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comparison fastq_to_fasta.xml @ 2:4844c1810c16 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit f2582539542b33240234e8ea6093e25d0aee9b6a
author devteam
date Sat, 30 Sep 2017 13:56:09 -0400
parents 723b5b38d88a
children a64c24430f5e
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1:723b5b38d88a 2:4844c1810c16
1 <tool id="fastq_to_fasta_python" name="FASTQ to FASTA" version="1.0.0"> 1 <tool id="fastq_to_fasta_python" name="FASTQ to FASTA" version="1.1.1">
2 <description>converter</description> 2 <description>converter</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.0.0">galaxy_sequence_utils</requirement> 4 <requirement type="package" version="1.1.1">galaxy_sequence_utils</requirement>
5 </requirements> 5 </requirements>
6 <command interpreter="python">fastq_to_fasta.py '$input_file' '$output_file' '${input_file.extension[len( 'fastq' ):]}'</command> 6 <command><![CDATA[
7 <inputs> 7 gx-fastq-to-fasta '$input_file' '$output_file' '${input_file.extension[len('fastq'):]}'
8 <param name="input_file" type="data" format="fastq" label="FASTQ file to convert" /> 8 ]]></command>
9 </inputs> 9 <inputs>
10 <outputs> 10 <param name="input_file" type="data" format="fastq,fastq.gz,fastq.bz2" label="FASTQ file to convert" />
11 <data name="output_file" format="fasta" /> 11 </inputs>
12 </outputs> 12 <outputs>
13 <tests> 13 <data name="output_file" format="fasta" />
14 <!-- basic test --> 14 </outputs>
15 <test> 15 <tests>
16 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> 16 <!-- basic test -->
17 <output name="output_file" file="fastq_to_fasta_python_1.out" /> 17 <test>
18 </test> 18 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
19 <!-- color space test --> 19 <output name="output_file" file="fastq_to_fasta_python_1.out" />
20 <test> 20 </test>
21 <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastqcssanger" /> 21 <!-- color space test -->
22 <output name="output_file" file="fastq_to_fasta_python_2.out" /> 22 <test>
23 </test> 23 <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastqcssanger" />
24 <!-- test of ignoring invalid score values: this input has ascii characters falling outside of illumina range, but they should not matter --> 24 <output name="output_file" file="fastq_to_fasta_python_2.out" />
25 <test> 25 </test>
26 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqillumina" /> 26 <!-- test of ignoring invalid score values: this input has ascii characters falling outside of illumina range, but they should not matter -->
27 <output name="output_file" file="fastq_to_fasta_python_1.out" /> 27 <test>
28 </test> 28 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqillumina" />
29 </tests> 29 <output name="output_file" file="fastq_to_fasta_python_1.out" />
30 <help> 30 </test>
31 </tests>
32 <help><![CDATA[
31 **What it does** 33 **What it does**
32 34
33 This tool converts FASTQ sequencing reads to FASTA sequences. 35 This tool converts FASTQ sequencing reads to FASTA sequences.
34 36 ]]></help>
35 37 <citations>
36 </help> 38 <citation type="doi">10.1093/bioinformatics/btq281</citation>
37 39 </citations>
38 <citations>
39 <citation type="doi">10.1093/bioinformatics/btq281</citation>
40 </citations>
41
42 </tool> 40 </tool>