Mercurial > repos > iuc > seqtk
annotate seqtk_cutN.xml @ 3:bc7d99f46a5d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
author | iuc |
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date | Mon, 05 Jun 2017 13:27:11 -0400 |
parents | f73729b62b51 |
children | ecf1c30da3a2 |
rev | line source |
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0 | 1 <?xml version="1.0"?> |
2 <tool id="seqtk_cutN" name="seqtk_cutN" version="@WRAPPER_VERSION@.0"> | |
3
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
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3 <description>cut sequence at long N</description> |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
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4 <macros> |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
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5 <import>macros.xml</import> |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
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6 </macros> |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
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changeset
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7 <expand macro="requirements"/> |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents:
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8 <expand macro="stdio"/> |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
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9 <command><![CDATA[ |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
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diff
changeset
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10 seqtk cutN |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents:
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11 -n $n |
0 | 12 -p $p |
13 $g | |
3
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
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14 '$in_file' |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
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15 > '$default' |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
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16 ]]></command> |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents:
2
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17 <inputs> |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents:
2
diff
changeset
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18 <expand macro="in_faq"/> |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents:
2
diff
changeset
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19 <param argument="-n" type="integer" value="1000" label="Minimum size of N tract" /> |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents:
2
diff
changeset
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20 <param argument="-p" type="integer" value="10" label="Penalty for a non-N" /> |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents:
2
diff
changeset
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21 <param argument="-g" type="boolean" truevalue="-g" falsevalue="" checked="false" label="Print gaps only, no sequence" /> |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents:
2
diff
changeset
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22 </inputs> |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents:
2
diff
changeset
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23 <outputs> |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents:
2
diff
changeset
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24 <data name="default" format_source="in_file" label="$in_file.name split on N runs longer than $n"/> |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents:
2
diff
changeset
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25 </outputs> |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents:
2
diff
changeset
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26 <tests> |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents:
2
diff
changeset
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27 <test> |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents:
2
diff
changeset
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28 <param name="in_file" value="seqtk_cutn.fa"/> |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents:
2
diff
changeset
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29 <param name="n" value="1"/> |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents:
2
diff
changeset
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30 <output name="default" file="seqtk_cutn.out" ftype="fasta"/> |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents:
2
diff
changeset
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31 </test> |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents:
2
diff
changeset
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32 </tests> |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents:
2
diff
changeset
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33 <help><![CDATA[ |
0 | 34 **What it does** |
35 | |
36 Splits long sequences with runs of Ns | |
37 | |
38 :: | |
39 | |
40 >test | |
41 AACTGATCGATCGATCGNNNNNNNNNNNACATG | |
42 | |
43 This will be split into the component sequences without the ambiguity. | |
44 | |
45 :: | |
46 | |
47 >test:1-17 | |
48 AACTGATCGATCGATCG | |
49 >test:29-33 | |
50 ACATG | |
51 | |
52 @ATTRIBUTION@ | |
3
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents:
2
diff
changeset
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53 ]]></help> |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents:
2
diff
changeset
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54 <expand macro="citation" /> |
0 | 55 </tool> |