Mercurial > repos > iuc > seqtk
annotate seqtk_cutN.xml @ 7:55e75a28fde7 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 344140b8df53b8b7024618bb04594607a045c03a
| author | iuc |
|---|---|
| date | Mon, 04 May 2015 22:47:23 -0400 |
| parents | 33ded39275c3 |
| children | 16f2535c08bf |
| rev | line source |
|---|---|
| 0 | 1 <?xml version="1.0"?> |
| 2 <tool id="seqtk_cutN" name="seqtk_cutN" version="@WRAPPER_VERSION@.0"> | |
| 3 <description>cut sequence at long N</description> | |
| 4 <macros> | |
| 5 <import>macros.xml</import> | |
| 6 </macros> | |
| 7 <expand macro="requirements"/> | |
| 8 <expand macro="stdio"/> | |
| 9 <command><![CDATA[seqtk cutN -n $n | |
| 10 -p $p | |
| 11 $g | |
| 12 $in_file | |
| 13 > $default]]></command> | |
| 14 <inputs> | |
| 15 <expand macro="in_faq"/> | |
| 16 <param label="min size of N tract" help="(-n)" name="n" type="integer" value="1000"/> | |
| 17 <param label="penalty for a non-N" help="(-p)" name="p" type="integer" value="10"/> | |
| 18 <param checked="false" label="print gaps only, no sequence" help="(-g)" name="g" type="boolean" falsevalue="" truevalue="-g"/> | |
| 19 </inputs> | |
| 20 <outputs> | |
| 21 <data format_source="in_file" hidden="false" name="default" label="$in_file.name split on N runs longer than $n"/> | |
| 22 </outputs> | |
| 23 <tests> | |
| 24 <test> | |
| 25 <param name="in_file" value="seqtk_cutn.fa"/> | |
| 26 <param name="n" value="1"/> | |
| 27 <output name="default" file="seqtk_cutn.out" ftype="fasta"/> | |
| 28 </test> | |
| 29 </tests> | |
| 30 <help><![CDATA[ | |
| 31 **What it does** | |
| 32 | |
| 33 Splits long sequences with runs of Ns | |
| 34 | |
| 35 :: | |
| 36 | |
| 37 >test | |
| 38 AACTGATCGATCGATCGNNNNNNNNNNNACATG | |
| 39 | |
| 40 This will be split into the component sequences without the ambiguity. | |
| 41 | |
| 42 :: | |
| 43 | |
| 44 >test:1-17 | |
| 45 AACTGATCGATCGATCG | |
| 46 >test:29-33 | |
| 47 ACATG | |
| 48 | |
| 49 | |
| 50 @ATTRIBUTION@ | |
|
7
55e75a28fde7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
0
diff
changeset
|
51 ]]></help> |
|
55e75a28fde7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
0
diff
changeset
|
52 <expand macro="citation" /> |
| 0 | 53 </tool> |