| Previous changeset 3:e0b44bf2543e (2018-08-05) Next changeset 5:3e2551a37201 (2018-08-10) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 761a954744119f6317afe28eb50bd4f3fdea4984 |
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modified:
fastp.xml |
| b |
| diff -r e0b44bf2543e -r 7c82cb2a90c4 fastp.xml --- a/fastp.xml Sun Aug 05 18:02:58 2018 -0400 +++ b/fastp.xml Wed Aug 08 08:49:26 2018 -0400 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="fastp" name="fastp" version="@WRAPPER_VERSION@.0"> +<tool id="fastp" name="fastp" version="@WRAPPER_VERSION@.1"> <description>- fast all-in-one preprocessing for FASTQ files</description> <macros> <import>macros.xml</import> @@ -8,44 +8,42 @@ </requirements> <version_command>fastp -v</version_command> <command detect_errors="exit_code"><![CDATA[ +#import re + ## Link input files #if $in1.is_of_type('fastq.gz') - #set ext = 'fastq.gz' + #set ext = '.fastq.gz' #else - #set ext = 'fastq' + #set ext = '.fastq' #end if -ln -s '$in1' input1.$ext && +#set $in1_name = re.sub('[^\w\-\s]', '_', str($in1.element_identifier)) + $ext +ln -s '$in1' $in1_name && #if str($single_paired.single_paired_selector) == 'paired': - ln -s '$in2' input2.$ext && + #set $in2_name = re.sub('[^\w\-\s]', '_', str($in2.element_identifier)) + $ext + ln -s '$in2' $in2_name && #end if -## Set filename for output report - -#import re -#set $filename = re.sub('[^\w\-\s]', '_', str($in1.element_identifier)) - - ## Run fastp fastp --thread \${GALAXY_SLOTS:-1} ---report_title 'fastp report for $filename' +--report_title 'fastp report for $in1_name' #if $in1.is_of_type('fastqillumina', 'fastqsolexa', 'fastqillumina.gz', 'fastqsolexa.gz'): --phred64 #end if --i input1.$ext --o first.$ext +-i $in1_name +-o first${ext} #if str($single_paired.single_paired_selector) == 'paired': - -I input2.$ext - -O second.$ext + -I $in2_name + -O second${ext} #end if @@ -184,10 +182,10 @@ && -mv first.$ext '${out1}' +mv first${ext} '${out1}' #if str($single_paired.single_paired_selector) == 'paired': && - mv second.$ext '${out2}' + mv second${ext} '${out2}' #end if ]]></command> <inputs> @@ -309,7 +307,7 @@ <section name="output_options" title="Output Options" expanded="False"> <param name="report_html" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Output HTML report" help="fastp provides a QC report for the data Before and After filtering within a single HTML page, which enables comparison of the quality statistics changed by the preprocessing step directly"/> - <param name="report_json" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output JSON report" help="The JSON report contains all the data visualized in the HTML report. The format of the JSON report is manually optimized to be easily readable by humans"/> + <param name="report_json" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output JSON report" help="The JSON report contains all the data visualized in the HTML report. The format of the JSON report is manually optimized to be easily readable by humans and is compatible with MultiQC"/> </section> </inputs> @@ -469,7 +467,7 @@ Optionally, under **Output Options** you can choose to output * HTML report (default is Yes) - * JSON report + * JSON report (compatible with MultiQC) .. _fastp: https://github.com/OpenGene/fastp |