes/PopA_02.matches.tsv" />
122 <element name="PopA_02.snps.tsv" ftype="tabular" value="genotypes/PopA_02.snps.tsv" />
123 <element name="PopA_02.tags.tsv" ftype="tabular" value="genotypes/PopA_02.tags.tsv" />
124 </collection>
125 </param>
126 <param name="reads" value="demultiplexed/PopA_01.2.fq,demultiplexed/PopA_02.2.fq" ftype="fastqsanger" />
127 <param name="velvet|use_velvet" value="true" />
128 <param name="velvet|contig_length" value="20" />
129
130 <output_collection name="collated">
131 <element name="1">
132 <assert_contents>
133 <has_text text="CCGATCAGCATCAGTAGTTTTCAACGAGCTGGCCCAATGGTGTATAACTATGTGGTAGAGAGAAACTGCTGCTATCACTCACGATATAAGCCCTCTGACG" />
134 </assert_contents>
135 </element>
136 </output_collection>
137
138 <output name="contigs">
139 <assert_contents>
140 <has_text text="TGTATTCTCCCATGCGACAGCAGGACATCCCATCCCCCTCTGATGTTATCAATCATAAGA" />
141 </assert_contents>
142 </output>
143 </test>
144 </tests>
145
146 <help>
147 <![CDATA[
148 .. class:: infomark
149
150 **What it does**
151
152 This program will run each of the Stacks sort_read_pairs.pl and exec_velvet.pl utilities to assemble pair-end reads from STACKS pipeline results
153
154 --------
155
156 **Input file**
157
158 Output from denovo_map or ref_map
159
160
161 **Output file**
162
163 A collated.fa file containing assembled contigs for each locus
164
165 @STACKS_INFOS@
166 ]]>
167 </help>
168 <expand macro="citation" />
169 </tool>