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comparison tarfast5.xml @ 2:e660e8605dd8 draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit 62909f7108d2d371e6461a4e3f8040ebb54f1ec0"
author artbio
date Sun, 16 May 2021 18:20:09 +0000
parents 436f11e1ed6d
children 75ae798e310b
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1:436f11e1ed6d 2:e660e8605dd8
1 <tool id="tarfast5" name="tarfast5" version="0.4"> 1 <tool id="tarfast5" name="tarfast5" version="0.5.2">
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>
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}.h5 &&
13 #end for 13 #end for
14 #if $output_format == "gzip":
14 export PIGZ="-p \${GALAXY_SLOTS:-4}" && 15 export PIGZ="-p \${GALAXY_SLOTS:-4}" &&
15 tar -cvh --use-compress-program=pigz -f $compressed_output *.h5 16 tar -cvh --use-compress-program=pigz -f $output *.h5
17 #else:
18 tar -cvh -f $output *.h5
19 #end if
16 ]]></command> 20 ]]></command>
17 <inputs> 21 <inputs>
18 <param name="inputs" type="data" format="h5" label="fast5 sequence files" multiple="true" /> 22 <param name="inputs" type="data" format="h5" label="fast5 sequence files" multiple="true" />
23 <param name="output_format" type="select" label="compression of the tar archive" display="radio">
24 <option value="tar">tar (no compression)</option>
25 <option value="gzip" selected="true">tar.gz</option>
26 </param>
19 </inputs> 27 </inputs>
20 28
21 <outputs> 29 <outputs>
22 <data format="fast5.tar.gz" name="compressed_output" label="tar.gz archive of fast5" /> 30 <data format="fast5.tar" name="output" label="Archive of fast5" >
31 <change_format>
32 <when input="output_format" value="gzip" format="fast5.tar.gz"/>
33 </change_format>
34 </data>
35
36
23 </outputs> 37 </outputs>
24 38
25 <tests> 39 <tests>
26 <test> <!-- 0 --> 40 <test> <!-- tar -->
41 <param name="inputs" value="F1.fast5.h5" ftype="h5" />
42 <param name="output_format" value="tar" />
43 <output file="archive.tar" name="output" compare="sim_size" delta="3000" />
44 </test>
45
46 <test> <!-- tar.gz -->
27 <param name="inputs" value="F1.fast5.h5,F2.fast5.h5" ftype="h5" /> 47 <param name="inputs" value="F1.fast5.h5,F2.fast5.h5" ftype="h5" />
28 <output file="archive.tar.gz" name="compressed_output" compare="sim_size" delta="3000" /> 48 <param name="output_format" value="gzip" />
49 <output file="archive.tar.gz" name="output" compare="sim_size" delta="3000" />
29 </test> 50 </test>
30 </tests> 51 </tests>
31 <help> 52 <help>
32 53
33 **What it does** 54 **What it does**