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comparison read_hexamer.xml @ 63:27e16a30667a draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit d7544582d5599c67a284faf9232cd2ccc4daa1de
author iuc
date Tue, 09 Apr 2024 11:24:55 +0000
parents 5968573462fa
children
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equal deleted inserted replaced
62:473382134e56 63:27e16a30667a
4 </description> 4 </description>
5 <macros> 5 <macros>
6 <import>rseqc_macros.xml</import> 6 <import>rseqc_macros.xml</import>
7 </macros> 7 </macros>
8 <expand macro="bio_tools"/> 8 <expand macro="bio_tools"/>
9 <expand macro="requirements" /> 9 <expand macro="requirements"/>
10 10 <expand macro="stdio"/>
11 <expand macro="stdio" />
12
13 <version_command><![CDATA[read_hexamer.py --version]]></version_command> 11 <version_command><![CDATA[read_hexamer.py --version]]></version_command>
14
15 <command><![CDATA[ 12 <command><![CDATA[
16 #import re 13 #import re
17 #set $input_list = [] 14 #set $input_list = []
18 #for $i, $input in enumerate($inputs): 15 #for $i, $input in enumerate($inputs):
19 16
37 -g '${refgene}' 34 -g '${refgene}'
38 #end if 35 #end if
39 > '${output}' 36 > '${output}'
40 ]]> 37 ]]>
41 </command> 38 </command>
42
43 <inputs> 39 <inputs>
44 <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" /> 40 <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"/>
45 <param name="refgenome" type="data" label="Reference genome seqeunce (fasta)" format="fasta" optional="true" help="(--refgenome)" /> 41 <param name="refgenome" type="data" label="Reference genome seqeunce (fasta)" format="fasta" optional="true" help="(--refgenome)"/>
46 <param name="refgene" type="data" label="Reference mRNA sequence (fasta)" format="fasta" optional="true" help="(--refgene)" /> 42 <param name="refgene" type="data" label="Reference mRNA sequence (fasta)" format="fasta" optional="true" help="(--refgene)"/>
47 </inputs> 43 </inputs>
48
49 <outputs> 44 <outputs>
50 <data name="output" format="tabular" label="${tool.name} on ${on_string}" /> 45 <data name="output" format="tabular" label="${tool.name} on ${on_string}"/>
51 </outputs> 46 </outputs>
52
53 <tests> 47 <tests>
54 <test> 48 <test expect_num_outputs="1">
55 <param name="inputs" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.R1.fastq"/> 49 <param name="inputs" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.R1.fastq"/>
56 <output name="output"> 50 <output name="output">
57 <assert_contents> 51 <assert_contents>
58 <has_line line="Hexamer&#009;pairend_strandspecific_51mer_hg19_chr1_1-100000_R1_fastq" /> 52 <has_line line="Hexamer&#9;pairend_strandspecific_51mer_hg19_chr1_1-100000_R1_fastq"/>
59 <has_text text="0.002173913043478261" /> 53 <has_text text="0.002173913043478261"/>
60 </assert_contents> 54 </assert_contents>
61 </output> 55 </output>
62 </test> 56 </test>
63 <test> 57 <test expect_num_outputs="1">
64 <param name="inputs" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.R1.fastq.gz" ftype="fastqsanger.gz"/> 58 <param name="inputs" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.R1.fastq.gz" ftype="fastqsanger.gz"/>
65 <output name="output"> 59 <output name="output">
66 <assert_contents> 60 <assert_contents>
67 <has_line line="Hexamer&#009;pairend_strandspecific_51mer_hg19_chr1_1-100000_R1_fastq_gz" /> 61 <has_line line="Hexamer&#9;pairend_strandspecific_51mer_hg19_chr1_1-100000_R1_fastq_gz"/>
68 <has_text text="0.002173913043478261" /> 62 <has_text text="0.002173913043478261"/>
69 </assert_contents> 63 </assert_contents>
70 </output> 64 </output>
71 </test> 65 </test>
72 <test> 66 <test expect_num_outputs="1">
73 <param name="inputs" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.R1.fastq,pairend_strandspecific_51mer_hg19_chr1_1-100000.R2.fastq"/> 67 <param name="inputs" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.R1.fastq,pairend_strandspecific_51mer_hg19_chr1_1-100000.R2.fastq"/>
74 <output name="output"> 68 <output name="output">
75 <assert_contents> 69 <assert_contents>
76 <has_line line="Hexamer&#009;pairend_strandspecific_51mer_hg19_chr1_1-100000_R1_fastq&#009;pairend_strandspecific_51mer_hg19_chr1_1-100000_R2_fastq" /> 70 <has_line line="Hexamer&#9;pairend_strandspecific_51mer_hg19_chr1_1-100000_R1_fastq&#9;pairend_strandspecific_51mer_hg19_chr1_1-100000_R2_fastq"/>
77 <has_text text="0.002173913043478261" /> 71 <has_text text="0.002173913043478261"/>
78 </assert_contents> 72 </assert_contents>
79 </output> 73 </output>
80 </test> 74 </test>
81 <test> 75 <test expect_num_outputs="1">
82 <param name="inputs" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.R1.fastq,pairend_strandspecific_51mer_hg19_chr1_1-100000.R1.fastq"/> 76 <param name="inputs" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.R1.fastq,pairend_strandspecific_51mer_hg19_chr1_1-100000.R1.fastq"/>
83 <output name="output"> 77 <output name="output">
84 <assert_contents> 78 <assert_contents>
85 <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" /> 79 <has_line line="Hexamer&#9;pairend_strandspecific_51mer_hg19_chr1_1-100000_R1_fastq&#9;pairend_strandspecific_51mer_hg19_chr1_1-100000_R1_fastq.1"/>
86 <has_text text="0.002173913043478261" /> 80 <has_text text="0.002173913043478261"/>
87 </assert_contents> 81 </assert_contents>
88 </output> 82 </output>
89 </test> 83 </test>
90 <!-- Unable to test with collections at the moment (requires type="data_collection" on the input) 84 <!-- Unable to test with collections at the moment (requires type="data_collection" on the input)
91 <test> 85 <test>
97 </param> 91 </param>
98 <output name="output" file="output.read_hexamer.2.txt" /> 92 <output name="output" file="output.read_hexamer.2.txt" />
99 </test> 93 </test>
100 --> 94 -->
101 </tests> 95 </tests>
102
103 <help><![CDATA[ 96 <help><![CDATA[
104 read_hexamer.py 97 read_hexamer.py
105 +++++++++++++++++++++ 98 +++++++++++++++++++++
106 99
107 Calculate hexamer (6mer) frequency. If ‘-r’ was specified, hexamer frequency 100 Calculate hexamer (6mer) frequency. If ‘-r’ was specified, hexamer frequency
128 121
129 @ABOUT@ 122 @ABOUT@
130 123
131 ]]> 124 ]]>
132 </help> 125 </help>
133 126 <expand macro="citations"/>
134 <expand macro="citations" />
135
136 </tool> 127 </tool>