| Previous changeset 0:401afd3c5220 (2018-05-16) Next changeset 2:285d48249ba2 (2023-12-13) |
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Commit message:
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit 33e1e0491fc6ba65ac9777c06a7f736592f6d2e3" |
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modified:
gzip.xml |
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| diff -r 401afd3c5220 -r 32b19379cd25 gzip.xml --- a/gzip.xml Wed May 16 12:59:10 2018 -0400 +++ b/gzip.xml Wed Apr 06 10:12:12 2022 +0000 |
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| @@ -1,37 +1,30 @@ -<tool id="justgzip" name="Gzip sequence datasets" version="0.1.0"> +<tool id="justgzip" name="Gzip datasets" version="0.2" profile="21.01"> <description></description> <stdio> <exit_code range="1:" level="fatal" description="Tool exception" /> </stdio> <command detect_errors="exit_code"><![CDATA[ -gzip -ck '${input1}' > $output +gzip -c '${input1}' > '$output' +#if ($input1.ext.startswith("fastq") and not $input1.ext.endswith(".gz")) or $input1.ext in ["fasta", "paf", "gff3", "nii1", "nii2", "gii", "tabular"]: + #set ext = $input1.ext + ".gz" +#else + #set ext = "gz" +#end if +&& echo '{"output": {"ext": "$ext"}}' >> galaxy.json ]]></command> <inputs> - <param format="fastq" name="input1" type="data" label="Input file" help="file to compress" /> - <param name="datatype" type="select" label="Input file datatype" help="Input file datatype" > - <option value="sanger" >fastqsanger </option> - <option value="illumina" >fastqillumina </option> - <option value="fastq" selected="true" >fastq </option> - </param> + <param format="data" name="input1" type="data" label="Input file" help="file to compress" /> </inputs> <outputs> - - <data name="output" format="fastq.gz" label="$input1.name " > - <change_format> - <when input="datatype" value="sanger" format="fastqsanger.gz" /> - <when input="datatype" value="illumina" format="fastqillumina.gz" /> - </change_format> - </data> + <data name="output" format="auto" label="${input1.name}.gz" /> </outputs> <tests> <test> <param name="input1" value="file1" ftype="fastq" /> - <param name="datatype" value="fastq" /> <output name="output" file="file1.gz" decompress="True" ftype="fastq.gz"/> </test> <test> <param name="input1" value="file1" ftype="fastqsanger" /> - <param name="datatype" value="sanger" /> <output name="output" file="file1.gz" decompress="True" ftype="fastqsanger.gz" /> </test> @@ -42,7 +35,7 @@ **What it does** -Just **gzip** fastq, fastqillumina and fastqsanger datasets. +Just **gzip** datasets. </help> </tool> |