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Merge pull request #3145 from mvdbeek/fastqgz

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Support for gzipped fastq formats
This commit is contained in:
John Chilton
2017-01-11 21:18:22 -05:00
committed by GitHub
parent 34458725b8 296889d0df
commit a87feb11ff
19 changed files with 380 additions and 32 deletions
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test/functional/tools/compressed_bz2_fastq_conversion.xml
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<tool id="compressed_bz2_fastq_conversion" name="Confirm fastq.bz2 is converted to fastq on demand">
<command>
cat '$input1' > '$out_file1'
</command>
<inputs>
<param name="input1" type="data" format="fastq" label="Concatenate Dataset"/>
</inputs>
<outputs>
<data name="out_file1" format="fastq"/>
</outputs>
<tests>
<test>
<param name="input1" value="1.fastqsanger.bz2"/>
<output name="out_file1" file="1.fastqsanger"/>
</test>
</tests>
<help>
</help>
</tool>
test/functional/tools/compressed_bz2_fastq_no_conversion.xml
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<tool id="compressed_bz2_fastq_cat" name="Confirm fastq.bz2 is not uncompressed">
<command>
cat '$input1' > '$out_file1'
</command>
<inputs>
<param name="input1" type="data" format="fastq.bz2" label="Concatenate Dataset"/>
</inputs>
<outputs>
<data name="out_file1" format="fastq.bz2"/>
</outputs>
<tests>
<test>
<param name="input1" value="1.fastqsanger.bz2"/>
<output name="out_file1" file="1.fastqsanger.bz2" ftype="fastq.bz2"/>
</test>
</tests>
<help>
</help>
</tool>
test/functional/tools/compressed_gz_fastq_conversion.xml
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<tool id="compressed_gz_fastq_conversion" name="Confirm fastq.gz is converted to fastq on demand">
<command>
cat '$input1' > '$out_file1'
</command>
<inputs>
<param name="input1" type="data" format="fastq" label="Concatenate Dataset"/>
</inputs>
<outputs>
<data name="out_file1" format="fastq"/>
</outputs>
<tests>
<test>
<param name="input1" value="1.fastqsanger.gz"/>
<output name="out_file1" file="1.fastqsanger"/>
</test>
</tests>
<help>
</help>
</tool>
test/functional/tools/compressed_gz_fastq_no_conversion.xml
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<tool id="compressed_gz_fastq_cat" name="Confirm fastq.gz is not uncompressed">
<command>
cat '$input1' > '$out_file1'
</command>
<inputs>
<param name="input1" type="data" format="fastq.gz" label="Concatenate Dataset"/>
</inputs>
<outputs>
<data name="out_file1" format="fastq.gz"/>
</outputs>
<tests>
<test>
<param name="input1" value="1.fastqsanger.gz"/>
<output name="out_file1" file="1.fastqsanger.gz" ftype="fastq.gz"/>
</test>
</tests>
<help>
</help>
</tool>