Mercurial > repos > drosofff > parse_srbowtie_alignment
changeset 0:67610b7c0a40 draft
Uploaded
author | drosofff |
---|---|
date | Mon, 23 Jun 2014 03:55:41 -0400 |
parents | |
children | 06e465694fd1 |
files | sRbowtieParser.xml |
diffstat | 1 files changed, 67 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sRbowtieParser.xml Mon Jun 23 03:55:41 2014 -0400 @@ -0,0 +1,67 @@ +<tool id="sRbowtieParser" name="Parse items in sRbowtie alignment" version="0.9.1"> + <description></description> + <requirements><requirement type='package'>bowtie-inspect</requirement></requirements> + <parallelism method="basic"></parallelism> +<command interpreter="python"> + sRbowtieParser.py + #if $refGenomeSource.genomeSource == "history": + $refGenomeSource.ownFile ## index source + --do_not_extract_index + #else: + #silent reference= filter( lambda x: str( x[0] ) == str( $input_list.dbkey ), $__app__.tool_data_tables[ 'bowtie_indexes' ].get_fields() )[0][-1] + $reference ## index source + --extract_index + #end if + $output + $polarity + #for $i in $refGenomeSource.input_list + $i $i.ext "$i.name" + #end for + +</command> + <inputs> + <conditional name="refGenomeSource"> + <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options"> + <option value="indexed">Use a built-in index</option> + <option value="history">Use one from the history</option> + </param> + <when value="indexed"> + <param name="input_list" type="data" label="Select multiple alignments to parse" multiple="true"> + <validator type="dataset_metadata_in_data_table" table_name="bowtie_indexes" metadata_name="dbkey" metadata_column="0" message="database not set for this bowtie output. Select the database(=genome used for matching) manually, or select a reference fasta from your history."/> + </param> + </when> + <when value="history"> + <param name="ownFile" type="data" format="fasta" label="Select the fasta reference" /> + <param name="input_list" type="data" label="Select multiple alignments to parse" multiple="true"/> + </when> + </conditional> <!-- refGenomeSource --> + <param name="polarity" type="select" label="how to count sense and antisense reads"> + <option value="both">count both sense and antisense reads</option> + <option value="forward">count only sense reads</option> + <option value="reverse">count only antisense reads</option> + </param> + </inputs> + <outputs> + <data format="tabular" name="output" label="Read Count Lists"/> + </outputs> + <help> + +**What it does** + +Parses read counts from one or several sRBowtie alignments (in tabular, Sam or Bam format). + +Here a bowtie match done against an index composed of a set of items is parsed and expressed as a hit list of the corresponding items + +Sense, antisense or both sense and antisense alignments can be counted + +The library labels are infered from the input dataset names in the galaxy history. + +**It is thus essential that input datasets are appropriately renamed** + +**it is preferable that you do not put any space in this input dataset names. You may edit these names in the history** + + + + </help> +</tool> +