Mercurial > repos > iuc > umi_tools_whitelist
changeset 4:095c349b4343 draft
planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
| author | iuc |
|---|---|
| date | Mon, 16 Apr 2018 16:38:19 -0400 |
| parents | 853f74e08009 |
| children | a211847807c4 |
| files | macros.xml umi-tools_whitelist.xml |
| diffstat | 2 files changed, 71 insertions(+), 65 deletions(-) [+] |
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--- a/macros.xml Sat Mar 31 17:36:28 2018 -0400 +++ b/macros.xml Mon Apr 16 16:38:19 2018 -0400 @@ -1,5 +1,41 @@ <?xml version="1.0"?> <macros> + <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." > + </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> @@ -20,4 +56,33 @@ </requirements> </xml> <token name="@VERSION@">0.5.3</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>
--- a/umi-tools_whitelist.xml Sat Mar 31 17:36:28 2018 -0400 +++ b/umi-tools_whitelist.xml Mon Apr 16 16:38:19 2018 -0400 @@ -2,51 +2,10 @@ <description>Extract cell barcodes from FASTQ files</description> <macros> <import>macros.xml</import> - <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."> - </param> - </when> - </conditional> - </macro> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![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 '$input_type.input_readpair.reverse' input_read2.txt && - #end if - #end if + @COMMAND_LINK@ umi_tools whitelist --bc-pattern='$bc_pattern' @@ -65,7 +24,7 @@ --stdin=input_read1.txt --read2-in=input_read2.txt #end if - #if $input_type.barcode.barcode_select == "1": + #if $input_type.barcode.barcode_select == "both_reads": --bc-pattern2='$input_type.barcode.bc_pattern2' #end if #end if @@ -105,25 +64,7 @@ mv OUT_cell_thresholds.tsv '$out_thresh' ]]></command> <inputs> - <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> + <expand macro="input_types" /> <param name="bc_pattern" argument="--bc-pattern" type="text" label="Barcode pattern for first read" help="Use this option to specify the format of the UMI/barcode. Use Ns to represent the random positions and Xs to indicate the bc positions. @@ -180,8 +121,8 @@ <param name="type" value="paired" /> <param name="input_read1" value="t_R1.fastq.gz" ftype="fastq" /> <param name="input_read2" value="t_R2.fastq.gz" ftype="fastq" /> - <param name="barcode_select" value="both_reads" /> - <param name="bc_pattern" value="CCCNNNNNNNNXXXXX" /> + <param name="barcode_select" value="first_read_only" /> + <param name="bc_pattern" value="CCCNNNNNNNNXXXXX" /> <param name="bc_pattern2" value="CCCCCCCCNNNNNNNN" /> <param name="method" value="reads" /> <param name="prime3" value="false" /> @@ -202,7 +143,7 @@ <element name="reverse" ftype="fastq.gz" value="t_R2.fastq.gz" /> </collection> </param> - <param name="barcode_select" value="both_reads" /> + <param name="barcode_select" value="first_read_only" /> <param name="bc_pattern" value="CCCNNNNNNNNXXXXX" /> <param name="bc_pattern2" value="CCCCCCCCNNNNNNNN" /> <param name="method" value="reads" />