comparison tarfast5.xml @ 4:56b8caf469f3 draft

"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit 249d82b663920626adc7d5300ffef43c065c1205"
author artbio
date Sat, 22 May 2021 12:35:41 +0000
parents 75ae798e310b
children 03034755a509
comparison
equal deleted inserted replaced
3:75ae798e310b 4:56b8caf469f3
1 <tool id="tarfast5" name="tarfast5" version="0.5.3"> 1 <tool id="tarfast5" name="tarfast5" version="0.6.0">
2 <description></description> 2 <description></description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.6">pigz</requirement> 4 <requirement type="package" version="2.6">pigz</requirement>
5 <requirement type="package" version="1.34">tar</requirement> 5 <requirement type="package" version="1.34">tar</requirement>
6 </requirements> 6 </requirements>
7 <stdio> 7 <stdio>
8 <exit_code range="1:" level="fatal" description="Tool exception" /> 8 <exit_code range="1:" level="fatal" description="Tool exception" />
9 </stdio> 9 </stdio>
10 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
11 #for $file in $inputs: 11 #for $file in $inputs:
12 ln -s $file ${file.element_identifier}.h5 && 12 ln -s $file ${file.element_identifier}.fast5 &&
13 #end for 13 #end for
14 #if $output_format == "gzip": 14 #if $output_format == "gzip":
15 export PIGZ="-p \${GALAXY_SLOTS:-4}" && 15 export PIGZ="-p \${GALAXY_SLOTS:-4}" &&
16 tar -cvh --use-compress-program=pigz -f $output *.h5 16 tar -cvh --use-compress-program=pigz -f $output *.fast5
17 #else: 17 #else:
18 tar -cvh -f $output *.h5 18 tar -cvh -f $output *.fast5
19 #end if 19 #end if
20 ]]></command> 20 ]]></command>
21 <inputs> 21 <inputs>
22 <param name="inputs" type="data" format="h5" label="fast5 sequence files" multiple="true" /> 22 <param name="inputs" type="data" format="h5,fast5.tar" label="fast5 sequence files" multiple="true" />
23 <param name="output_format" type="select" label="compression of the tar archive" display="radio"> 23 <param name="output_format" type="select" label="compression of the tar archive" display="radio">
24 <option value="tar">tar (no compression)</option> 24 <option value="tar">tar (no compression)</option>
25 <option value="gzip" selected="true">tar.gz</option> 25 <option value="gzip" selected="true">tar.gz</option>
26 </param> 26 </param>
27 </inputs> 27 </inputs>