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comparison read_hexamer.xml @ 51:09846d5169fa draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
author iuc
date Tue, 14 Mar 2017 10:23:21 -0400
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50:f242ee103277 51:09846d5169fa
1 <tool id="rseqc_read_hexamer" name="Hexamer frequency" version="@WRAPPER_VERSION@">
2 <description>
3 calculates hexamer (6mer) frequency for reads, genomes, and mRNA sequences
4 </description>
5
6 <macros>
7 <import>rseqc_macros.xml</import>
8 </macros>
9
10 <expand macro="requirements" />
11
12 <expand macro="stdio" />
13
14 <version_command><![CDATA[read_hexamer.py --version]]></version_command>
15
16 <command><![CDATA[
17 #import re
18 #set $input_list = []
19 #for $i, $input in enumerate($inputs):
20
21 #set $safename = re.sub('[^\w\-_]', '_', $input.element_identifier)
22 #if $safename in $input_list:
23 #set $safename = str($safename) + "." + str($i)
24 #end if
25 $input_list.append($safename)
26
27 #if $input.is_of_type("fastq.gz", "fastqsanger.gz"):
28 gunzip -c '${input}' > "${safename}" &&
29 #else:
30 ln -sf '${input}' "${safename}" &&
31 #end if
32 #end for
33 read_hexamer.py -i '${ ','.join( [ $name for $name in $input_list ] ) }'
34 #if $refgenome:
35 -r '${refgenome}'
36 #end if
37 #if $refgene:
38 -g '${refgene}'
39 #end if
40 > '${output}'
41 ]]>
42 </command>
43
44 <inputs>
45 <param name="inputs" type="data" label="Read sequences in fasta or fastq format" format="fasta,fastq,fastqsanger,fastq.gz,fastqsanger.gz" help="(--input)" multiple="true" />
46 <param name="refgenome" type="data" label="Reference genome seqeunce (fasta)" format="fasta" optional="true" help="(--refgenome)" />
47 <param name="refgene" type="data" label="Reference mRNA sequence (fasta)" format="fasta" optional="true" help="(--refgene)" />
48 </inputs>
49
50 <outputs>
51 <data name="output" format="tabular" label="${tool.name} on ${on_string}" />
52 </outputs>
53
54 <tests>
55 <test>
56 <param name="inputs" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.R1.fastq"/>
57 <output name="output">
58 <assert_contents>
59 <has_line line="Hexamer&#009;pairend_strandspecific_51mer_hg19_chr1_1-100000_R1_fastq" />
60 <has_line line="AAAAAA&#009;0.00217391304348" />
61 </assert_contents>
62 </output>
63 </test>
64 <test>
65 <param name="inputs" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.R1.fastq.gz" ftype="fastqsanger.gz"/>
66 <output name="output">
67 <assert_contents>
68 <has_line line="Hexamer&#009;pairend_strandspecific_51mer_hg19_chr1_1-100000_R1_fastq_gz" />
69 <has_line line="AAAAAA&#009;0.00217391304348" />
70 </assert_contents>
71 </output>
72 </test>
73 <test>
74 <param name="inputs" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.R1.fastq,pairend_strandspecific_51mer_hg19_chr1_1-100000.R2.fastq"/>
75 <output name="output">
76 <assert_contents>
77 <has_line line="Hexamer&#009;pairend_strandspecific_51mer_hg19_chr1_1-100000_R1_fastq&#009;pairend_strandspecific_51mer_hg19_chr1_1-100000_R2_fastq" />
78 <has_line line="AAAAAA&#009;0.00217391304348&#009;0.00534759358289" />
79 </assert_contents>
80 </output>
81 </test>
82 <test>
83 <param name="inputs" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.R1.fastq,pairend_strandspecific_51mer_hg19_chr1_1-100000.R1.fastq"/>
84 <output name="output">
85 <assert_contents>
86 <has_line line="Hexamer&#009;pairend_strandspecific_51mer_hg19_chr1_1-100000_R1_fastq&#009;pairend_strandspecific_51mer_hg19_chr1_1-100000_R1_fastq.1" />
87 <has_line line="AAAAAA&#009;0.00217391304348&#009;0.00217391304348" />
88 </assert_contents>
89 </output>
90 </test>
91 <!-- Unable to test with collections at the moment (requires type="data_collection" on the input)
92 <test>
93 <param name="inputs">
94 <collection type="list">
95 <element name="read_1" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.R1.fastq" />
96 <element name="read_2" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.R2.fastq" />
97 </collection>
98 </param>
99 <output name="output" file="output.read_hexamer.2.txt" />
100 </test>
101 -->
102 </tests>
103
104 <help><![CDATA[
105 read_hexamer.py
106 +++++++++++++++++++++
107
108 Calculate hexamer (6mer) frequency. If ‘-r’ was specified, hexamer frequency
109 is also calculated for the reference genome. If ‘-g’ was provided, hexamer
110 frequency is also calculated for the mRNA sequences.
111
112 Inputs
113 ++++++++++++++
114
115 Input reads file
116 Read sequences in fasta or fastq format.
117
118 Reference Genome
119 Reference genome sequence in fasta format.
120
121 Reference Gene
122 Reference mRNA sequences in fasta format.
123
124
125 Outputs
126 ++++++++++++++
127
128 Tabular file of hexamer frequences in for each input.
129
130 @ABOUT@
131
132 ]]>
133 </help>
134
135 <expand macro="citations" />
136
137 </tool>