Mercurial > repos > iuc > umi_tools_whitelist
view macros.xml @ 13:49bfe13676a1 draft
"planemo upload commit 2da1197aac6a18df9252e5da096645d2ecaece88"
author | iuc |
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date | Wed, 10 Feb 2021 19:29:21 +0000 |
parents | b9e787edcbbd |
children | 345bdf4546fd |
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<?xml version="1.0"?> <macros> <macro name="barcode_sanitizer" > <sanitizer invalid_char=""> <valid initial="string.letters,string.digits"> <add value="*" /><!-- asterisk --> <add value="," /><!-- comma --> <add value="." /><!-- period --> <add value="<" /><!-- less than --> <add value="=" /><!-- equals sign --> <add value=">" /><!-- greater than --> <add value="?" /><!-- question mark --> <add value="_" /><!-- underscore --> <add value="(" /><!-- left bracket --> <add value=")" /><!-- right bracket --> <add value="["/> <!-- left square bracket --> <add value="]"/> <!-- right square bracket --> <add value="{"/><!-- left brace --> <add value="}"/><!-- right brace --> <add value="^"/> <!-- caret --> <add value="-"/> <add value="!"/> </valid> </sanitizer> </macro> <macro name="barcode2_conditional" > <conditional name="barcode"> <param name="barcode_select" argument="--split-barcode" type="select" label="Barcode on both reads?"> <option value="first_read_only">Barcode on first read only</option> <option value="both_reads">Barcode on both reads</option> </param> <when value="first_read_only"/> <when value="both_reads"> <param name="bc_pattern2" argument="--bc-pattern2" type="text" value="" label="Barcode pattern for second read" help="Use this option to specify the format of the UMI/barcode for the second read pair if required." > <expand macro="barcode_sanitizer" /> </param> </when> </conditional> </macro> <xml name="input_types"> <conditional name="input_type"> <param name="type" type="select" label="Library type"> <option value="single">Single-end</option> <option value="paired">Paired-end</option> <option value="paired_collection">Paired-end Dataset Collection</option> </param> <when value="single"> <param name="input_single" type="data" format="fastq,fastq.gz" label="Reads in FASTQ format" /> </when> <when value="paired"> <param name="input_read1" type="data" format="fastq,fastq.gz" label="Reads in FASTQ format" /> <param name="input_read2" type="data" format="fastq,fastq.gz" label="Reads in FASTQ format" /> <expand macro="barcode2_conditional" /> </when> <when value="paired_collection"> <param name="input_readpair" type="data_collection" collection_type="paired" format="fastq,fastq.gz" label="Reads in FASTQ format" /> <expand macro="barcode2_conditional" /> </when> </conditional> </xml> <xml name="citations"> <citations> <citation type="doi">10.1101/gr.209601.116</citation> <citation type="bibtex"> @misc{githubUMI-tools, title = {UMI-tools}, publisher = {GitHub}, journal = {GitHub repository}, url = {https://github.com/CGATOxford/UMI-tools}, } </citation> </citations> </xml> <xml name="requirements"> <requirements> <requirement type="package" version="@VERSION@">umi_tools</requirement> <yield /> </requirements> </xml> <token name="@VERSION@">0.5.5</token> <token name="@COMMAND_LINK@"><![CDATA[ #set $gz = False #if $input_type.type == 'single': #if $input_type.input_single.is_of_type("fastq.gz", "fastqsanger.gz"): ln -s '$input_type.input_single' input_single.gz && #set $gz = True #else ln -s '$input_type.input_single' input_single.txt && #end if #elif $input_type.type == 'paired': #if $input_type.input_read1.is_of_type("fastq.gz", "fastqsanger.gz"): ln -s '$input_type.input_read1' input_read1.gz && ln -s '$input_type.input_read2' input_read2.gz && #set $gz = True #else ln -s '$input_type.input_read1' input_read1.txt && ln -s '$input_type.input_read2' input_read2.txt && #end if #else ## paired_collection #if $input_type.input_readpair.forward.is_of_type("fastq.gz", "fastqsanger.gz"): ln -s '$input_type.input_readpair.forward' input_read1.gz && ln -s '$input_type.input_readpair.reverse' input_read2.gz && #set $gz = True #else ln -s '$input_type.input_readpair.forward' input_read1.txt && ln -s '$input_type.input_readpair.reverse' input_read2.txt && #end if #end if ]]></token> </macros>