Mercurial > repos > drosofff > parse_srbowtie_alignment
comparison sRbowtieParser.xml @ 0:67610b7c0a40 draft
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| author | drosofff |
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| date | Mon, 23 Jun 2014 03:55:41 -0400 |
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| -1:000000000000 | 0:67610b7c0a40 |
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| 1 <tool id="sRbowtieParser" name="Parse items in sRbowtie alignment" version="0.9.1"> | |
| 2 <description></description> | |
| 3 <requirements><requirement type='package'>bowtie-inspect</requirement></requirements> | |
| 4 <parallelism method="basic"></parallelism> | |
| 5 <command interpreter="python"> | |
| 6 sRbowtieParser.py | |
| 7 #if $refGenomeSource.genomeSource == "history": | |
| 8 $refGenomeSource.ownFile ## index source | |
| 9 --do_not_extract_index | |
| 10 #else: | |
| 11 #silent reference= filter( lambda x: str( x[0] ) == str( $input_list.dbkey ), $__app__.tool_data_tables[ 'bowtie_indexes' ].get_fields() )[0][-1] | |
| 12 $reference ## index source | |
| 13 --extract_index | |
| 14 #end if | |
| 15 $output | |
| 16 $polarity | |
| 17 #for $i in $refGenomeSource.input_list | |
| 18 $i $i.ext "$i.name" | |
| 19 #end for | |
| 20 | |
| 21 </command> | |
| 22 <inputs> | |
| 23 <conditional name="refGenomeSource"> | |
| 24 <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"> | |
| 25 <option value="indexed">Use a built-in index</option> | |
| 26 <option value="history">Use one from the history</option> | |
| 27 </param> | |
| 28 <when value="indexed"> | |
| 29 <param name="input_list" type="data" label="Select multiple alignments to parse" multiple="true"> | |
| 30 <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."/> | |
| 31 </param> | |
| 32 </when> | |
| 33 <when value="history"> | |
| 34 <param name="ownFile" type="data" format="fasta" label="Select the fasta reference" /> | |
| 35 <param name="input_list" type="data" label="Select multiple alignments to parse" multiple="true"/> | |
| 36 </when> | |
| 37 </conditional> <!-- refGenomeSource --> | |
| 38 <param name="polarity" type="select" label="how to count sense and antisense reads"> | |
| 39 <option value="both">count both sense and antisense reads</option> | |
| 40 <option value="forward">count only sense reads</option> | |
| 41 <option value="reverse">count only antisense reads</option> | |
| 42 </param> | |
| 43 </inputs> | |
| 44 <outputs> | |
| 45 <data format="tabular" name="output" label="Read Count Lists"/> | |
| 46 </outputs> | |
| 47 <help> | |
| 48 | |
| 49 **What it does** | |
| 50 | |
| 51 Parses read counts from one or several sRBowtie alignments (in tabular, Sam or Bam format). | |
| 52 | |
| 53 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 | |
| 54 | |
| 55 Sense, antisense or both sense and antisense alignments can be counted | |
| 56 | |
| 57 The library labels are infered from the input dataset names in the galaxy history. | |
| 58 | |
| 59 **It is thus essential that input datasets are appropriately renamed** | |
| 60 | |
| 61 **it is preferable that you do not put any space in this input dataset names. You may edit these names in the history** | |
| 62 | |
| 63 | |
| 64 | |
| 65 </help> | |
| 66 </tool> | |
| 67 |