Mercurial > repos > drosofff > msp_sr_bowtie_parser
annotate sRbowtieParser.xml @ 17:7b5e0fba8e74 draft default tip
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie_parser commit 30a73e24eabb05f9d46150fd03471ff853579ad2-dirty
| author | mvdbeek |
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| date | Mon, 18 Apr 2016 09:52:54 -0400 |
| parents | bfeaf4415eba |
| children |
| rev | line source |
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bfeaf4415eba
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie_parser commit 30a73e24eabb05f9d46150fd03471ff853579ad2-dirty
mvdbeek
parents:
15
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changeset
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1 <tool id="sRbowtieParser" name="Parse items in sRbowtie alignment" version="1.0.6"> |
| 0 | 2 <description></description> |
| 3 <requirements> | |
| 4 <requirement type="package" version="0.12.7">bowtie</requirement> | |
| 5 <requirement type="package" version="0.7.7">pysam</requirement> | |
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115af29c4f57
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
mvdbeek
parents:
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6 <requirement type="package" version="1.9">numpy</requirement> |
| 0 | 7 </requirements> |
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bfeaf4415eba
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie_parser commit 30a73e24eabb05f9d46150fd03471ff853579ad2-dirty
mvdbeek
parents:
15
diff
changeset
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8 <command> |
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17
7b5e0fba8e74
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie_parser commit 30a73e24eabb05f9d46150fd03471ff853579ad2-dirty
mvdbeek
parents:
16
diff
changeset
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9 python $__tool_directory__/sRbowtieParser.py |
| 0 | 10 #if $refGenomeSource.genomeSource == "history": |
| 11 --IndexSource $refGenomeSource.ownFile | |
| 12 --ExtractDirective fastaSource | |
| 13 #else: | |
| 14 #silent reference= filter( lambda x: str( x[0] ) == str( $input_list.dbkey ), $__app__.tool_data_tables[ 'bowtie_indexes' ].get_fields() )[0][-1] | |
| 15 --IndexSource $reference | |
| 16 --ExtractDirective bowtieIndex | |
| 17 #end if | |
| 18 --output $output | |
| 19 --polarity $polarity | |
| 20 --alignmentSource | |
| 21 #for $i in $refGenomeSource.input_list | |
| 22 $i | |
| 23 #end for | |
| 24 --alignmentFormat | |
| 25 #for $i in $refGenomeSource.input_list | |
| 26 $i.ext | |
| 27 #end for | |
| 28 --alignmentLabel | |
| 29 #for $i in $refGenomeSource.input_list | |
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16
bfeaf4415eba
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie_parser commit 30a73e24eabb05f9d46150fd03471ff853579ad2-dirty
mvdbeek
parents:
15
diff
changeset
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30 "$i.element_identifier" |
| 0 | 31 #end for |
| 32 | |
| 33 </command> | |
| 34 <inputs> | |
| 35 <conditional name="refGenomeSource"> | |
| 36 <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"> | |
| 37 <option value="indexed">Use a built-in index</option> | |
| 38 <option value="history">Use one from the history</option> | |
| 39 </param> | |
| 40 <when value="indexed"> | |
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a39761c27e77
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
14
diff
changeset
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41 <param name="input_list" type="data" format="tabular,sam,bam" label="Select multiple alignments to parse" multiple="true"> |
| 0 | 42 <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."/> |
| 43 </param> | |
| 44 </when> | |
| 45 <when value="history"> | |
| 46 <param name="ownFile" type="data" format="fasta" label="Select the fasta reference" /> | |
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15
a39761c27e77
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
14
diff
changeset
|
47 <param name="input_list" type="data" format="tabular,sam,bam" label="Select multiple alignments to parse" multiple="true"/> |
| 0 | 48 </when> |
| 49 </conditional> <!-- refGenomeSource --> | |
| 50 <param name="polarity" type="select" label="how to count sense and antisense reads"> | |
| 51 <option value="both">count both sense and antisense reads</option> | |
| 52 <option value="forward">count only sense reads</option> | |
| 53 <option value="reverse">count only antisense reads</option> | |
| 54 </param> | |
| 55 </inputs> | |
| 56 <outputs> | |
| 57 <data format="tabular" name="output" label="Read Count Lists"/> | |
| 58 </outputs> | |
| 59 <help> | |
| 60 | |
| 61 **What it does** | |
| 62 | |
| 63 Parses read counts from one or several sRBowtie alignments (in tabular, Sam or Bam format). | |
| 64 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 | |
| 65 | |
| 66 Sense, antisense or both sense and antisense alignments can be counted | |
| 67 | |
| 68 The library labels are infered from the input dataset names in the galaxy history. | |
| 69 | |
| 70 **It is thus essential that input datasets are appropriately renamed** | |
| 71 | |
| 72 **it is preferable that you do not put any space in this input dataset names. You may edit these names in the history** | |
| 73 | |
| 74 </help> | |
| 1 | 75 <tests> |
| 76 <test> | |
| 0 | 77 <param name="genomeSource" value="history" /> |
| 78 <param name="ownFile" value ="dme-mir-v20" ftype="fasta" /> | |
| 1 | 79 <param name="input_list" value="matchedSample_1,matchedSample_2" ftype="tabular" /> |
| 0 | 80 <param name="polarity" value="forward" /> |
| 1 | 81 <output name="output" ftype="tabular" file="Read_Count_Lists.tab" /> |
| 82 </test> | |
| 83 </tests> | |
| 0 | 84 </tool> |
| 85 |