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comparison fasta_compute_length.xml @ 4:e12f68d2cc4e draft

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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
author devteam
date Sun, 01 Mar 2020 07:24:10 -0500
parents 2051602a5f97
children 7d37cfda8e00
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3:2051602a5f97 4:e12f68d2cc4e
1 <?xml version="1.0"?> 1 <tool id="fasta_compute_length" name="Compute sequence length" version="1.0.2" profile="16.04">
2 <tool id="fasta_compute_length" name="Compute sequence length" version="1.0.2">
3 <description></description> 2 <description></description>
3 <requirements>
4 <requirement type="package" version="3.7">python</requirement>
5 </requirements>
4 <command> 6 <command>
5 #if $ref.ref_source == 'dbkey': 7 #if $ref.ref_source == 'dbkey':
6 cp '${ref.index.fields.len_path}' '$output' 8 cp '${ref.index.fields.len_path}' '$output'
7 #else: 9 #else:
8 python $__tool_directory__/fasta_compute_length.py 10 python '$__tool_directory__/fasta_compute_length.py'
9 #if $ref.ref_source == 'history': 11 #if $ref.ref_source == 'history':
10 '$input' 12 '$input'
11 #else: 13 #else:
12 '${ref.index.fields.path}' 14 '${ref.index.fields.path}'
13 #end if 15 #end if
83 <param name="ref|ref_source" value="dbkey" /> 85 <param name="ref|ref_source" value="dbkey" />
84 <param name="ref|index" value="test_id"/> 86 <param name="ref|index" value="test_id"/>
85 <output name="output" file="merged.tab" /> 87 <output name="output" file="merged.tab" />
86 </test> 88 </test>
87 </tests> 89 </tests>
88 <help> 90 <help><![CDATA[
89 91
90 **What it does** 92 **What it does**
91 93
92 This tool counts the length of each fasta sequence in the file. The output file has two columns per line (separated by tab): fasta titles and lengths of the sequences. The option *How many characters to keep?* allows to select a specified number of letters from the beginning of each FASTA entry. 94 This tool counts the length of each fasta sequence in the file. The output file has two columns per line (separated by tab): fasta titles and lengths of the sequences. The option *How many characters to keep?* allows to select a specified number of letters from the beginning of each FASTA entry.
93 95
95 97
96 **Example** 98 **Example**
97 99
98 Suppose you have the following FASTA formatted sequences from a Roche (454) FLX sequencing run:: 100 Suppose you have the following FASTA formatted sequences from a Roche (454) FLX sequencing run::
99 101
100 &gt;EYKX4VC02EQLO5 length=108 xy=1826_0455 region=2 run=R_2007_11_07_16_15_57_ 102 >EYKX4VC02EQLO5 length=108 xy=1826_0455 region=2 run=R_2007_11_07_16_15_57_
101 TCCGCGCCGAGCATGCCCATCTTGGATTCCGGCGCGATGACCATCGCCCGCTCCACCACG 103 TCCGCGCCGAGCATGCCCATCTTGGATTCCGGCGCGATGACCATCGCCCGCTCCACCACG
102 TTCGGCCGGCCCTTCTCGTCGAGGAATGACACCAGCGCTTCGCCCACG 104 TTCGGCCGGCCCTTCTCGTCGAGGAATGACACCAGCGCTTCGCCCACG
103 &gt;EYKX4VC02D4GS2 length=60 xy=1573_3972 region=2 run=R_2007_11_07_16_15_57_ 105 &gt;EYKX4VC02D4GS2 length=60 xy=1573_3972 region=2 run=R_2007_11_07_16_15_57_
104 AATAAAACTAAATCAGCAAAGACTGGCAAATACTCACAGGCTTATACAATACAAATGTAAfa 106 AATAAAACTAAATCAGCAAAGACTGGCAAATACTCACAGGCTTATACAATACAAATGTAAfa
105 107
108 EYKX4VC02EQLO5 108 110 EYKX4VC02EQLO5 108
109 EYKX4VC02D4GS2 60 111 EYKX4VC02D4GS2 60
110 112
111 However, if your IDs are not all the same length, you may wish to just keep the fasta ID, and not the description:: 113 However, if your IDs are not all the same length, you may wish to just keep the fasta ID, and not the description::
112 114
113 &gt;EYKX4VC02EQLO5 length=108 xy=1826_0455 region=2 run=R_2007_11_07_16_15_57_ 115 >EYKX4VC02EQLO5 length=108 xy=1826_0455 region=2 run=R_2007_11_07_16_15_57_
114 TCCGCGCCGAGCATGCCCATCTTGGATTCCGGCGCGATGACCATCGCCCGCTCCACCACG 116 TCCGCGCCGAGCATGCCCATCTTGGATTCCGGCGCGATGACCATCGCCCGCTCCACCACG
115 TTCGGCCGGCCCTTCTCGTCGAGGAATGACACCAGCGCTTCGCCCACG 117 TTCGGCCGGCCCTTCTCGTCGAGGAATGACACCAGCGCTTCGCCCACG
116 &gt;EYKX4VC length=60 xy=1573_3972 region=2 run=R_2007_11_07_16_15_57_ 118 >EYKX4VC length=60 xy=1573_3972 region=2 run=R_2007_11_07_16_15_57_
117 AATAAAACTAAATCAGCAAAGACTGGCAAATACTCACAGGCTTATACAATACAAATGTAAfa 119 AATAAAACTAAATCAGCAAAGACTGGCAAATACTCACAGGCTTATACAATACAAATGTAAfa
118 120
119 Running this tool with **Strip fasta description from header** set to **True** and **How many characters to keep?** set to **0** will produce:: 121 Running this tool with **Strip fasta description from header** set to **True** and **How many characters to keep?** set to **0** will produce::
120 122
121 EYKX4VC02EQLO5 108 123 EYKX4VC02EQLO5 108
122 EYKX4VC 60 124 EYKX4VC 60
123 125
124 126
125 </help> 127 ]]></help>
126 <citations> 128 <citations>
127 <citation type="doi">10.1093/bioinformatics/btq281</citation> 129 <citation type="doi">10.1093/bioinformatics/btq281</citation>
128 </citations> 130 </citations>
129 </tool> 131 </tool>