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comparison fastx_collapser.xml @ 3:7bda0f25191f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_collapser commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
author iuc
date Tue, 08 May 2018 12:51:34 -0400
parents 17bfc147c9ea
children 1e76bd67fb73
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2:17bfc147c9ea 3:7bda0f25191f
1 <tool id="cshl_fastx_collapser" version="1.0.0" name="Collapse"> 1 <tool id="cshl_fastx_collapser" version="1.0.1" name="Collapse">
2 <description>sequences</description> 2 <description>sequences</description>
3 <requirements> 3 <macros>
4 <requirement type="package" version="0.0.13">fastx_toolkit</requirement> 4 <import>macros.xml</import>
5 </requirements> 5 </macros>
6 <command> 6 <expand macro="requirements" />
7 <![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 zcat -f < '$input' | fastx_collapser -v -o '$output' 8 @CATS@ fastx_collapser -v
9 #if $input.ext == "fastqsanger": 9 -o '$output'
10 -Q 33 10 @FQQUAL@
11 #end if 11 ]]></command>
12 ]]>
13 </command>
14 12
15 <inputs> 13 <inputs>
16 <param format="fasta,fastqsanger,fastqsolexa" name="input" type="data" label="Library to collapse" /> 14 <expand macro="fastx_input" />
17 </inputs> 15 </inputs>
18 <outputs> 16 <outputs>
19 <data format="fasta" name="output" metadata_source="input" /> 17 <data name="output" format="fasta" metadata_source="input" />
20 </outputs> 18 </outputs>
21 <!-- The order of sequences in the test output differ between 32 bit and 64 bit machines.
22 <tests> 19 <tests>
23 <test> 20 <test>
24 <param name="input" value="fasta_collapser1.fasta" /> 21 <param name="input" value="fasta_collapser1.fasta" />
25 <param name="output" file="fasta_collapser1.out" /> 22 <!-- The output is sorted differently depending on architecture,
23 so the sort attribute is needed here -->
24 <output name="output" file="fasta_collapser1.out" sort="true" />
26 </test> 25 </test>
27 </tests> 26 </tests>
28 --> 27 <help><![CDATA[
29 <help>
30 **What it does** 28 **What it does**
31 29
32 This tool collapses identical sequences in a FASTA file into a single sequence. 30 This tool collapses identical sequences in a FASTA file into a single sequence.
33 31
34 -------- 32 --------
78 >2-4 76 >2-4
79 ATAT 77 ATAT
80 78
81 means that the sequence "ATAT" is the second sequence in the file, and it appeared 4 times in the input FASTA file. 79 means that the sequence "ATAT" is the second sequence in the file, and it appeared 4 times in the input FASTA file.
82 80
83
84 ------ 81 ------
85 82
86 This tool is based on `FASTX-toolkit`__ by Assaf Gordon. 83 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
87 84
88 .. __: http://hannonlab.cshl.edu/fastx_toolkit/ 85 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
89 </help> 86 ]]></help>
87 <expand macro="citations" />
90 </tool> 88 </tool>