Mercurial > repos > artbio > justgzip

changeset 1:32b19379cd25 draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit 33e1e0491fc6ba65ac9777c06a7f736592f6d2e3"
author artbio
date Wed, 06 Apr 2022 10:12:12 +0000
parents 401afd3c5220
children 285d48249ba2
files gzip.xml
diffstat 1 files changed, 11 insertions(+), 18 deletions(-) [+]
line wrap: on
line diff
--- a/gzip.xml	Wed May 16 12:59:10 2018 -0400
+++ b/gzip.xml	Wed Apr 06 10:12:12 2022 +0000
@@ -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>