Mercurial > repos > artbio > tarfast5
comparison tarfast5.xml @ 4:56b8caf469f3 draft
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit 249d82b663920626adc7d5300ffef43c065c1205"
author | artbio |
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date | Sat, 22 May 2021 12:35:41 +0000 |
parents | 75ae798e310b |
children | 03034755a509 |
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3:75ae798e310b | 4:56b8caf469f3 |
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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> |