| Previous changeset 1:dac4e7dc837d (2018-03-27) Next changeset 3:853f74e08009 (2018-03-31) |
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Commit message:
planemo upload commit e274ffd67bede657f4f5a2c6524023ff57f0db87 |
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modified:
umi-tools_whitelist.xml |
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| diff -r dac4e7dc837d -r c1743022a8cd umi-tools_whitelist.xml --- a/umi-tools_whitelist.xml Tue Mar 27 14:26:15 2018 -0400 +++ b/umi-tools_whitelist.xml Thu Mar 29 18:24:04 2018 -0400 |
| [ |
| @@ -1,7 +1,22 @@ -<tool id="umi_tools_whitelist" name="UMI-tools whitelist" version="@VERSION@.0"> +<tool id="umi_tools_whitelist" name="UMI-tools whitelist" version="@VERSION@.1"> <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[ @@ -11,12 +26,18 @@ ln -s '$input_type.input_single' input_single.gz && #set $gz = True #end if - #else + #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 #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 $gz = True + #end if #end if umi_tools whitelist --bc-pattern='$bc_pattern' @@ -27,7 +48,7 @@ #else --stdin='$input_type.input_single' #end if - #else: + #else: ## equally valid for both 'paired' and 'paired_collection' #if $gz: --stdin=input_read1.gz --read2-in=input_read2.gz @@ -57,7 +78,7 @@ --log='$out_log' #end if - --log2stderr + --log2stderr > '$out_whitelist' && @@ -79,6 +100,7 @@ <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" /> @@ -86,19 +108,11 @@ <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" /> - <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> + <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> <param name="bc_pattern" argument="--bc-pattern" type="text" label="Barcode pattern for first read" @@ -171,6 +185,28 @@ <output name="out_html_report" file="out_wl_paired.html" /> <output name="out_thresh" file="out_wl_paired.tresh.tab" /> </test> + <test expect_num_outputs="4"> <!-- As previous, identical outputs but paired collection input --> + <param name="type" value="paired_collection" /> + <param name="input_readpair" > + <collection type="paired"> + <element name="forward" ftype="fastq.gz" value="t_R1.fastq.gz" /> + <element name="reverse" ftype="fastq.gz" value="t_R2.fastq.gz" /> + </collection> + </param> + <param name="barcode_select" value="both_reads" /> + <param name="bc_pattern" value="CCCNNNNNNNNXXXXX" /> + <param name="bc_pattern2" value="CCCCCCCCNNNNNNNN" /> + <param name="method" value="reads" /> + <param name="prime3" value="false" /> + <param name="use_cell_opts" value="advanced" /> + <param name="expect_cells" value="5" /> + <param name="error_correct_thresh" value="3" /> + <param name="log" value="true" /> + <output name="out_whitelist" file="out_wl_paired.txt" /> + <output name="out_log" file="out_wl_paired.log" lines_diff="40" /> + <output name="out_html_report" file="out_wl_paired.html" /> + <output name="out_thresh" file="out_wl_paired.tresh.tab" /> + </test> </tests> <help><![CDATA[ |