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comparison sRbowtieCascade.xml @ 0:ecb041b49cd7 draft

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author drosofff
date Mon, 03 Nov 2014 10:26:15 -0500
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1 <tool id="sRbowtie_cascade" name="Annotate smRNA datasets" version="1.0.0">
2 <description>Using iterative sRbowtie Alignments</description>
3 <requirements>
4 <requirement type="package" version="0.12.7">bowtie</requirement>
5 </requirements>
6 <parallelism method="basic"></parallelism>
7 <command interpreter="python"> sRbowtieCascade.py --output $output
8 --num-threads \${GALAXY_SLOTS:-4} ## number of processors to be handled by bowtie
9 --mismatch $mismatches
10 --input
11 #for $i in $input:
12 $i
13 #end for
14 --label
15 #for $i in $input:
16 "$i.name"
17 #end for
18 --index
19 #if $refGenomeSource1.genomeSource == "history":
20 $refGenomeSource1.ownFile
21 #else:
22 $refGenomeSource1.index.fields.path
23 #end if
24 #for $i in $AdditionalQueries:
25 #if $i.refGenomeSource.genomeSource == "history":
26 $i.refGenomeSource.ownFile
27 #else:
28 $i.refGenomeSource.index.fields.path
29 #end if
30 #end for
31 --indexing-flags
32 $refGenomeSource1.genomeSource
33 #for $i in $AdditionalQueries:
34 $i.refGenomeSource.genomeSource
35 #end for
36 --indexName
37 #if $refGenomeSource1.genomeSource == "history":
38 "$refGenomeSource1.ownFile.name"
39 #else:
40 "$refGenomeSource1.index.fields.name"
41 #end if
42 #for $i in $AdditionalQueries:
43 #if $i.refGenomeSource.genomeSource == "history":
44 "$i.refGenomeSource.ownFile.name"
45 #else:
46 "$i.refGenomeSource.index.fields.name"
47 #end if
48 #end for
49 </command>
50 <inputs>
51 <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"/>
52 <param name="mismatches" type="select" label="Number of mismatches allowed" help="specify the number of mismatches allowed during alignments">
53 <option value="0">0</option>
54 <option value="1" selected="true">1</option>
55 <option value="2">2</option>
56 <option value="3">3</option>
57 </param>
58 <!-- First bowtie index selection -->
59 <conditional name="refGenomeSource1">
60 <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">
61 <option value="indexed">Use a built-in index</option>
62 <option value="history">Use one from the history</option>
63 </param>
64 <when value="indexed">
65 <param name="index" type="select" label="Select a DNA reference index" help="if your genome of interest is not listed - contact GED team">
66 <options from_data_table="bowtie_indexes"/>
67 </param>
68 </when>
69 <when value="history">
70 <param name="ownFile" type="data" format="fasta" label="Select a fasta file, to serve as index reference" />
71 </when>
72 </conditional>
73 <!-- End of first bowtie index selection -->
74 <!-- other bowtie index selections -->
75 <repeat name="AdditionalQueries" title="Additional Alignment Step">
76 <conditional name="refGenomeSource">
77 <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">
78 <option value="indexed">Use a built-in index</option>
79 <option value="history">Use one from the history</option>
80 </param>
81 <when value="indexed">
82 <param name="index" type="select" label="Select a DNA reference index" help="if your genome of interest is not listed - contact GED team">
83 <options from_data_table="bowtie_indexes"/>
84 </param>
85 </when>
86 <when value="history">
87 <param name="ownFile" type="data" format="fasta" label="Select a fasta file, to serve as index reference" />
88 </when>
89 </conditional>
90 </repeat>
91 <!-- End of other bowtie index selections -->
92 </inputs>
93 <outputs>
94 <data format="tabular" name="output" label="Cascade Annotation Analysis"/>
95 </outputs>
96
97 <test>
98 </test>
99
100 <help>
101
102 **Intro**
103
104 Bowtie_ is a short read aligner designed to be ultrafast and memory-efficient.
105 A generic "Map with Bowtie for Illumina" Galaxy tool is available in the main Galaxy distribution.
106 However, this Bowtie wrapper tool only takes FASTQ files as inputs.
107
108 Here The sRbowtie wrapper specifically works with short reads FASTA inputs (-v bowtie mode, with -k 1)
109
110 .. _Bowtie: http://bowtie-bio.sourceforge.net/index.shtml
111
112
113 ------
114
115 **What it does**
116
117 .. class:: infomark
118
119 This script uses the sRbowtie wrapper to iteratively match reads on a reference indexes.
120
121 Reads are Matched on DNA references as fast as possible, without taking care of mapping issues
122
123 *-v [0,1,2,3] -k 1 --best -p 12 --suppress 6,7,8*
124
125 unaligned reads at step N are used as input for sRbowtie at step N+1
126
127 -----
128
129 **Input formats**
130
131 .. class:: warningmark
132
133 *The only accepted format for the script is a raw fasta list of reads, clipped from their adapter*
134
135 -----
136
137 **OUTPUTS**
138
139 **Annotation table**
140
141 </help>
142 </tool>