Mercurial > repos > crusoe > khmer
diff do-partition.xml @ 45:0b238b083f77
2 more tools
| author | Michael R. Crusoe <mcrusoe@msu.edu> |
|---|---|
| date | Sat, 12 Jul 2014 11:13:21 -0400 |
| parents | |
| children | 3d65329a491d |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/do-partition.xml Sat Jul 12 11:13:21 2014 -0400 @@ -0,0 +1,93 @@ +<tool id="gedlab-khmer-do-partition" + name="Sequence partition all-in-one" + version="1.1-1" + force_history_refresh="true"> + + <description> + Load, partition, and annotate FAST[AQ] sequences + </description> + <macros> + <token name="@BINARY@">do-parition.py</token> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command> +mkdir -p output; +@BINARY@ +@TABLEPARAMS@ +@THREADS@ +output +#for input in $inputs +$input +#end for ; +mv output.info $infomation ; +mv *.part output/ + </command> + + <inputs> + <expand macro="input_sequences_filenames" /> + </inputs> + <outputs> + <data name="information" + format="text" + label="${tool.name} summary for #echo ','.join(map(str, $inputs ))#" /> + <expand macro="output_sequences" /> + </outputs> + <stdio> + <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> + <exit_code range="1:" + level="fatal" /> + </stdio> + +<!-- <tests> + <test interactor="api"> + <conditional name="parameters"> + <param name="type" value="specific" /> + <param name="inputs" value="test-abund-read-2.fa"/> + <param name="cutoff" value="1" /> + <param name="ksize" value="17" /> + </conditional> + <output name="output"> + <discover_dataset name="test-abund-read-2.fa.keep"> + <assert_contents> + <has_line_matching expression="GGTTGACGGGGCTCAGGGGG" /> + </assert_contents> + </discover_dataset> + </output> + </test> + <test interactor="api"> + <param name="inputs" value="test-abund-read-2.fa" /> + <param name="cutoff" value="2" /> + <param name="ksize" value="17" /> + <output name="output"> + <discover_dataset name="test-abund-read-2.fa.keep"> + <assert_contents> + <has_line_matching expression="GGTTGACGGGGCTCAGGGGG" /> + <has_line_matching expression="GGTTGACGGGGCTCAGGG" /> + </assert_contents> + </discover_dataset> + </output> + </test> + <test interactor="api"> + <param name="inputs" value="test-abund-read-paired.fa" /> + <param name="cutoff" value="1" /> + <param name="ksize" value="17" /> + <param name="paired" value="true" /> + <output name="output"> + <discover_dataset name="test-abund-read-paired.fa.keep"> + <assert_contents> + <has_line_matching expression="GGTTGACGGGGCTCAGGGGG" /> + <has_line_matching expression="GGTTGACGGGGCTCAGGG" /> + </assert_contents> + </discover_dataset> + </output> + </test> + + </tests> + --> + <!-- [OPTIONAL] Help displayed in Galaxy --> + <!-- + <help> + </help> + --> +</tool>