Mercurial > repos > drosofff > msp_sr_bowtie_parser
annotate sRbowtieParser.xml @ 10:21a7875d3e9f draft
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
| author | mvdbeek |
|---|---|
| date | Fri, 12 Jun 2015 09:46:05 -0400 |
| parents | 2c25b9005680 |
| children | e64fec3de201 |
| rev | line source |
|---|---|
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aa3620d405b1
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
mvdbeek
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1 <tool id="sRbowtieParser" name="Parse items in sRbowtie alignment" version="1.0.4"> |
| 0 | 2 <description></description> |
| 3 <requirements> | |
| 4 <requirement type="package" version="0.12.7">bowtie</requirement> | |
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3fcc752a7101
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
mvdbeek
parents:
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diff
changeset
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5 <requirement type="package" version="1.2">samtools</requirement> |
| 0 | 6 <requirement type="package" version="0.7.7">pysam</requirement> |
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21a7875d3e9f
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
mvdbeek
parents:
9
diff
changeset
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7 <requirement type="package" version="0.12.0">scipy</requirement> |
| 0 | 8 </requirements> |
| 9 <command interpreter="python"> | |
| 10 sRbowtieParser.py | |
| 11 #if $refGenomeSource.genomeSource == "history": | |
| 12 --IndexSource $refGenomeSource.ownFile | |
| 13 --ExtractDirective fastaSource | |
| 14 #else: | |
| 15 #silent reference= filter( lambda x: str( x[0] ) == str( $input_list.dbkey ), $__app__.tool_data_tables[ 'bowtie_indexes' ].get_fields() )[0][-1] | |
| 16 --IndexSource $reference | |
| 17 --ExtractDirective bowtieIndex | |
| 18 #end if | |
| 19 --output $output | |
| 20 --polarity $polarity | |
| 21 --alignmentSource | |
| 22 #for $i in $refGenomeSource.input_list | |
| 23 $i | |
| 24 #end for | |
| 25 --alignmentFormat | |
| 26 #for $i in $refGenomeSource.input_list | |
| 27 $i.ext | |
| 28 #end for | |
| 29 --alignmentLabel | |
| 30 #for $i in $refGenomeSource.input_list | |
| 31 "$i.name" | |
| 32 #end for | |
| 33 | |
| 34 </command> | |
| 35 <inputs> | |
| 36 <conditional name="refGenomeSource"> | |
| 37 <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"> | |
| 38 <option value="indexed">Use a built-in index</option> | |
| 39 <option value="history">Use one from the history</option> | |
| 40 </param> | |
| 41 <when value="indexed"> | |
| 42 <param name="input_list" type="data" label="Select multiple alignments to parse" multiple="true"> | |
| 43 <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."/> | |
| 44 </param> | |
| 45 </when> | |
| 46 <when value="history"> | |
| 47 <param name="ownFile" type="data" format="fasta" label="Select the fasta reference" /> | |
| 48 <param name="input_list" type="data" label="Select multiple alignments to parse" multiple="true"/> | |
| 49 </when> | |
| 50 </conditional> <!-- refGenomeSource --> | |
| 51 <param name="polarity" type="select" label="how to count sense and antisense reads"> | |
| 52 <option value="both">count both sense and antisense reads</option> | |
| 53 <option value="forward">count only sense reads</option> | |
| 54 <option value="reverse">count only antisense reads</option> | |
| 55 </param> | |
| 56 </inputs> | |
| 57 <outputs> | |
| 58 <data format="tabular" name="output" label="Read Count Lists"/> | |
| 59 </outputs> | |
| 60 <help> | |
| 61 | |
| 62 **What it does** | |
| 63 | |
| 64 Parses read counts from one or several sRBowtie alignments (in tabular, Sam or Bam format). | |
| 65 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 | |
| 66 | |
| 67 Sense, antisense or both sense and antisense alignments can be counted | |
| 68 | |
| 69 The library labels are infered from the input dataset names in the galaxy history. | |
| 70 | |
| 71 **It is thus essential that input datasets are appropriately renamed** | |
| 72 | |
| 73 **it is preferable that you do not put any space in this input dataset names. You may edit these names in the history** | |
| 74 | |
| 75 </help> | |
| 1 | 76 <tests> |
| 77 <test> | |
| 0 | 78 <param name="genomeSource" value="history" /> |
| 79 <param name="ownFile" value ="dme-mir-v20" ftype="fasta" /> | |
| 1 | 80 <param name="input_list" value="matchedSample_1,matchedSample_2" ftype="tabular" /> |
| 0 | 81 <param name="polarity" value="forward" /> |
| 1 | 82 <output name="output" ftype="tabular" file="Read_Count_Lists.tab" /> |
| 83 </test> | |
| 84 </tests> | |
| 0 | 85 </tool> |
| 86 |