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comparison fastx_barcode_splitter.xml @ 2:32304398ef67 draft

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planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit c3b0be52079831f6ae58ff64e42d8ff54ce501e4
author lparsons
date Fri, 13 Nov 2015 12:43:14 -0500
parents b7b3d008e2d3
children e7b7cdc1834d
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1:b7b3d008e2d3 2:32304398ef67
1 <tool id="cshl_princeton_fastx_barcode_splitter" version="1.1" name="Barcode Splitter" force_history_refresh="True"> 1 <tool id="cshl_princeton_fastx_barcode_splitter" version="1.1" name="Barcode Splitter">
2 <description></description> 2 <description></description>
3 <command interpreter="bash"><![CDATA[ 3 <command interpreter="bash"><![CDATA[
4 fastx_barcode_splitter_galaxy_wrapper.sh $BARCODE $input "primary_$output.id" "$__new_file_path__" $input.extension --mismatches $mismatches --partial $partial 4 fastx_barcode_splitter_galaxy_wrapper.sh $BARCODE $input "split/" $input.extension --mismatches $mismatches --partial $partial
5 #if $refBarcodeLocation.barcodeLocation == "idxfile": 5 #if $refBarcodeLocation.barcodeLocation == "idxfile":
6 --idxfile $refBarcodeLocation.idxfile 6 --idxfile $refBarcodeLocation.idxfile
7 #else: 7 #else:
8 $refBarcodeLocation.EOL 8 $refBarcodeLocation.EOL
9 #end if 9 #end if
37 <param name="partial" type="integer" size="3" value="0" label="Number of allowed barcodes nucleotide deletions" /> 37 <param name="partial" type="integer" size="3" value="0" label="Number of allowed barcodes nucleotide deletions" />
38 38
39 </inputs> 39 </inputs>
40 40
41 <outputs> 41 <outputs>
42 <data format="html" name="output" /> 42 <data format="html" name="output">
43 <discover_datasets pattern="__designation_and_ext__" directory="split" visible="true" label="${tool.name}: ${designation}"/>
44 </data>
43 </outputs> 45 </outputs>
44 46
45 <tests> 47 <tests>
46 <test> 48 <test>
47 <!-- Split a FASTQ file --> 49 <!-- Split a FASTQ file -->
48 <param name="BARCODE" value="fastx_barcode_splitter1.txt" /> 50 <param name="BARCODE" value="fastx_barcode_splitter1.txt" />
49 <param name="input" value="fastx_barcode_splitter1.fastq" ftype="fastqsolexa" /> 51 <param name="input" value="fastx_barcode_splitter1.fastq" ftype="fastqsolexa" />
50 <param name="barcodeLocation" value="bol" /> 52 <param name="barcodeLocation" value="bol" />
51 <param name="mismatches" value="2" /> 53 <param name="mismatches" value="2" />
52 <param name="partial" value="0" /> 54 <param name="partial" value="0" />
53 <output name="output" file="fastx_barcode_splitter1.out" /> 55 <output name="output" file="fastx_barcode_splitter1.out">
56 <discovered_dataset designation="BC1" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC1.out" />
57 <discovered_dataset designation="BC2" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC2.out" />
58 <discovered_dataset designation="BC3" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC3.out" />
59 <discovered_dataset designation="BC4" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC4.out" />
60 <discovered_dataset designation="unmatched" ftype="fastqsolexa" file="fastx_barcode_splitter1_unmatched.out" />
61 </output>
54 </test> 62 </test>
55 </tests> 63 </tests>
56 64
57 <help><![CDATA[ 65 <help><![CDATA[
58 **What it does** 66 **What it does**
83 ]]> 91 ]]>
84 </help> 92 </help>
85 93
86 <!-- FASTX-barcode-splitter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) --> 94 <!-- FASTX-barcode-splitter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
87 <citations> 95 <citations>
88 <citation type="bibtex"> 96 <citation type="bibtex">
89 @misc{gordon_fastx-toolkit_????, 97 @misc{gordon_fastx-toolkit_????,
90 title = {{FASTX}-{Toolkit}}, 98 title = {{FASTX}-{Toolkit}},
91 url = {http://hannonlab.cshl.edu/fastx_toolkit/index.html}, 99 url = {http://hannonlab.cshl.edu/fastx_toolkit/index.html},
92 author = {Gordon, Assaf} 100 author = {Gordon, Assaf}
93 } 101 }