Mercurial > repos > iuc > seqtk
annotate seqtk_mergefa.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_mergefa" name="seqtk_mergefa" version="@WRAPPER_VERSION@.0"> | |
3
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
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3 <description>merge two FASTA/Q files</description> |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
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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
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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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7 <expand macro="requirements"/> |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
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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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10 seqtk mergefa |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
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11 -q $q |
0 | 12 $i |
13 $m | |
14 $r | |
15 $h | |
3
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
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16 '$in_fa1' |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
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17 '$in_fa2' |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
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18 > '$default' |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
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19 ]]></command> |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
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20 <inputs> |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
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21 <param name="in_fa1" type="data" format="fasta,fastq" label="Input FASTA/Q file #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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22 <param name="in_fa2" type="data" format="fasta,fastq" label="Input FASTA/Q file #2"/> |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents:
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23 <param argument="-q" type="integer" value="0" label="Quality threshold"/> |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents:
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24 <param argument="-i" type="boolean" truevalue="-i" falsevalue="" checked="false" label="Take intersection" /> |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents:
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25 <param argument="-m" type="boolean" truevalue="-m" falsevalue="" checked="false" label="Convert to lowercase when one of the input base is N" /> |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents:
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26 <param argument="-r" type="boolean" truevalue="-r" falsevalue="" checked="false" label="Pick a random allele from het" /> |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents:
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27 <param argument="-h" type="boolean" truevalue="-h" falsevalue="" checked="false" label="Suppress hets in the input" /> |
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 </inputs> |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents:
2
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changeset
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29 <outputs> |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
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30 <data name="default" format_source="in_fa1" label="Merger of $in_fa1.name and $in_fa2.name"/> |
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 </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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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 <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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34 <param name="in_fa1" value="seqtk_mergefa1.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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35 <param name="in_fa2" value="seqtk_mergefa2.fa"/> |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents:
2
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changeset
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36 <output name="default" file="seqtk_mergefa.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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37 </test> |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents:
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diff
changeset
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38 <test> |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents:
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diff
changeset
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39 <param name="in_fa1" value="seqtk_mergefa1.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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40 <param name="in_fa2" value="seqtk_mergefa2.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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41 <param name="m" value="True" /> |
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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42 <output name="default" file="seqtk_mergefa2.out" ftype="fasta"/> |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents:
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43 </test> |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents:
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44 </tests> |
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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45 <help><![CDATA[ |
0 | 46 **What it does** |
47 | |
48 Merges two fasta files, using ambiguity codes | |
49 | |
50 :: | |
51 | |
52 # seq1.fa | |
53 >test0 | |
54 ACTGACTGAAA | |
55 | |
56 # seq2.fa | |
57 >test0 | |
58 ACTGAMTGCGN | |
59 | |
60 In the following the `-m` option has been set to highlight seqtk-mergefa's features. | |
61 | |
62 :: | |
63 | |
64 >test0 | |
65 ACTGACTGxxa | |
66 | |
67 @ATTRIBUTION@ | |
3
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
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68 ]]></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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69 <expand macro="citation" /> |
0 | 70 </tool> |