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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
author | iuc |
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date | Mon, 12 Mar 2018 12:53:10 -0400 |
parents | |
children | a8d69aee190e |
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<?xml version="1.0"?> <tool id="samtools_fastx" name="Samtools extract" version="@TOOL_VERSION@"> <description>FASTA or FASTQ from a SAM file</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <expand macro="version_command" /> <command detect_errors="exit_code"> <![CDATA[ samtools $output.output_format #if $output.output_format == 'fastq': -v $output.default_quality $output.output_quality #end if #if $reference: --reference '$reference' #end if $copy_flags $omit_read_number -0 '$nonspecific' -1 '$forward' -2 '$reverse' #if str($inclusive_filter) != 'None': #set $filter = $inclusive_filter @FLAGS@ -f $flags #end if #if str($exclusive_filter) != 'None': #set $filter = $exclusive_filter @FLAGS@ -F $flags #end if '$input' ]]> </command> <inputs> <param name="input" type="data" format="bam,sam" label="BAM or SAM file to convert" /> <param argument="--reference" type="data" format="fasta" optional="True" label="Reference FASTA" /> <param name="copy_flags" argument="-t" type="boolean" truevalue="-t" falsevalue="" label="Copy RG/BC/QT flags to output header" /> <param name="omit_read_number" argument="-n" type="boolean" truevalue="-n" falsevalue="" label="Do not append /1 and /2 to read names" /> <param name="inclusive_filter" argument="-f" type="select" multiple="True" label="Require that these flags be set"> <expand macro="filter_options" /> </param> <param name="exclusive_filter" argument="-F" type="select" multiple="True" label="Exclude reads with the following flags set"> <expand macro="filter_options" /> </param> <conditional name="output"> <param name="output_format" type="select" label="Output format"> <option value="fasta">FASTA</option> <option value="fastq">FASTQ</option> </param> <when value="fastq"> <param name="default_quality" argument="-v" type="integer" value="1" label="Default quality if none is given" /> <param name="output_quality" argument="-O" type="boolean" truevalue="-O" falsevalue="" label="Output quality in the OQ tag if available" /> </when> <when value="fasta" /> </conditional> </inputs> <outputs> <data name="nonspecific" format="fasta" label="${on_string} converted to ${output.output_format} (Neither or both)"> <change_format> <when input="output_format" value="fastq" format="fastq" /> </change_format> </data> <data name="forward" format="fasta" label="${on_string} converted to ${output.output_format} (READ1)"> <change_format> <when input="output_format" value="fastq" format="fastq" /> </change_format> </data> <data name="reverse" format="fasta" label="${on_string} converted to ${output.output_format} (READ2)"> <change_format> <when input="output_format" value="fastq" format="fastq" /> </change_format> </data> </outputs> <tests> <test> <param name="input" value="samtools_fastx-in1.bam" ftype="bam" /> <param name="output_format" value="fasta" /> <output name="nonspecific" file="samtools_fastx-out1-1.fasta" /> <output name="forward" file="samtools_fastx-out1-2.fasta" /> <output name="reverse" file="samtools_fastx-out1-3.fasta" /> </test> <test> <param name="input" value="samtools_fastx-in2.bam" ftype="bam" /> <param name="output_format" value="fastq" /> <output name="nonspecific" file="samtools_fastx-out2-1.fastq" /> <output name="forward" file="samtools_fastx-out2-2.fastq" /> <output name="reverse" file="samtools_fastx-out2-3.fastq" /> </test> <test> <param name="input" value="samtools_fastx-in3.sam" ftype="sam" /> <param name="output_format" value="fasta" /> <output name="nonspecific" file="samtools_fastx-out3-1.fasta" /> <output name="forward" file="samtools_fastx-out3-2.fasta" /> <output name="reverse" file="samtools_fastx-out3-3.fasta" /> </test> </tests> <help> <![CDATA[ This tool uses `Samtools <http://www.htslib.org/>`_ to extract sequences from a SAM or BAM file in FASTA or FASTQ format. ]]> </help> <expand macro="citations" /> </tool>