Mercurial > repos > iuc > filtlong
changeset 1:8880fb74ef56 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 914aebf765a006b3d284388aba0584d0035a8a66
| author | iuc |
|---|---|
| date | Wed, 19 Sep 2018 08:21:21 -0400 |
| parents | a64b45c8b174 |
| children | a72af9de6bf5 |
| files | filtlong.xml |
| diffstat | 1 files changed, 10 insertions(+), 10 deletions(-) [+] |
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--- a/filtlong.xml Mon Sep 17 16:16:07 2018 -0400 +++ b/filtlong.xml Wed Sep 19 08:21:21 2018 -0400 @@ -43,7 +43,7 @@ '$input_file' > output.fastq ]]></command> <inputs> - <param name="input_file" type="data" format="fastq" label="Input FASTQ" help="FASTQ of input reads"/> + <param name="input_file" type="data" format="fastqsanger" label="Input FASTQ" help="FASTQ of input reads"/> <section name="output_thresholds" title="Output thresholds"> <param argument="--target_bases" type="integer" min="0" optional="True" label="Total bases" help="Keep only the best reads up to this many total bases"/> <param argument="--keep_percent" type="float" min="0" max="100" optional="True" label="Keep percentage" help="Keep only this percentage of the best reads (measured by bases)"/> @@ -53,8 +53,8 @@ </section> <section name="external_references" title="External references"> <param argument="--assembly" type="data" format="fasta" optional="True" label="Reference assembly" help="Reference assembly in FASTA format"/> - <param argument="--illumina_1" type="data" format="fastq,fastq.gz" optional="True" label="Reference Illumina read" help="Reference Illumina reads in FASTQ format"/> - <param argument="--illumina_2" type="data" format="fastq,fastq.gz" optional="True" label="Reference Illumina read" help="Reference Illumina reads in FASTQ format"/> + <param argument="--illumina_1" type="data" format="fastqsanger,fastqsanger.gz" optional="True" label="Reference Illumina read" help="Reference Illumina reads in FASTQ format"/> + <param argument="--illumina_2" type="data" format="fastqsanger,fastqsanger.gz" optional="True" label="Reference Illumina read" help="Reference Illumina reads in FASTQ format"/> </section> <section name="score_weights" title="Score weights"> <param argument="--length_weight" type="float" min="0" value="1" optional="True" label="Weight length score" help="Weight given to the length score (default: 1)"/> @@ -70,26 +70,26 @@ </section> </inputs> <outputs> - <data name="outfile" format="fastq" from_work_dir="output.fastq" label="${tool.name} on ${on_string}: Filtered FASTQ"/> + <data name="outfile" format="fastqsanger" from_work_dir="output.fastq" label="${tool.name} on ${on_string}: Filtered FASTQ"/> </outputs> <tests> <test> - <param name="input_file" ftype="fastq" value="test.fastq"/> + <param name="input_file" ftype="fastqsanger" value="test.fastq"/> <param name="min_length" value="1000"/> <param name="keep_percent" value="50"/> <param name="target_bases" value="500000000"/> - <output name="outfile" ftype="fastq" file="output.fastq"/> + <output name="outfile" ftype="fastqsanger" file="output.fastq"/> </test> <test> - <param name="input_file" ftype="fastq" value="test_reference.fasta"/> - <param name="illumina_1" ftype="fastq.gz" value="test_reference_1.fastq.gz"/> - <param name="illumina_2" ftype="fastq.gz" value="test_reference_2.fastq.gz"/> + <param name="input_file" ftype="fastqsanger" value="test_reference.fasta"/> + <param name="illumina_1" ftype="fastqsanger.gz" value="test_reference_1.fastq.gz"/> + <param name="illumina_2" ftype="fastqsanger.gz" value="test_reference_2.fastq.gz"/> <param name="min_length" value="1000"/> <param name="keep_percent" value="90"/> <param name="target_bases" value="500000000"/> <param name="trim" value="True"/> <param name="split" value="500"/> - <output name="outfile" ftype="fastq" file="output_reference.fastq"/> + <output name="outfile" ftype="fastqsanger" file="output_reference.fastq"/> </test> </tests> <help><![CDATA[