Mercurial > repos > iuc > seqtk
annotate seqtk_seq.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_seq" name="seqtk_seq" version="@WRAPPER_VERSION@.0"> | |
| 3 <description>common transformation 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 seq -q $q | |
| 10 -X $X | |
| 11 #if $n and $n != "None" and $n is not None and $n != "": | |
| 12 -n "$n" | |
| 13 #end if | |
| 14 -l $l | |
| 15 -Q $Q | |
| 16 -s $s | |
| 17 -f $f | |
| 18 #if $M and $M != "None" and $M is not None and $M != "": | |
| 19 -M "$M" | |
| 20 #end if | |
| 21 -L $L | |
| 22 $c | |
| 23 $r | |
| 24 $A | |
| 25 $C | |
| 26 $N | |
| 27 $x1 | |
| 28 $x2 | |
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f73729b62b51
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 2249d643284ee782d882cd200729a86a2c6bb744
iuc
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29 #if $in_file.ext == "fastqillumina" |
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f73729b62b51
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 2249d643284ee782d882cd200729a86a2c6bb744
iuc
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0
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changeset
|
30 -V |
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f73729b62b51
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 2249d643284ee782d882cd200729a86a2c6bb744
iuc
parents:
0
diff
changeset
|
31 #end if |
| 0 | 32 |
| 33 $in_file | |
| 34 > $default]]></command> | |
| 35 <inputs> | |
| 36 <expand macro="in_faq"/> | |
| 37 <param label="mask bases with quality lower than INT" help="(-q)" name="q" type="integer" value="0"/> | |
| 38 <param label="mask bases with quality higher than INT" help="(-X)" name="X" type="integer" value="255"/> | |
| 39 <param area="false" default="0" label="masked bases converted to CHAR; 0 for lowercase" help="(-n)" name="n" type="text"/> | |
| 40 <param label="number of residues per line; 0 for 2^32-1" help="(-l)" name="l" type="integer" value="0"/> | |
| 41 <param label="quality shift: ASCII-INT gives base quality" help="(-Q)" name="Q" type="integer" value="33"/> | |
| 42 <param label="random seed" help="effective with -f (-s)" name="s" type="integer" value="11"/> | |
| 43 <param label="sample fraction of sequences" help="(-f)" name="f" type="float" value="1"/> | |
| 44 <param area="false" default="null" label="mask regions in BED or name list FILE" help="(-M)" name="M" type="text"/> | |
| 45 <param label="drop sequences with length shorter than INT" help="(-L)" name="L" type="integer" value="0"/> | |
| 46 <param checked="false" label="mask complement region" help="effective with -M (-c)" name="c" type="boolean" falsevalue="" truevalue="-c"/> | |
| 47 <param checked="false" label="reverse complement" help="(-r)" name="r" type="boolean" falsevalue="" truevalue="-r"/> | |
| 48 <param checked="false" label="force FASTA output (discard quality)" help="(-A)" name="A" type="boolean" falsevalue="" truevalue="-A"/> | |
| 49 <param checked="false" label="drop comments at the header lines" help="(-C)" name="C" type="boolean" falsevalue="" truevalue="-C"/> | |
| 50 <param checked="false" label="drop sequences containing ambiguous bases" help="(-N)" name="N" type="boolean" falsevalue="" truevalue="-N"/> | |
| 51 <param checked="false" label="output the 2n-1 reads only" help="(-1)" name="x1" type="boolean" falsevalue="" truevalue="-1"/> | |
| 52 <param checked="false" label="output the 2n reads only" help="(-2)" name="x2" type="boolean" falsevalue="" truevalue="-2"/> | |
| 53 </inputs> | |
| 54 <outputs> | |
| 55 <data format_source="in_file" hidden="false" name="default"/> | |
| 56 </outputs> | |
| 57 <tests> | |
| 58 <test> | |
| 59 <!-- This is a sorry excuse for a test for a tool which does way more | |
| 60 than it should, but upstream decided to put a TON of functionality | |
| 61 into a single tool rather than using the single responsibility | |
| 62 principle. --> | |
| 63 <param name="in_file" value="seqtk_seq.fa"/> | |
| 64 <param name="r" value="True"/> | |
| 65 <param name="n" value=""/> | |
| 66 <param name="M" value=""/> | |
| 67 <output name="default" file="seqtk_seq_revcom.fa" ftype="fasta"/> | |
| 68 </test> | |
| 69 </tests> | |
| 70 <help><![CDATA[ | |
| 71 **What it does** | |
| 72 | |
| 73 Various utilities for transforming FASTA/Q data | |
| 74 | |
| 75 @ATTRIBUTION@ | |
| 76 ]]></help> | |
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2
f73729b62b51
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 2249d643284ee782d882cd200729a86a2c6bb744
iuc
parents:
0
diff
changeset
|
77 <expand macro="citation" /> |
| 0 | 78 </tool> |