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comparison sRbowtieParser.xml @ 0:3a510730e3fc draft

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author drosofff
date Mon, 03 Nov 2014 10:27:20 -0500
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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 </requirements>
8 <parallelism method="basic"></parallelism>
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>
76 <test>
77 <param name="genomeSource" value="history" />
78 <param name="ownFile" value ="dme-mir-v20" ftype="fasta" />
79 <param name="input_list" value="matchedSample_1, matchedSample_2" ftype="tabular" />
80 <param name="polarity" value="forward" />
81 <output name="output" ftype="tabular" value="Read_Count_Lists.tab" />
82 </test>
83
84 </tool>
85