Mercurial > repos > drosofff > msp_sr_bowtie_parser
comparison sRbowtieParser.xml @ 0:b996480cd604 draft
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
| author | drosofff |
|---|---|
| date | Wed, 27 May 2015 17:19:15 -0400 |
| parents | |
| children | ca3845fb0b31 |
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| -1:000000000000 | 0:b996480cd604 |
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| 1 <tool id="sRbowtieParser" name="Parse items in sRbowtie alignment" version="1.0.1"> | |
| 2 <description></description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="0.12.7">bowtie</requirement> | |
| 5 <requirement type="package" version="0.1.18">samtools</requirement> | |
| 6 <requirement type="package" version="0.7.7">pysam</requirement> | |
| 7 <requirement type="package" version="1.9">numpy</requirement> | |
| 8 <requirement type="package" version="0.14">scipy</requirement> | |
| 9 </requirements> | |
| 10 <command interpreter="python"> | |
| 11 sRbowtieParser.py | |
| 12 #if $refGenomeSource.genomeSource == "history": | |
| 13 --IndexSource $refGenomeSource.ownFile | |
| 14 --ExtractDirective fastaSource | |
| 15 #else: | |
| 16 #silent reference= filter( lambda x: str( x[0] ) == str( $input_list.dbkey ), $__app__.tool_data_tables[ 'bowtie_indexes' ].get_fields() )[0][-1] | |
| 17 --IndexSource $reference | |
| 18 --ExtractDirective bowtieIndex | |
| 19 #end if | |
| 20 --output $output | |
| 21 --polarity $polarity | |
| 22 --alignmentSource | |
| 23 #for $i in $refGenomeSource.input_list | |
| 24 $i | |
| 25 #end for | |
| 26 --alignmentFormat | |
| 27 #for $i in $refGenomeSource.input_list | |
| 28 $i.ext | |
| 29 #end for | |
| 30 --alignmentLabel | |
| 31 #for $i in $refGenomeSource.input_list | |
| 32 "$i.name" | |
| 33 #end for | |
| 34 | |
| 35 </command> | |
| 36 <inputs> | |
| 37 <conditional name="refGenomeSource"> | |
| 38 <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"> | |
| 39 <option value="indexed">Use a built-in index</option> | |
| 40 <option value="history">Use one from the history</option> | |
| 41 </param> | |
| 42 <when value="indexed"> | |
| 43 <param name="input_list" type="data" label="Select multiple alignments to parse" multiple="true"> | |
| 44 <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."/> | |
| 45 </param> | |
| 46 </when> | |
| 47 <when value="history"> | |
| 48 <param name="ownFile" type="data" format="fasta" label="Select the fasta reference" /> | |
| 49 <param name="input_list" type="data" label="Select multiple alignments to parse" multiple="true"/> | |
| 50 </when> | |
| 51 </conditional> <!-- refGenomeSource --> | |
| 52 <param name="polarity" type="select" label="how to count sense and antisense reads"> | |
| 53 <option value="both">count both sense and antisense reads</option> | |
| 54 <option value="forward">count only sense reads</option> | |
| 55 <option value="reverse">count only antisense reads</option> | |
| 56 </param> | |
| 57 </inputs> | |
| 58 <outputs> | |
| 59 <data format="tabular" name="output" label="Read Count Lists"/> | |
| 60 </outputs> | |
| 61 <help> | |
| 62 | |
| 63 **What it does** | |
| 64 | |
| 65 Parses read counts from one or several sRBowtie alignments (in tabular, Sam or Bam format). | |
| 66 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 | |
| 67 | |
| 68 Sense, antisense or both sense and antisense alignments can be counted | |
| 69 | |
| 70 The library labels are infered from the input dataset names in the galaxy history. | |
| 71 | |
| 72 **It is thus essential that input datasets are appropriately renamed** | |
| 73 | |
| 74 **it is preferable that you do not put any space in this input dataset names. You may edit these names in the history** | |
| 75 | |
| 76 </help> | |
| 77 <tests> | |
| 78 <test> | |
| 79 <param name="genomeSource" value="history" /> | |
| 80 <param name="ownFile" value ="dme-mir-v20" ftype="fasta" /> | |
| 81 <param name="input_list" value="matchedSample_1,matchedSample_2" ftype="tabular" /> | |
| 82 <param name="polarity" value="forward" /> | |
| 83 <output name="output" ftype="tabular" file="Read_Count_Lists.tab" /> | |
| 84 </test> | |
| 85 </tests> | |
| 86 </tool> | |
| 87 |