Mercurial > repos > iuc > seqtk
annotate seqtk_mergefa.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_mergefa" name="seqtk_mergefa" version="@WRAPPER_VERSION@.0"> | |
| 3 <description>merge two FASTA/Q files</description> | |
| 4 <macros> | |
| 5 <import>macros.xml</import> | |
| 6 </macros> | |
| 7 <expand macro="requirements"/> | |
| 8 <expand macro="stdio"/> | |
| 9 <command><![CDATA[seqtk mergefa -q $q | |
| 10 $i | |
| 11 $m | |
| 12 $r | |
| 13 $h | |
| 14 | |
| 15 $in_fa1 | |
| 16 $in_fa2 | |
| 17 | |
| 18 > $default]]></command> | |
| 19 <inputs> | |
| 20 <param name="in_fa1" type="data" format="fasta,fastq" label="Input FASTA/Q file #1"/> | |
| 21 <param name="in_fa2" type="data" format="fasta,fastq" label="Input FASTA/Q file #2"/> | |
| 22 <param label="quality threshold" help="(-q)" name="q" type="integer" value="0"/> | |
| 23 <param checked="false" label="take intersection" help="(-i)" name="i" type="boolean" falsevalue="" truevalue="-i"/> | |
| 24 <param checked="false" label="convert to lowercase when one of the input base is N" help="(-m)" name="m" type="boolean" falsevalue="" truevalue="-m"/> | |
| 25 <param checked="false" label="pick a random allele from het" help="(-r)" name="r" type="boolean" falsevalue="" truevalue="-r"/> | |
| 26 <param checked="false" label="suppress hets in the input" help="(-h)" name="h" type="boolean" falsevalue="" truevalue="-h"/> | |
| 27 </inputs> | |
| 28 <outputs> | |
| 29 <data format_source="in_fa1" hidden="false" name="default" label="Merger of $in_fa1.name and $in_fa2.name"/> | |
| 30 </outputs> | |
| 31 <tests> | |
| 32 <test> | |
| 33 <param name="in_fa1" value="seqtk_mergefa1.fa"/> | |
| 34 <param name="in_fa2" value="seqtk_mergefa2.fa"/> | |
| 35 <output name="default" file="seqtk_mergefa.out" ftype="fasta"/> | |
| 36 </test> | |
| 37 <test> | |
| 38 <param name="in_fa1" value="seqtk_mergefa1.fa"/> | |
| 39 <param name="in_fa2" value="seqtk_mergefa2.fa"/> | |
| 40 <param name="m" value="True" /> | |
| 41 <output name="default" file="seqtk_mergefa2.out" ftype="fasta"/> | |
| 42 </test> | |
| 43 </tests> | |
| 44 <help><![CDATA[ | |
| 45 **What it does** | |
| 46 | |
| 47 Merges two fasta files, using ambiguity codes | |
| 48 | |
| 49 :: | |
| 50 | |
| 51 # seq1.fa | |
| 52 >test0 | |
| 53 ACTGACTGAAA | |
| 54 | |
| 55 # seq2.fa | |
| 56 >test0 | |
| 57 ACTGAMTGCGN | |
| 58 | |
| 59 In the following the `-m` option has been set to highlight seqtk-mergefa's features. | |
| 60 | |
| 61 :: | |
| 62 | |
| 63 >test0 | |
| 64 ACTGACTGxxa | |
| 65 | |
| 66 @ATTRIBUTION@ | |
| 67 ]]></help> | |
|
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55e75a28fde7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
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68 <expand macro="citation" /> |
| 0 | 69 </tool> |