preppereadsforveletfasta: preppereads

annotate preppereads_fasta.xml @ 0:4d237a31970b default tip

Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

author	konradpaszkiewicz
date	Tue, 07 Jun 2011 17:42:21 -0400
parents
children

rev	line source
0 4d237a31970b Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	1 <tool id="preppereadsforveletfasta" name="Prepare reads for use with velvet (FASTA)" version="1.0.0">
4d237a31970b Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	2 <description>Prepare paired-end reads for use with Velvet</description>
4d237a31970b Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	3 <command interpreter="python">
4d237a31970b Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	4 preppereads_fasta.py
4d237a31970b Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	5 '$__app__.config.new_file_path'
4d237a31970b Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	6 '$input1'
4d237a31970b Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	7 '$input2'
4d237a31970b Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	8 '$outpe'
4d237a31970b Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	9 '$outsingletons'; exit 0
4d237a31970b Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	10 </command>
4d237a31970b Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	11 <inputs>
4d237a31970b Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	12 <param name="input1" type="data" format="fasta" label="Read 1 of paired-end dataset"/>
4d237a31970b Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	13 <param name="input2" type="data" format="fasta" label="Read 2 of paired-end dataset"/>
4d237a31970b Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	14 </inputs>
4d237a31970b Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	15 <outputs>
4d237a31970b Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	16 <data format="fasta" name="outpe" label="Merged paired-end reads ready for velvet"/>
4d237a31970b Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	17 <data format="fasta" name="outsingletons" label="Singleton reads reads for velvet"/>
4d237a31970b Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	18
4d237a31970b Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	19 </outputs>
4d237a31970b Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	20 <requirements>
4d237a31970b Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	21 </requirements>
4d237a31970b Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	22 <help>
4d237a31970b Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	23 Paired-end reads preparation for velvet
4d237a31970b Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	24
4d237a31970b Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	25 Velvet requires paired-end reads to be in the same file in an interleaved FASTQ format. This format specifies that read 1 should be followed immediately by read 2.
4d237a31970b Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	26
4d237a31970b Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	27 This script is useful to ensure reads are in the correct order prior to passing the data to Velvet.
4d237a31970b Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	28
4d237a31970b Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	29 Singleton reads can also be produced if quality trimming or other filtering criteria have removed the read's mate. These can also be passed to Velvet using a second short read channel.
4d237a31970b Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	30
4d237a31970b Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	31 </help>
4d237a31970b Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	32 </tool>

Mercurial > repos > konradpaszkiewicz > preppereadsforveletfasta

annotate preppereads_fasta.xml @ 0:4d237a31970b default tip