Mercurial > repos > rnateam > ribotaper

comparison ribotaper_part1_create_annotation_files.xml @ 2:9dda0cc9ff98 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ commit 9a59864f0bfb9937309d2c18b8cf3715c8067808
author rnateam
date Wed, 30 Nov 2016 16:57:07 -0500
parents a56343c142d5
children 579b3be2559f
comparison
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1:a56343c142d5 2:9dda0cc9ff98
32 <param name="appris" type="boolean" falsevalue="false" truevalue="true" checked="true" label="Use appris? (valid for Human Gencode 19 and Mouse Gencode M3 )" 32 <param name="appris" type="boolean" falsevalue="false" truevalue="true" checked="true" label="Use appris? (valid for Human Gencode 19 and Mouse Gencode M3 )"
33 help=" If yes, only exons/transcripts with the appris tag will be used, using only 1 transcript per appris gene (the appris_principal transcript or other appris transcript). If a gene does not have appris transcript, all the annotated transcript structures are used. 33 help=" If yes, only exons/transcripts with the appris tag will be used, using only 1 transcript per appris gene (the appris_principal transcript or other appris transcript). If a gene does not have appris transcript, all the annotated transcript structures are used.
34 "/> 34 "/>
35 </inputs> 35 </inputs>
36 <outputs> 36 <outputs>
37 <data name="output1" type="data" format="bed" from_work_dir="annotation_path/start_stops_FAR.bed" label="start_stops_FAR"/> 37 <data name="output1" format="bed" from_work_dir="annotation_path/start_stops_FAR.bed" label="start_stops_FAR"/>
38 <data name="output2" type="data" format="zip" label="annotation_path"/> 38 <data name="output2" format="tar" label="annotation_path"/>
39 </outputs> 39 </outputs>
40 <tests> 40 <tests>
41 <test> 41 <test>
42 <param name="gtf" value="test.gtf"/> 42 <param name="gtf" value="test.gtf"/>
43 <param name="fa" value="test.fa"/> 43 <param name="fa" value="test.fa"/>
77 exon sequences and transcript structures. 77 exon sequences and transcript structures.
78 78
79 ``Ribotaper part 1`` generates two files: 79 ``Ribotaper part 1`` generates two files:
80 80
81 - **start_stops_FAR** in BED format 81 - **start_stops_FAR** in BED format
82 - **annotation_path** in format of zip 82 - **annotation_path** in format of tar
83 83
84 *Start_stops_FAR* 84 *Start_stops_FAR*
85 is used as an input for ``ribotaper part 2``. 85 is used as an input for ``ribotaper part 2``.
86 *Annotation_path* 86 *Annotation_path*
87 is used as an input for ``ribotaper part 3``. 87 is used as an input for ``ribotaper part 3``.