Mercurial > repos > devteam > fastx_collapser
comparison fastx_collapser.xml @ 3:7ce1891db6f5 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_collapser commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
author | iuc |
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date | Tue, 08 May 2018 13:27:36 -0400 |
parents | 421f0af4ee95 |
children | 07497255281e |
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2:421f0af4ee95 | 3:7ce1891db6f5 |
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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> |