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comparison fastx_artifacts_filter.xml @ 3:dd3737e40dce draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
author iuc
date Tue, 08 May 2018 13:27:02 -0400
parents 09070cacefd8
children 567d5b3c52b1
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2:09070cacefd8 3:dd3737e40dce
1 <tool id="cshl_fastx_artifacts_filter" version="1.0.0" name="Remove sequencing artifacts"> 1 <tool id="cshl_fastx_artifacts_filter" version="1.0.1" name="Remove sequencing artifacts">
2 <description></description> 2 <description></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 < '$input' | fastx_artifacts_filter -v -o '$output' 8 @CATS@ fastx_artifacts_filter
9 #if $input.ext == "fastqsanger": 9 -v
10 -Q 33 10 -o '$output'
11 #end if 11 @FQQUAL@
12 ]]> 12 ]]></command>
13 </command>
14 13
15 <inputs> 14 <inputs>
16 <param format="fasta,fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="Library to filter" /> 15 <expand macro="fastx_input" />
17 </inputs> 16 </inputs>
18 <outputs> 17 <outputs>
19 <data format_source="input" name="output" metadata_source="input" /> 18 <data name="output" format_source="input" metadata_source="input" />
20 </outputs> 19 </outputs>
21 <tests> 20 <tests>
22 <test> 21 <test>
23 <!-- Filter FASTA file --> 22 <!-- Filter FASTA file -->
24 <param name="input" value="fastx_artifacts1.fasta" /> 23 <param name="input" value="fastx_artifacts1.fasta" />
28 <!-- Filter FASTQ file --> 27 <!-- Filter FASTQ file -->
29 <param name="input" value="fastx_artifacts2.fastq" ftype="fastqsanger" /> 28 <param name="input" value="fastx_artifacts2.fastq" ftype="fastqsanger" />
30 <output name="output" ftype="fastqsanger" file="fastx_artifacts2.out" /> 29 <output name="output" ftype="fastqsanger" file="fastx_artifacts2.out" />
31 </test> 30 </test>
32 </tests> 31 </tests>
33 <help> 32 <help><![CDATA[
34 **What it does** 33 **What it does**
35 34
36 This tool filters sequencing artifacts (reads with all but 3 identical bases). 35 This tool filters sequencing artifacts (reads with all but 3 identical bases).
37 36
38 -------- 37 --------
85 ------ 84 ------
86 85
87 This tool is based on `FASTX-toolkit`__ by Assaf Gordon. 86 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
88 87
89 .. __: http://hannonlab.cshl.edu/fastx_toolkit/ 88 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
90 </help> 89 ]]></help>
90 <expand macro="citations" />
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>