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comparison fastx_artifacts_filter.xml @ 2:09070cacefd8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
author devteam
date Wed, 11 Nov 2015 12:38:23 -0500
parents c8808979ba33
children dd3737e40dce
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1:c8808979ba33 2:09070cacefd8
1 <tool id="cshl_fastx_artifacts_filter" version="1.0.0" name="Remove sequencing artifacts"> 1 <tool id="cshl_fastx_artifacts_filter" version="1.0.0" name="Remove sequencing artifacts">
2 <description></description> 2 <description></description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.0.13">fastx_toolkit</requirement> 4 <requirement type="package" version="0.0.13">fastx_toolkit</requirement>
5 </requirements> 5 </requirements>
6 <command>zcat -f '$input' | fastx_artifacts_filter -v -o "$output" 6 <command>
7 <![CDATA[
8 zcat -f < '$input' | fastx_artifacts_filter -v -o '$output'
7 #if $input.ext == "fastqsanger": 9 #if $input.ext == "fastqsanger":
8 -Q 33 10 -Q 33
9 #end if 11 #end if
10 </command> 12 ]]>
13 </command>
11 14
12 <inputs> 15 <inputs>
13 <param format="fasta,fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="Library to filter" /> 16 <param format="fasta,fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="Library to filter" />
14 17 </inputs>
15 </inputs> 18 <outputs>
16 19 <data format_source="input" name="output" metadata_source="input" />
17 <tests> 20 </outputs>
18 <test> 21 <tests>
19 <!-- Filter FASTA file --> 22 <test>
20 <param name="input" value="fastx_artifacts1.fasta" /> 23 <!-- Filter FASTA file -->
21 <param name="output" file="fastx_artifacts1.out" /> 24 <param name="input" value="fastx_artifacts1.fasta" />
22 </test> 25 <output name="output" ftype="fasta" file="fastx_artifacts1.out" />
23 <test> 26 </test>
24 <!-- Filter FASTQ file --> 27 <test>
25 <param name="input" value="fastx_artifacts2.fastq" ftype="fastqsanger" /> 28 <!-- Filter FASTQ file -->
26 <param name="output" file="fastx_artifacts2.out" /> 29 <param name="input" value="fastx_artifacts2.fastq" ftype="fastqsanger" />
27 </test> 30 <output name="output" ftype="fastqsanger" file="fastx_artifacts2.out" />
28 </tests> 31 </test>
29 32 </tests>
30 <outputs> 33 <help>
31 <data format="input" name="output" metadata_source="input" />
32 </outputs>
33 <help>
34 **What it does** 34 **What it does**
35 35
36 This tool filters sequencing artifacts (reads with all but 3 identical bases). 36 This tool filters sequencing artifacts (reads with all but 3 identical bases).
37 37
38 -------- 38 --------
79 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 79 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
80 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 80 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
81 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAA 81 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAA
82 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAA 82 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAA
83 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAA 83 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAA
84 84
85 ------ 85 ------
86 86
87 This tool is based on `FASTX-toolkit`__ by Assaf Gordon. 87 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
88 88
89 .. __: http://hannonlab.cshl.edu/fastx_toolkit/ 89 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
90 </help> 90 </help>
91 <!-- FASTX-Artifacts-filter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) --> 91 <!-- FASTX-Artifacts-filter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
92 </tool> 92 </tool>