Mercurial > repos > drosofff > yac_clipper
annotate yac.xml @ 4:621df8f400a5 draft
planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 1136a0c5b7398eddc5420113784914c0d471bfbf
| author | drosofff |
|---|---|
| date | Thu, 03 Sep 2015 11:32:55 -0400 |
| parents | a70911a01f36 |
| children | 416f6fbc7ff3 |
| rev | line source |
|---|---|
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4
621df8f400a5
planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 1136a0c5b7398eddc5420113784914c0d471bfbf
drosofff
parents:
2
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changeset
|
1 <tool id="yac" name="Clip adapter" version="1.3.6"> |
| 1 | 2 <description /> |
| 3 <command interpreter="python">yac.py --input $input | |
| 0 | 4 --output $output |
| 1 | 5 --output_format "$out_format" |
| 0 | 6 --adapter_to_clip $clip_source.clip_sequence |
| 7 --min $min | |
| 8 --max $max | |
| 9 --Nmode $Nmode | |
| 10 </command> | |
| 1 | 11 <inputs> |
| 12 <param format="fastq" label="Source file" name="input" type="data" /> | |
| 13 <param label="min size" name="min" size="4" type="integer" value="15" /> | |
| 14 <param label="max size" name="max" size="4" type="integer" value="36" /> | |
| 15 <param label="Select output format" name="out_format" type="select"> | |
| 16 <option selected="true" value="fasta">Fasta format</option> | |
| 17 <option value="fastq">Fastq format</option> | |
| 18 </param> | |
| 19 <param label="Accept reads containing N?" name="Nmode" type="select"> | |
| 20 <option selected="True" value="accept">accept</option> | |
| 21 <option value="reject">reject</option> | |
| 22 </param> | |
| 23 <conditional name="clip_source"> | |
| 24 <param help="Built-in adapters or User-provided" label="Source" name="clip_source_list" type="select"> | |
| 25 <option selected="True" value="prebuilt">Use a built-in adapter (select from the list below)</option> | |
| 26 <option value="user">Use custom sequence</option> | |
| 27 </param> | |
| 28 <when value="prebuilt"> | |
| 29 <param help="if your adapter is not listed, input your own sequence" label="Select Adapter to clip" name="clip_sequence" type="select"> | |
| 30 <option value="TCGTATGCCGTCTTCTGCTTG">Solexa TCGTATGCCGTCTTCTGCTTG</option> | |
| 31 <option value="ATCTCGTATGCCGTCTTCTGCTT">Illumina ATCTCGTATGCCGTCTTCTGCTT</option> | |
| 32 <option selected="True" value="TGGAATTCTCGGGTGCCAAG">Illumina TruSeq TGGAATTCTCGGGTGCCAAG</option> | |
| 33 <option value="CTGTAGGCACCATCAATCGT">IdT CTGTAGGCACCATCAATCGT</option> | |
| 34 </param> | |
| 35 </when> | |
| 36 <when value="user"> | |
| 37 <param label="Enter your Sequence" name="clip_sequence" size="35" type="text" value="GAATCC" /> | |
| 38 </when> | |
| 39 </conditional> | |
| 40 </inputs> | |
| 41 <outputs> | |
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2
a70911a01f36
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
1
diff
changeset
|
42 <data format="fasta" metadata_source="input" name="output"> |
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a70911a01f36
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
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diff
changeset
|
43 <change_format> |
|
a70911a01f36
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
1
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44 <when input="out_format" value="fastq" format="fastq" /> |
|
a70911a01f36
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
1
diff
changeset
|
45 </change_format> |
|
a70911a01f36
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
1
diff
changeset
|
46 </data> |
| 1 | 47 </outputs> |
| 48 <tests> | |
| 49 <test> | |
| 50 <param ftype="fastqsanger" name="input" value="yac.fastq" /> | |
| 51 <param name="min" value="18" /> | |
| 52 <param name="max" value="29" /> | |
| 53 <param name="clip_source_list" value="prebuilt" /> | |
| 54 <param name="clip_sequence" value="ATCTCGTATGCCGTCTTCTGCTT" /> | |
| 55 <param name="Nmode" value="accept" /> | |
| 56 <output file="yac.out" name="output" /> | |
| 57 </test> | |
| 58 <test> | |
| 59 <param ftype="fastqsanger" name="input" value="yac.fastq" /> | |
| 60 <param name="min" value="18" /> | |
| 61 <param name="max" value="29" /> | |
| 62 <param name="clip_source_list" value="prebuilt" /> | |
| 63 <param name="clip_sequence" value="ATCTCGTATGCCGTCTTCTGCTT" /> | |
| 64 <param name="Nmode" value="accept" /> | |
| 65 <param name="out_format" value="fastq" /> | |
| 66 <output file="yac_fastq.out" name="output" /> | |
| 67 </test> | |
| 68 </tests> | |
| 69 <help> | |
| 70 This tool clips adapter sequences from a fastq file and outputs either a | |
| 71 fasta or fastq file of clipped reads with renumbered fasta/fastq headers. | |
| 0 | 72 |
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4
621df8f400a5
planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 1136a0c5b7398eddc5420113784914c0d471bfbf
drosofff
parents:
2
diff
changeset
|
73 By default clipped sequences with unknown nucleotides are kept, but |
| 1 | 74 can be discarded by setting "Accept reads containing N?" to reject. |
| 0 | 75 |
| 76 Min size and max size filter clipped reads on their size. | |
| 77 | |
| 78 Note that unclipped reads that satisfy the min and max size conditions are kept. | |
| 79 </help> | |
| 80 </tool> |