Mercurial > repos > serranop > usearch
comparison usearch_fastq_mergepairs.xml @ 28:dcad0a24bafa draft
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| author | serranop |
|---|---|
| date | Sat, 14 Sep 2013 12:20:18 -0400 |
| parents | 4c11ec2ae1c0 |
| children | 29cb532fc1ee |
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| 27:4c11ec2ae1c0 | 28:dcad0a24bafa |
|---|---|
| 41 <param name="input_reverse" type="data" format="fastq,fastqsanger,fastqcssanger" label="2. File with reverse reads" /> | 41 <param name="input_reverse" type="data" format="fastq,fastqsanger,fastqcssanger" label="2. File with reverse reads" /> |
| 42 <param name="minovlen" type="integer" value="0" label="3. Minimum length of the overlap" help="'0' means no minimum." /> | 42 <param name="minovlen" type="integer" value="0" label="3. Minimum length of the overlap" help="'0' means no minimum." /> |
| 43 <param name="minmergelen" type="integer" value="0" label="4. Minimum length of the merged read" help="'0' means no minimum." /> | 43 <param name="minmergelen" type="integer" value="0" label="4. Minimum length of the merged read" help="'0' means no minimum." /> |
| 44 <param name="maxmergelen" type="integer" value="0" label="5. Maximum length of the merged read" help="'0' means no maximum." /> | 44 <param name="maxmergelen" type="integer" value="0" label="5. Maximum length of the merged read" help="'0' means no maximum." /> |
| 45 <param name="maxdiffs" type="integer" value="0" label="6. Maximum number of mismatches allowed in the overlap region" help="'0' means any number of mismatches allowed" /> | 45 <param name="maxdiffs" type="integer" value="0" label="6. Maximum number of mismatches allowed in the overlap region" help="'0' means any number of mismatches allowed" /> |
| 46 <param name="truncqual" type="integer" value="0" label="7. Truncate the forward and reverse reads at the first Q<=q, if present. This truncation is performed before aligning the pair. With Illumina paired reads, it is recommended to set this to 2 or higher, as low-quality tails will otherwise often cause alignment of the pair to fail." help="'0' means no quality truncation." /> | 46 <param name="truncqual" type="integer" value="0" label="7. Truncate the forward and reverse reads at the first Q<=q, if present. This truncation is performed before aligning the pair. With Illumina paired reads, it is recommended to set this to 2 or higher, as low-quality tails will otherwise often cause alignment of the pair to fail" help="'0' means no quality truncation." /> |
| 47 <param name="minlen" type="integer" value="0" label="8. Minimum length of the forward and reverse read, after truncating per option 7 if applicable." help="'0' means no minimum." /> | 47 <param name="minlen" type="integer" value="0" label="8. Minimum length of the forward and reverse read, after truncating per option 7 if applicable" help="'0' means no minimum." /> |
| 48 <param name="allowmergestagger" type="boolean" truevalue="-fastq_allowmergestagger" falsevalue="" checked="false" label="9. Allow merge of a pair where the alignment is staggered" help="By default, pairs with staggered alignments are discarded." /> | 48 <param name="allowmergestagger" type="boolean" truevalue="-fastq_allowmergestagger" falsevalue="" checked="false" label="9. Allow merge of a pair where the alignment is staggered" help="By default, pairs with staggered alignments are discarded." /> |
| 49 <param name="ascii" type="integer" value="33" label="10. ASCII_BASE constant" help="See http://drive5.com/usearch/manual/fastq_params.html" /> | 49 <param name="ascii" type="integer" value="33" label="10. ASCII_BASE constant" help="See http://drive5.com/usearch/manual/fastq_params.html" /> |
| 50 <param name="qmin" type="integer" value="0" label="11. Minimum Q score" /> | 50 <param name="qmin" type="integer" value="0" label="11. Minimum Q score" /> |
| 51 <param name="qmax" type="integer" value="41" label="12. Maximum Q score for input files" /> | 51 <param name="qmax" type="integer" value="41" label="12. Maximum Q score for input files" /> |
| 52 <param name="qmaxout" type="integer" value="41" label="13. Maximum Q score for output files" /> | 52 <param name="qmaxout" type="integer" value="41" label="13. Maximum Q score for output files" /> |
| 60 <when value="fastq"></when> | 60 <when value="fastq"></when> |
| 61 <when value="fasta"></when> | 61 <when value="fasta"></when> |
| 62 </conditional> | 62 </conditional> |
| 63 </inputs> | 63 </inputs> |
| 64 <outputs> | 64 <outputs> |
| 65 <data name="output" format="${output_format.format}" label="Merge result" /> | 65 <data format="fastq" name="output" label="Merge output"> |
| 66 <change_format> | |
| 67 <when input="format" value="fasta" format="fasta" /> | |
| 68 </change_format> | |
| 69 </data> | |
| 66 </outputs> | 70 </outputs> |
| 67 <tests> | 71 <tests> |
| 68 <test> | 72 <test> |
| 69 <param name="input_forward" value="fastq_mergepairs_input1.fq" ftype="fastqsanger" /> | 73 <param name="input_forward" value="fastq_mergepairs_input1.fq" ftype="fastqsanger" /> |
| 70 <param name="input_reverse" value="fastq_mergepairs_input2.fq" ftype="fastqsanger" /> | 74 <param name="input_reverse" value="fastq_mergepairs_input2.fq" ftype="fastqsanger" /> |