Mercurial > repos > artbio > tarfast5
changeset 2:e660e8605dd8 draft
"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 |
| files | archive.tar archive.tar.gz tarfast5.xml test-data/F1.fast5.h5 test-data/F1_filename_mapping.txt test-data/F2.fast5.h5 test-data/F2_filename_mapping.txt test-data/archive.tar test-data/archive.tar.gz |
| diffstat | 7 files changed, 36 insertions(+), 5 deletions(-) [+] |
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--- a/tarfast5.xml Thu May 06 23:12:50 2021 +0000 +++ b/tarfast5.xml Sun May 16 18:20:09 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="tarfast5" name="tarfast5" version="0.4"> +<tool id="tarfast5" name="tarfast5" version="0.5.2"> <description></description> <requirements> <requirement type="package" version="2.6">pigz</requirement> @@ -11,21 +11,42 @@ #for $file in $inputs: ln -s $file ${file.element_identifier}.h5 && #end for + #if $output_format == "gzip": export PIGZ="-p \${GALAXY_SLOTS:-4}" && - tar -cvh --use-compress-program=pigz -f $compressed_output *.h5 + tar -cvh --use-compress-program=pigz -f $output *.h5 + #else: + tar -cvh -f $output *.h5 + #end if ]]></command> <inputs> <param name="inputs" type="data" format="h5" label="fast5 sequence files" multiple="true" /> + <param name="output_format" type="select" label="compression of the tar archive" display="radio"> + <option value="tar">tar (no compression)</option> + <option value="gzip" selected="true">tar.gz</option> + </param> </inputs> <outputs> - <data format="fast5.tar.gz" name="compressed_output" label="tar.gz archive of fast5" /> + <data format="fast5.tar" name="output" label="Archive of fast5" > + <change_format> + <when input="output_format" value="gzip" format="fast5.tar.gz"/> + </change_format> + </data> + + </outputs> <tests> - <test> <!-- 0 --> + <test> <!-- tar --> + <param name="inputs" value="F1.fast5.h5" ftype="h5" /> + <param name="output_format" value="tar" /> + <output file="archive.tar" name="output" compare="sim_size" delta="3000" /> + </test> + + <test> <!-- tar.gz --> <param name="inputs" value="F1.fast5.h5,F2.fast5.h5" ftype="h5" /> - <output file="archive.tar.gz" name="compressed_output" compare="sim_size" delta="3000" /> + <param name="output_format" value="gzip" /> + <output file="archive.tar.gz" name="output" compare="sim_size" delta="3000" /> </test> </tests> <help>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/F1_filename_mapping.txt Sun May 16 18:20:09 2021 +0000 @@ -0,0 +1,5 @@ +02184968-3def-4785-bd81-0bff70a57da4 batch0.fast5 +0335884d-20f0-4b7f-8f1c-ef57cd739ce6 batch0.fast5 +03bd0764-2e1f-4d60-841b-9519ea9d39cb batch0.fast5 +07b9016b-e5db-449f-b161-79f17eae34df batch0.fast5 +02343944-ac7b-41ac-85b9-dd0b040bfd6c batch0.fast5
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/F2_filename_mapping.txt Sun May 16 18:20:09 2021 +0000 @@ -0,0 +1,5 @@ +03bd0764-2e1f-4d60-841b-9519ea9d39cb batch0.fast5 +02343944-ac7b-41ac-85b9-dd0b040bfd6c batch0.fast5 +02184968-3def-4785-bd81-0bff70a57da4 batch0.fast5 +07b9016b-e5db-449f-b161-79f17eae34df batch0.fast5 +0335884d-20f0-4b7f-8f1c-ef57cd739ce6 batch0.fast5