Mercurial > repos > devteam > fastx_barcode_splitter
comparison fastx_barcode_splitter.xml @ 1:7b5eb2503f6d
Remove spurious version strings.
| author | Dave Bouvier <dave@bx.psu.edu> |
|---|---|
| date | Tue, 26 Nov 2013 12:46:41 -0500 |
| parents | 6cbe88c680bb |
| children | 1a20fbb8bad8 |
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| 0:6cbe88c680bb | 1:7b5eb2503f6d |
|---|---|
| 4 <requirement type="package" version="0.0.13">fastx_toolkit</requirement> | 4 <requirement type="package" version="0.0.13">fastx_toolkit</requirement> |
| 5 </requirements> | 5 </requirements> |
| 6 <command interpreter="bash">fastx_barcode_splitter_galaxy_wrapper.sh $BARCODE $input "$input.name" "$output.files_path" --mismatches $mismatches --partial $partial $EOL > $output </command> | 6 <command interpreter="bash">fastx_barcode_splitter_galaxy_wrapper.sh $BARCODE $input "$input.name" "$output.files_path" --mismatches $mismatches --partial $partial $EOL > $output </command> |
| 7 | 7 |
| 8 <inputs> | 8 <inputs> |
| 9 <param format="txt" version="1.0.0" name="BARCODE" type="data" label="Barcodes to use" /> | 9 <param format="txt" name="BARCODE" type="data" label="Barcodes to use" /> |
| 10 <param format="fasta,fastqsanger,fastqsolexa,fastqillumina" version="1.0.0" name="input" type="data" label="Library to split" /> | 10 <param format="fasta,fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="Library to split" /> |
| 11 | 11 |
| 12 <param version="1.0.0" name="EOL" type="select" label="Barcodes found at"> | 12 <param name="EOL" type="select" label="Barcodes found at"> |
| 13 <option value="--bol">Start of sequence (5' end)</option> | 13 <option value="--bol">Start of sequence (5' end)</option> |
| 14 <option value="--eol">End of sequence (3' end)</option> | 14 <option value="--eol">End of sequence (3' end)</option> |
| 15 </param> | 15 </param> |
| 16 | 16 |
| 17 <param version="1.0.0" name="mismatches" type="integer" size="3" value="2" label="Number of allowed mismatches" /> | 17 <param name="mismatches" type="integer" size="3" value="2" label="Number of allowed mismatches" /> |
| 18 | 18 |
| 19 <param version="1.0.0" name="partial" type="integer" size="3" value="0" label="Number of allowed barcodes nucleotide deletions" /> | 19 <param name="partial" type="integer" size="3" value="0" label="Number of allowed barcodes nucleotide deletions" /> |
| 20 | 20 |
| 21 </inputs> | 21 </inputs> |
| 22 | 22 |
| 23 <tests> | 23 <tests> |
| 24 <test> | 24 <test> |
| 25 <!-- Split a FASTQ file --> | 25 <!-- Split a FASTQ file --> |
| 26 <param version="1.0.0" name="BARCODE" value="fastx_barcode_splitter1.txt" /> | 26 <param name="BARCODE" value="fastx_barcode_splitter1.txt" /> |
| 27 <param version="1.0.0" name="input" value="fastx_barcode_splitter1.fastq" ftype="fastqsolexa" /> | 27 <param name="input" value="fastx_barcode_splitter1.fastq" ftype="fastqsolexa" /> |
| 28 <param version="1.0.0" name="EOL" value="Start of sequence (5' end)" /> | 28 <param name="EOL" value="Start of sequence (5' end)" /> |
| 29 <param version="1.0.0" name="mismatches" value="2" /> | 29 <param name="mismatches" value="2" /> |
| 30 <param version="1.0.0" name="partial" value="0" /> | 30 <param name="partial" value="0" /> |
| 31 <output version="1.0.0" name="output" file="fastx_barcode_splitter1.out" /> | 31 <output name="output" file="fastx_barcode_splitter1.out" /> |
| 32 </test> | 32 </test> |
| 33 </tests> | 33 </tests> |
| 34 | 34 |
| 35 <outputs> | 35 <outputs> |
| 36 <data format="html" version="1.0.0" name="output" /> | 36 <data format="html" name="output" /> |
| 37 </outputs> | 37 </outputs> |
| 38 <help> | 38 <help> |
| 39 | 39 |
| 40 **What it does** | 40 **What it does** |
| 41 | 41 |