Mercurial > repos > iuc > filtlong
diff filtlong.xml @ 2:a72af9de6bf5 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit fe7fac8c3287f5de0fe92d20fc39f71045240889"
author | iuc |
---|---|
date | Wed, 31 Mar 2021 08:19:02 +0000 |
parents | 8880fb74ef56 |
children | 41b2ad601cf0 |
line wrap: on
line diff
--- a/filtlong.xml Wed Sep 19 08:21:21 2018 -0400 +++ b/filtlong.xml Wed Mar 31 08:19:02 2021 +0000 @@ -1,8 +1,9 @@ -<tool id="filtlong" name="filtlong" version="0.2.0"> +<tool id="filtlong" name="filtlong" version="@WRAPPER_VERSION@+galaxy1" profile="@PROFILE@"> <description>Filtering long reads by quality</description> - <requirements> - <requirement type="package" version="0.2.0">filtlong</requirement> - </requirements> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> <version_command>filtlong --version</version_command> <command detect_errors="exit_code"><![CDATA[ filtlong @@ -43,7 +44,7 @@ '$input_file' > output.fastq ]]></command> <inputs> - <param name="input_file" type="data" format="fastqsanger" label="Input FASTQ" help="FASTQ of input reads"/> + <param name="input_file" type="data" format="fastqsanger,fastqsanger.gz" 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)"/> @@ -52,7 +53,7 @@ <param argument="--min_window_q" type="float" min="0" optional="True" label="Min. window quality" help="Minimum window quality threshold"/> </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="--assembly" type="data" format="fasta,fasta.gz" optional="True" label="Reference assembly" help="Reference assembly in FASTA 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> @@ -74,14 +75,15 @@ </outputs> <tests> <test> - <param name="input_file" ftype="fastqsanger" value="test.fastq"/> + <param name="input_file" ftype="fastqsanger" value="test.fastq.gz"/> <param name="min_length" value="1000"/> <param name="keep_percent" value="50"/> <param name="target_bases" value="500000000"/> <output name="outfile" ftype="fastqsanger" file="output.fastq"/> </test> <test> - <param name="input_file" ftype="fastqsanger" value="test_reference.fasta"/> + <param name="input_file" ftype="fastqsanger" value="test.fastq.gz"/> + <param name="assembly" ftype="fasta.gz" value="test_reference.fasta.gz"/> <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"/>