Mercurial > repos > iuc > fastqe
changeset 3:819b8c1657d5 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
| author | iuc |
|---|---|
| date | Fri, 19 Mar 2021 21:37:48 +0000 |
| parents | a252d8415583 |
| children | ecb38e2798cd |
| files | fastqe.xml test-data/test.fq.gz test-data/test2.fq.gz |
| diffstat | 3 files changed, 21 insertions(+), 13 deletions(-) [+] |
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--- a/fastqe.xml Fri Jul 24 14:30:21 2020 -0400 +++ b/fastqe.xml Fri Mar 19 21:37:48 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="fastqe" name="FASTQE" version="0.2.6+galaxy0"> +<tool id="fastqe" name="FASTQE" version="0.2.6+galaxy1"> <description>visualize fastq files with emoji's 🧬😎</description> <requirements> <requirement type="package" version="0.2.6">fastqe</requirement> @@ -6,32 +6,36 @@ </requirements> <command detect_errors="exit_code"> <![CDATA[ - #import re - #set $filenames = [re.sub('[^\w\-\s.]', '_', $i.element_identifier) for $i in $input] - #for $i, $filename in zip($input, $filenames): - ln -s '$i' '$filename' && + mkdir inputs && + #for $i in $input + #set identifier = re.sub('[^\w\-\s.]', '_', $i.element_identifier) + #if $i.ext.endswith(".gz") and not $identifier.endswith(".gz") + #set identifier+=".gz" + #end if + ln -s $i inputs/$identifier && #end for echo "<html><head><title>FASTQE Report 🤔</title></head><body><h1>FASTQE Report 🤔</h1>" > '$output' && fastqe - --mean $bin - --min + ${" ".join(str($tpe).split(","))} --long $long - --max - #for $filename in $filenames: - '$filename' - #end for - | sed 's/$/<br>/;s/^\([^\t]*\)\t\([^\t]*\)\t/<h2>\1: \2<\/h2>\n/' >> '$output' && + ./inputs/* + | sed 's/$/<br>/;s/^\.\/inputs\/\([^\t]*\)\t\([^\t]*\)\t/<h2>\1: \2<\/h2>\n/;' >> '$output' && echo "</body></html>" >> '$output' ]]></command> <inputs> - <param label="FastQ data" name="input" type="data" format="fastq" multiple="true"/> + <param label="FastQ data" name="input" type="data" format="fastq,fastq.gz" multiple="true"/> <param label="Bin scores" name="bin" type="boolean" truevalue="--bin" falsevalue="" /> + <param label="Score types to show" name="tpe" type="select" multiple="true"> + <option value="--min" selected="true">Minimum</option> + <option value="--mean" selected="true">Minimum</option> + <option value="--max" selected="true">Minimum</option> + </param> <param label="Maximum read length" name="long" type="integer" help="Enable long reads up to this many bp long." min="1" value="500"/> </inputs> <outputs> @@ -42,6 +46,10 @@ <param name="input" value="test.fq,test2.fq" /> <output name="output" file="out.html" /> </test> + <test> + <param name="input" value="test.fq.gz,test2.fq.gz" /> + <output name="output" file="out.html" lines_diff="12"/> + </test> </tests> <help><![CDATA[ FASTQ + Emoji = FASTQE 🤔