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<!--
~ Copyright (C) 2009-2010 Institute for Computational Biomedicine,
~ Weill Medical College of Cornell University
~
~ This program is free software; you can redistribute it and/or modify
~ it under the terms of the GNU General Public License as published by
~ the Free Software Foundation; either version 3 of the License, or
~ (at your option) any later version.
~
~ This program is distributed in the hope that it will be useful,
~ but WITHOUT ANY WARRANTY; without even the implied warranty of
~ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
~ GNU General Public License for more details.
~
~ You should have received a copy of the GNU General Public License
~ along with this program. If not, see <http://www.gnu.org/licenses/>.
-->
<jsap>
<parameters>
<flaggedOption>
<id>input</id>
<shortFlag>i</shortFlag>
<longFlag>input</longFlag>
<required>true</required>
<help>Input transcripts FASTA file. The transcript-ids and gene-ids need to be embedded into the Fasta reference in the header/comment lines. It is assumed that the comment / header line for each sequence will be in the format ">TRANSCRIPT_ID IGNORED_DATA gene:GENE_ID". For example ">ENST00000400845 cdna:known supercontig::GL000222.1:11792:16670:1 gene:ENSG00000215756" speciefies a transcript-id of "ENST00000400845" and a gene-id of "ENSG00000215756".</help>
</flaggedOption>
<flaggedOption>
<id>output</id>
<shortFlag>o</shortFlag>
<longFlag>output</longFlag>
<required>true</required>
<help>Base output path / filename. Several files will be created using this base including multiple FASTA files and a config file.</help>
</flaggedOption>
<flaggedOption>
<id>max-entries-per-file</id>
<shortFlag>n</shortFlag>
<longFlag>max-entries-per-file</longFlag>
<required>false</required>
<stringParser>
<classname>IntegerStringParser</classname>
</stringParser>
<defaults>
<string>2147483647</string>
</defaults>
<help>Maximum number of entries that should be written to any given output file.</help>
</flaggedOption>
</parameters>
</jsap>
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