Mercurial > repos > devteam > fastq_to_fasta
diff fastq_to_fasta.xml @ 5:b8e3c0a52f33 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit 415a5c5de30530910f3039e5fc66aa15103c6f20
| author | iuc |
|---|---|
| date | Tue, 27 Jun 2023 17:37:16 +0000 |
| parents | 5dbca5fbdc45 |
| children | 0a759fe3fd43 |
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--- a/fastq_to_fasta.xml Thu Jan 30 18:26:18 2020 +0000 +++ b/fastq_to_fasta.xml Tue Jun 27 17:37:16 2023 +0000 @@ -9,7 +9,11 @@ $SKIPN $RENAMESEQ -v @FQQUAL@ -@GZIP@ > '$output' +#if $compress_output == 'yes' or ($compress_output == 'infer' and ($input.ext.endswith('.gz') or $input.ext.endswith('.bz2'))): + | gzip -c > '$output_gz' +#else: + > '$output' +#end if ]]></command> <inputs> <expand macro="fastq_input" /> @@ -21,32 +25,70 @@ <option value="-r">yes</option> <option value="">no</option> </param> + <param name="compress_output" type="select" label="Compress output FASTA"> + <option value="infer" selected="true">Infer from input data</option> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> </inputs> <outputs> - <data name="output" format="fasta" metadata_source="input" /> + <data name="output" format="fasta" metadata_source="input" label="${tool.name} on ${on_string}: FASTA"> + <filter> + compress_output == 'no' or compress_output == 'infer' and not (input.ext.endswith('.gz') or input.ext.endswith('.bz2')) + </filter> + </data> + <data name="output_gz" format="fasta.gz" metadata_source="input" label="${tool.name} on ${on_string}: FASTA.gz"> + <filter> + compress_output == 'yes' or compress_output == 'infer' and input.ext.endswith('.gz') or input.ext.endswith('.bz2') + </filter> + </data> </outputs> <tests> - <test> - <!-- FASTQ-To-FASTA, keep N, don't rename --> + <test expect_num_outputs="1" > + <!-- 1 FASTQ-To-FASTA, keep N, don't rename --> <param name="input" value="fastq_to_fasta1.fastq" ftype="fastqsolexa" /> <param name="SKIPN" value=""/> <param name="RENAMESEQ" value=""/> <output name="output" file="fastq_to_fasta1a.out" /> </test> - <test> - <!-- FASTQ-To-FASTA, discard N, rename --> + <test expect_num_outputs="1" > + <!-- 2 FASTQ-To-FASTA, discard N, rename --> <param name="input" value="fastq_to_fasta1.fastq" ftype="fastqsolexa" /> <param name="SKIPN" value="no"/> <param name="RENAMESEQ" value="yes"/> <output name="output" file="fastq_to_fasta1b.out" /> </test> - <test> - <!-- FASTQ-To-FASTA, discard N, rename --> + <test expect_num_outputs="1" > + <!-- 3 FASTQ-To-FASTA, discard N, rename --> <param name="input" value="fastq_to_fasta-in2.fastq" ftype="fastqsanger" /> <param name="SKIPN" value="no"/> <param name="RENAMESEQ" value="yes"/> <output name="output" file="fastq_to_fasta-out2.out" /> </test> + <test expect_num_outputs="1" > + <!-- 4 Infer FASTQ.GZ-To-FASTA.GZ --> + <param name="input" value="fastq_to_fasta-in2.fastq.gz" ftype="fastqsanger.gz" /> + <param name="SKIPN" value="no"/> + <param name="RENAMESEQ" value="yes"/> + <param name="compress_output" value="infer"/> + <output name="output" file="fastq_to_fasta-out2.out.gz" compare="sim_size" delta="50" /> + </test> + <test expect_num_outputs="1" > + <!-- 5 Force FASTQ.GZ-To-FASTA --> + <param name="input" value="fastq_to_fasta-in2.fastq.gz" ftype="fastqsanger.gz" /> + <param name="SKIPN" value="no"/> + <param name="RENAMESEQ" value="yes"/> + <param name="compress_output" value="no"/> + <output name="output" file="fastq_to_fasta-out2.out"/> + </test> + <test expect_num_outputs="1" > + <!-- 6 Force FASTQ-To-FASTA.GZ --> + <param name="input" value="fastq_to_fasta-in2.fastq" ftype="fastqsanger" /> + <param name="SKIPN" value="no"/> + <param name="RENAMESEQ" value="yes"/> + <param name="compress_output" value="yes"/> + <output name="output" file="fastq_to_fasta-out2.out.gz" compare="sim_size" delta="50" /> + </test> </tests> <help><![CDATA[ **What it does**