Mercurial > repos > devteam > fastq_to_fasta
changeset 5:8979c288aefb 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 17:37:28 +0000 |
| parents | e282bc27be9a |
| children | 77b41c89d856 |
| files | fastq_to_fasta.xml macros.xml test-data/fastq_to_fasta-in2.fastq.gz test-data/fastq_to_fasta-out2.out.gz |
| diffstat | 4 files changed, 52 insertions(+), 25 deletions(-) [+] |
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--- a/fastq_to_fasta.xml Thu Jan 30 13:29:38 2020 -0500 +++ b/fastq_to_fasta.xml Tue Jun 27 17:37:28 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**
--- a/macros.xml Thu Jan 30 13:29:38 2020 -0500 +++ b/macros.xml Tue Jun 27 17:37:28 2023 +0000 @@ -11,22 +11,13 @@ </token> <token name="@FQQUAL@"> <![CDATA[ - #if $input.is_of_type('fastqsanger', 'fastqsanger.gz', 'fastqsanger.bz2'): + #if 'fastqsanger' in $input.ext: -Q 33 - #elif $input.is_of_type('fastqsolexa', 'fastqsolexa.gz', 'fastqsolexa.bz2', 'fastqillumina', 'fastqillumina.gz', 'fastqillumina.bz2'): + #elif 'fastqsolexa' in $input.ext or 'fastqillumina' in $input.ext: -Q 64 #end if ]]> </token> - <token name="@GZIP@"> - <![CDATA[ - #if $input.is_of_type('fasta.gz', 'fastqsanger.gz', 'fastqsolexa.gz', 'fastqillumina.gz'): - | gzip -c - #elif $input.is_of_type('fastqsanger.bz2', 'fastqsolexa.bz2', 'fastqillumina.bz2'): - | bzip2 -c - #end if - ]]> - </token> <xml name="requirements"> <requirements> <requirement type="package" version="@VERSION@">fastx_toolkit</requirement> @@ -51,13 +42,7 @@ </citation> </citations> </xml> - <xml name="fasta_input"> - <param name="input" type="data" format="@FASTAS@" label="Input FASTA file" /> - </xml> <xml name="fastq_input"> <param name="input" type="data" format="@FASTQS@" label="Input FASTQ file" /> </xml> - <xml name="fastx_input"> - <param name="input" type="data" format="@FASTAS@,@FASTQS@" label="Input file in FASTA or FASTQ format" /> - </xml> </macros>