Mercurial > repos > iuc > seqtk
annotate seqtk_comp.xml @ 2:f73729b62b51 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 2249d643284ee782d882cd200729a86a2c6bb744
| author | iuc |
|---|---|
| date | Fri, 01 Jan 2016 14:49:42 -0500 |
| parents | e0a0fd938de4 |
| children | bc7d99f46a5d |
| rev | line source |
|---|---|
| 0 | 1 <?xml version="1.0"?> |
| 2 <tool id="seqtk_comp" name="seqtk_comp" version="@WRAPPER_VERSION@.0"> | |
| 3 <description>get the nucleotide composition of FASTA/Q</description> | |
| 4 <macros> | |
| 5 <import>macros.xml</import> | |
| 6 </macros> | |
| 7 <expand macro="requirements"/> | |
| 8 <expand macro="stdio"/> | |
| 9 <command><![CDATA[seqtk comp | |
| 10 #if $in_bed: | |
| 11 -r $in_bed | |
| 12 #end if | |
| 13 | |
| 14 $in_file | awk 'BEGIN{print "#chr\tlength\t#A\t#C\t#G\t#T\t#2\t#3\t#4\t#CpG\t#tv\t#ts\t#CpG-ts"}1' | |
| 15 | |
| 16 > $default]]></command> | |
| 17 <inputs> | |
| 18 <expand macro="in_faq"/> | |
| 19 <param name="in_bed" optional="True" type="data" format="bed" label="bed file"/> | |
| 20 </inputs> | |
| 21 <outputs> | |
| 22 <data format="tabular" hidden="false" name="default" label="Nucleotide composition of $in_file.name"/> | |
| 23 </outputs> | |
| 24 <tests> | |
| 25 <test> | |
| 26 <param name="in_file" value="seqtk_comp.fa" ftype="fasta"/> | |
| 27 <output name="default" file="seqtk_comp.out" ftype="tabular"/> | |
| 28 </test> | |
| 29 </tests> | |
| 30 <help><![CDATA[ | |
| 31 **What it does** | |
| 32 | |
| 33 Reports composition of fasta/fastq sequences. For an example sequence like | |
| 34 | |
| 35 :: | |
| 36 >test0 | |
| 37 ACTGACTGAA | |
| 38 >ambig_ref | |
| 39 ACGTCGTGTTVHDBN | |
| 40 | |
| 41 The seqtk tool will report: | |
| 42 | |
| 43 :: | |
| 44 | |
| 45 #chr length #A #C #G #T #2 #3 #4 #CpG #tv #ts #CpG-ts | |
| 46 test0 11 4 2 2 2 0 0 1 0 0 0 0 | |
| 47 ambig_ref 15 1 2 3 4 0 4 1 4 0 0 0 | |
| 48 | |
| 49 | |
| 50 @ATTRIBUTION@ | |
| 51 ]]></help> | |
|
2
f73729b62b51
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 2249d643284ee782d882cd200729a86a2c6bb744
iuc
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52 <expand macro="citation" /> |
| 0 | 53 </tool> |