Mercurial > repos > drosofff > msp_sr_bowtie_cascade
annotate sRbowtieCascade.xml @ 3:0052d1dd31df draft default tip
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
| author | drosofff |
|---|---|
| date | Mon, 29 Jun 2015 05:54:27 -0400 |
| parents | 0dfcb397699e |
| children |
| rev | line source |
|---|---|
| 1 | 1 <tool id="sRbowtie_cascade" name="Annotate smRNA datasets" version="1.0.1"> |
| 0 | 2 <description>Using iterative sRbowtie Alignments</description> |
| 3 <requirements> | |
| 4 <requirement type="package" version="0.12.7">bowtie</requirement> | |
| 5 </requirements> | |
| 6 <command interpreter="python"> sRbowtieCascade.py --output $output | |
| 7 --num-threads \${GALAXY_SLOTS:-4} ## number of processors to be handled by bowtie | |
| 8 --mismatch $mismatches | |
| 9 --input | |
| 10 #for $i in $input: | |
| 11 $i | |
| 12 #end for | |
| 13 --label | |
| 14 #for $i in $input: | |
| 15 "$i.name" | |
| 16 #end for | |
| 17 --index | |
| 18 #if $refGenomeSource1.genomeSource == "history": | |
| 19 $refGenomeSource1.ownFile | |
| 20 #else: | |
| 21 $refGenomeSource1.index.fields.path | |
| 22 #end if | |
| 23 #for $i in $AdditionalQueries: | |
| 24 #if $i.refGenomeSource.genomeSource == "history": | |
| 25 $i.refGenomeSource.ownFile | |
| 26 #else: | |
| 27 $i.refGenomeSource.index.fields.path | |
| 28 #end if | |
| 29 #end for | |
| 30 --indexing-flags | |
| 31 $refGenomeSource1.genomeSource | |
| 32 #for $i in $AdditionalQueries: | |
| 33 $i.refGenomeSource.genomeSource | |
| 34 #end for | |
| 35 --indexName | |
| 36 #if $refGenomeSource1.genomeSource == "history": | |
| 37 "$refGenomeSource1.ownFile.name" | |
| 38 #else: | |
| 39 "$refGenomeSource1.index.fields.name" | |
| 40 #end if | |
| 41 #for $i in $AdditionalQueries: | |
| 42 #if $i.refGenomeSource.genomeSource == "history": | |
| 43 "$i.refGenomeSource.ownFile.name" | |
| 44 #else: | |
| 45 "$i.refGenomeSource.index.fields.name" | |
| 46 #end if | |
| 47 #end for | |
| 48 </command> | |
| 49 <inputs> | |
| 50 <param name="input" type="data" format="fasta" label="Input fasta file: reads clipped from their adapter" help="Only with clipped, raw fasta files" multiple="true"/> | |
| 51 <param name="mismatches" type="select" label="Number of mismatches allowed" help="specify the number of mismatches allowed during alignments"> | |
| 52 <option value="0">0</option> | |
| 53 <option value="1" selected="true">1</option> | |
| 54 <option value="2">2</option> | |
| 55 <option value="3">3</option> | |
| 56 </param> | |
| 57 <!-- First bowtie index selection --> | |
| 58 <conditional name="refGenomeSource1"> | |
| 59 <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"> | |
| 60 <option value="indexed">Use a built-in index</option> | |
| 61 <option value="history">Use one from the history</option> | |
| 62 </param> | |
| 63 <when value="indexed"> | |
|
3
0052d1dd31df
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
1
diff
changeset
|
64 <param name="index" type="select" label="Select a DNA reference index" help="if your genome of interest is not listed - contact instance administrator"> |
| 0 | 65 <options from_data_table="bowtie_indexes"/> |
| 66 </param> | |
| 67 </when> | |
| 68 <when value="history"> | |
| 69 <param name="ownFile" type="data" format="fasta" label="Select a fasta file, to serve as index reference" /> | |
| 70 </when> | |
| 71 </conditional> | |
| 72 <!-- End of first bowtie index selection --> | |
| 73 <!-- other bowtie index selections --> | |
| 74 <repeat name="AdditionalQueries" title="Additional Alignment Step"> | |
| 75 <conditional name="refGenomeSource"> | |
| 76 <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"> | |
| 77 <option value="indexed">Use a built-in index</option> | |
| 78 <option value="history">Use one from the history</option> | |
| 79 </param> | |
| 80 <when value="indexed"> | |
|
3
0052d1dd31df
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
1
diff
changeset
|
81 <param name="index" type="select" label="Select a DNA reference index" help="if your genome of interest is not listed - contact instance administrator"> |
| 0 | 82 <options from_data_table="bowtie_indexes"/> |
| 83 </param> | |
| 84 </when> | |
| 85 <when value="history"> | |
| 86 <param name="ownFile" type="data" format="fasta" label="Select a fasta file, to serve as index reference" /> | |
| 87 </when> | |
| 88 </conditional> | |
| 89 </repeat> | |
| 90 <!-- End of other bowtie index selections --> | |
| 91 </inputs> | |
| 92 <outputs> | |
| 93 <data format="tabular" name="output" label="Cascade Annotation Analysis"/> | |
| 94 </outputs> | |
| 95 | |
| 96 | |
| 1 | 97 <tests> |
| 98 <test> | |
| 99 <param name="input" value ="sample1.fa,sample2.fa,sample3.fa" ftype="fasta" /> | |
| 100 <param name="genomeSource" value="history" /> | |
| 101 <param name="ownFile" value ="dmel-2L-r6.04.fasta" ftype="fasta" /> | |
| 102 <param name="AdditionalQueries_0|refGenomeSource|genomeSource" value="history"/> | |
| 103 <param name="AdditionalQueries_0|refGenomeSource|ownFile" value="dme_miR21_hairpin.fa" ftype="fasta" /> | |
| 104 <param name="AdditionalQueries_1|refGenomeSource|genomeSource" value="history"/> | |
| 105 <param name="AdditionalQueries_1|refGenomeSource|ownFile" value="Ensembl_transposon_set.fa" ftype="fasta" /> | |
| 106 <output name="output" ftype="tabular" file="Cascade_Annotation_Analysis.tab" /> | |
| 107 </test> | |
| 108 </tests> | |
| 0 | 109 <help> |
| 110 | |
| 111 **Intro** | |
| 112 | |
| 113 Bowtie_ is a short read aligner designed to be ultrafast and memory-efficient. | |
| 114 A generic "Map with Bowtie for Illumina" Galaxy tool is available in the main Galaxy distribution. | |
| 115 However, this Bowtie wrapper tool only takes FASTQ files as inputs. | |
| 116 | |
| 117 Here The sRbowtie wrapper specifically works with short reads FASTA inputs (-v bowtie mode, with -k 1) | |
| 118 | |
| 119 .. _Bowtie: http://bowtie-bio.sourceforge.net/index.shtml | |
| 120 | |
| 121 | |
| 122 ------ | |
| 123 | |
| 124 **What it does** | |
| 125 | |
| 126 .. class:: infomark | |
| 127 | |
| 128 This script uses the sRbowtie wrapper to iteratively match reads on a reference indexes. | |
| 129 | |
| 130 Reads are Matched on DNA references as fast as possible, without taking care of mapping issues | |
| 131 | |
| 132 *-v [0,1,2,3] -k 1 --best -p 12 --suppress 6,7,8* | |
| 133 | |
| 134 unaligned reads at step N are used as input for sRbowtie at step N+1 | |
| 135 | |
| 136 ----- | |
| 137 | |
| 138 **Input formats** | |
| 139 | |
| 140 .. class:: warningmark | |
| 141 | |
| 142 *The only accepted format for the script is a raw fasta list of reads, clipped from their adapter* | |
| 143 | |
| 144 ----- | |
| 145 | |
| 146 **OUTPUTS** | |
| 147 | |
| 148 **Annotation table** | |
| 149 | |
| 150 </help> | |
| 151 </tool> |