Mercurial > repos > devteam > fastx_collapser
annotate fastx_collapser.xml @ 2:421f0af4ee95 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_collapser commit a1517c9d22029095120643bbe2c8fa53754dd2b7
author | devteam |
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date | Wed, 11 Nov 2015 12:39:04 -0500 |
parents | 13c2d9e8c6d5 |
children | 7ce1891db6f5 |
rev | line source |
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0 | 1 <tool id="cshl_fastx_collapser" version="1.0.0" name="Collapse"> |
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421f0af4ee95
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_collapser commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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2 <description>sequences</description> |
0 | 3 <requirements> |
4 <requirement type="package" version="0.0.13">fastx_toolkit</requirement> | |
5 </requirements> | |
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421f0af4ee95
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_collapser commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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6 <command> |
421f0af4ee95
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_collapser commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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7 <![CDATA[ |
421f0af4ee95
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_collapser commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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8 zcat -f < '$input' | fastx_collapser -v -o '$output' |
0 | 9 #if $input.ext == "fastqsanger": |
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421f0af4ee95
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_collapser commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
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10 -Q 33 |
0 | 11 #end if |
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421f0af4ee95
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_collapser commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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12 ]]> |
421f0af4ee95
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_collapser commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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13 </command> |
0 | 14 |
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421f0af4ee95
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_collapser commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
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15 <inputs> |
421f0af4ee95
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_collapser commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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16 <param format="fasta,fastqsanger,fastqsolexa" name="input" type="data" label="Library to collapse" /> |
421f0af4ee95
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_collapser commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
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17 </inputs> |
421f0af4ee95
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_collapser commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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18 <outputs> |
421f0af4ee95
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_collapser commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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19 <data format="fasta" name="output" metadata_source="input" /> |
421f0af4ee95
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_collapser commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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20 </outputs> |
421f0af4ee95
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_collapser commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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21 <!-- The order of sequences in the test output differ between 32 bit and 64 bit machines. |
421f0af4ee95
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_collapser commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
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22 <tests> |
421f0af4ee95
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_collapser commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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23 <test> |
421f0af4ee95
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_collapser commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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24 <param name="input" value="fasta_collapser1.fasta" /> |
421f0af4ee95
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_collapser commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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25 <param name="output" file="fasta_collapser1.out" /> |
421f0af4ee95
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_collapser commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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26 </test> |
421f0af4ee95
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_collapser commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
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27 </tests> |
0 | 28 --> |
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421f0af4ee95
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_collapser commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
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changeset
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29 <help> |
0 | 30 **What it does** |
31 | |
32 This tool collapses identical sequences in a FASTA file into a single sequence. | |
33 | |
34 -------- | |
35 | |
36 **Example** | |
37 | |
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421f0af4ee95
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_collapser commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
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changeset
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38 Example Input File (Sequence "ATAT" appears multiple times):: |
0 | 39 |
40 >CSHL_2_FC0042AGLLOO_1_1_605_414 | |
41 TGCG | |
42 >CSHL_2_FC0042AGLLOO_1_1_537_759 | |
43 ATAT | |
44 >CSHL_2_FC0042AGLLOO_1_1_774_520 | |
45 TGGC | |
46 >CSHL_2_FC0042AGLLOO_1_1_742_502 | |
47 ATAT | |
48 >CSHL_2_FC0042AGLLOO_1_1_781_514 | |
49 TGAG | |
50 >CSHL_2_FC0042AGLLOO_1_1_757_487 | |
51 TTCA | |
52 >CSHL_2_FC0042AGLLOO_1_1_903_769 | |
53 ATAT | |
54 >CSHL_2_FC0042AGLLOO_1_1_724_499 | |
55 ATAT | |
56 | |
57 Example Output file:: | |
58 | |
59 >1-1 | |
60 TGCG | |
61 >2-4 | |
62 ATAT | |
63 >3-1 | |
64 TGGC | |
65 >4-1 | |
66 TGAG | |
67 >5-1 | |
68 TTCA | |
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421f0af4ee95
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_collapser commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
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changeset
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69 |
0 | 70 .. class:: infomark |
71 | |
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421f0af4ee95
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_collapser commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
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changeset
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72 Original Sequence Names / Lane descriptions (e.g. "CSHL_2_FC0042AGLLOO_1_1_742_502") are discarded. |
0 | 73 |
74 The output sequence name is composed of two numbers: the first is the sequence's number, the second is the multiplicity value. | |
75 | |
76 The following output:: | |
77 | |
78 >2-4 | |
79 ATAT | |
80 | |
81 means that the sequence "ATAT" is the second sequence in the file, and it appeared 4 times in the input FASTA file. | |
82 | |
83 | |
84 ------ | |
85 | |
86 This tool is based on `FASTX-toolkit`__ by Assaf Gordon. | |
87 | |
88 .. __: http://hannonlab.cshl.edu/fastx_toolkit/ | |
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421f0af4ee95
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_collapser commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
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changeset
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89 </help> |
0 | 90 </tool> |