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comparison fastx_barcode_splitter.xml @ 5:4bedca26c133 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter commit b2735803f9719ff955a49a5bde54a211d6d48bb5
author iuc
date Thu, 11 Oct 2018 09:35:51 -0400
parents 015dc921d814
children 0b7ec11b3c7c
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4:015dc921d814 5:4bedca26c133
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <command detect_errors="aggressive"><![CDATA[ 7 <command detect_errors="aggressive"><![CDATA[
8 mkdir split && 8 mkdir split &&
9 @CATS@ '$__tool_directory__/fastx_barcode_splitter.pl' --bcfile '$BARCODE' 9 @CATS@ '$__tool_directory__/fastx_barcode_splitter.pl' --bcfile '$BARCODE'
10 --prefix 'split/' 10 --prefix 'split/'
11 --suffix '.$input.extension' 11 --suffix
12 #if $input.is_of_type('fastqsanger', 'fastqsanger.gz', 'fastqsanger.bz2'):
13 '.fastqsanger'
14 #elif $input.is_of_type('fastqsolexa', 'fastqsolexa.gz', 'fastqsolexa.bz2'):
15 '.fastqsolexa'
16 #elif $input.is_of_type('fastqillumina', 'fastqillumina.gz', 'fastqillumina.bz2'):
17 '.fastqillumina'
18 #elif $input.is_of_type('fasta', 'fasta.gz'):
19 '.fasta'
20 #else:
21 '.$input.extension'
22 #end if
12 --mismatches $mismatches 23 --mismatches $mismatches
13 --partial $partial 24 --partial $partial
14 #if $refBarcodeLocation.barcodeLocation == "idxfile": 25 #if $refBarcodeLocation.barcodeLocation == "idxfile":
15 --idxfile '$refBarcodeLocation.idxfile' 26 --idxfile '$refBarcodeLocation.idxfile'
16 --idxidstrip $refBarcodeLocation.idxidstrip 27 --idxidstrip $refBarcodeLocation.idxidstrip
19 #end if 30 #end if
20 > '$summary' 31 > '$summary'
21 ]]></command> 32 ]]></command>
22 <inputs> 33 <inputs>
23 <param name="BARCODE" type="data" format="txt" label="Barcodes to use" /> 34 <param name="BARCODE" type="data" format="txt" label="Barcodes to use" />
24 <param name="input" type="data" format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina" label="Library to split" /> 35 <param name="input" type="data" format="@FASTAS@,@FASTQS@,fastq" label="Library to split" />
25
26 <conditional name="refBarcodeLocation"> 36 <conditional name="refBarcodeLocation">
27 <param name="barcodeLocation" type="select" label="Barcodes found at"> 37 <param name="barcodeLocation" type="select" label="Barcodes found at">
28 <option value="bol">Start of sequence (5' end)</option> 38 <option value="bol">Start of sequence (5' end)</option>
29 <option value="eol">End of sequence (3' end)</option> 39 <option value="eol">End of sequence (3' end)</option>
30 <option value="idxfile">Separate index file</option> 40 <option value="idxfile">Separate index file</option>
44 <param argument="--partial" type="integer" value="0" label="Number of allowed barcodes nucleotide deletions" /> 54 <param argument="--partial" type="integer" value="0" label="Number of allowed barcodes nucleotide deletions" />
45 </inputs> 55 </inputs>
46 56
47 <outputs> 57 <outputs>
48 <data name="summary" format="tabular" label="${tool.name} on ${on_string}: Summary" /> 58 <data name="summary" format="tabular" label="${tool.name} on ${on_string}: Summary" />
49 <collection name="split_output" type="list" format_source="input" label="${tool.name} on ${on_string}"> 59 <collection name="split_output" type="list" label="${tool.name} on ${on_string}">
50 <discover_datasets pattern="__designation_and_ext__" directory="split" visible="false" /> 60 <discover_datasets pattern="__designation_and_ext__" directory="split" visible="false" />
51 </collection> 61 </collection>
52 </outputs> 62 </outputs>
53 63
54 <tests> 64 <tests>
65 <element name="BC2" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC2.out" /> 75 <element name="BC2" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC2.out" />
66 <element name="BC3" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC3.out" /> 76 <element name="BC3" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC3.out" />
67 <element name="BC4" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC4.out" /> 77 <element name="BC4" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC4.out" />
68 <element name="unmatched" ftype="fastqsolexa" file="fastx_barcode_splitter1_unmatched.out" /> 78 <element name="unmatched" ftype="fastqsolexa" file="fastx_barcode_splitter1_unmatched.out" />
69 </output_collection> 79 </output_collection>
80 </test>
81
82 <test>
83 <!-- Split a FASTQ.gz file -->
84 <param name="BARCODE" value="fastx_barcode_splitter1.txt" />
85 <param name="input" value="fastx_barcode_splitter1.fastq.gz" ftype="fastqsolexa.gz" />
86 <param name="barcodeLocation" value="bol" />
87 <param name="mismatches" value="2" />
88 <param name="partial" value="0" />
89 <output name="summary" file="fastx_barcode_splitter1.out" />
90 <output_collection name="split_output" type="list">
91 <element name="BC1" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC1.out" />
92 <element name="BC2" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC2.out" />
93 <element name="BC3" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC3.out" />
94 <element name="BC4" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC4.out" />
95 <element name="unmatched" ftype="fastqsolexa" file="fastx_barcode_splitter1_unmatched.out" />
96 </output_collection>
70 </test> 97 </test>
71 98
72 <test> 99 <test>
73 <!-- Split a FASTQ file, using separate index read --> 100 <!-- Split a FASTQ file, using separate index read -->
74 <param name="BARCODE" value="fastx_barcode_splitter1.txt" /> 101 <param name="BARCODE" value="fastx_barcode_splitter1.txt" />