Mercurial > repos > iuc > seqtk
annotate seqtk_fqchk.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_fqchk" name="seqtk_fqchk" 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>fastq QC (base/quality summary)</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
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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
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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 fqchk |
0 | 11 -q $q |
3
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
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12 '$in_file' | awk '{if(NR<4){print "#"$0}else{print $0}}' |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
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13 > '$default' |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
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14 ]]></command> |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
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15 <inputs> |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
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16 <expand macro="in_fq"/> |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents:
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17 <param argument="-q" type="integer" value="20" label="Quality values" help="Use 0 to get the distribution of all quality values"/> |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
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18 </inputs> |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
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19 <outputs> |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
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20 <data name="default" format="tabular" label="Quality information for $in_file.name"/> |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents:
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21 </outputs> |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents:
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22 <tests> |
bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
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23 <test> |
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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24 <param name="in_file" value="seqtk_fqchk.fq"/> |
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 <output name="default" file="seqtk_fqchk.out" ftype="tabular"/> |
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 </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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27 </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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28 <help><![CDATA[ |
0 | 29 **What it does** |
30 | |
31 Returns quality score information base-by-base. | |
32 | |
33 :: | |
34 | |
35 @SEQ_ID1 | |
36 GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT | |
37 + | |
38 !''*((((***+))%%%++)(%%%%).1***-+*''))**55CCF>>>>>>CCCCCCC65 | |
39 | |
40 each based is examined individually and information reported: | |
41 | |
42 :: | |
43 | |
44 #min_len: 60; max_len: 60; avg_len: 60.00; 15 distinct quality values | |
45 #POS #bases %A %C %G %T %N avgQ errQ %low %high | |
46 #ALL 60 31.7 16.7 18.3 33.3 0.0 15.1 8.7 66.7 33.3 | |
47 1 1 0.0 0.0 100.0 0.0 0.0 0.0 3.0 100.0 0.0 | |
48 2 1 100.0 0.0 0.0 0.0 0.0 6.0 6.0 100.0 0.0 | |
49 3 1 0.0 0.0 0.0 100.0 0.0 6.0 6.0 100.0 0.0 | |
50 4 1 0.0 0.0 0.0 100.0 0.0 9.0 9.0 100.0 0.0 | |
51 5 1 0.0 0.0 0.0 100.0 0.0 7.0 7.0 100.0 0.0 | |
52 6 1 0.0 0.0 100.0 0.0 0.0 7.0 7.0 100.0 0.0 | |
53 7 1 0.0 0.0 100.0 0.0 0.0 7.0 7.0 100.0 0.0 | |
54 8 1 0.0 0.0 100.0 0.0 0.0 7.0 7.0 100.0 0.0 | |
55 9 1 0.0 0.0 100.0 0.0 0.0 9.0 9.0 100.0 0.0 | |
56 10 1 0.0 0.0 0.0 100.0 0.0 9.0 9.0 100.0 0.0 | |
57 | |
58 @ATTRIBUTION@ | |
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bc7d99f46a5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
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59 ]]></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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60 <expand macro="citation" /> |
0 | 61 </tool> |