Mercurial > repos > devteam > fastq_to_fasta
annotate fastq_to_fasta.xml @ 4:e282bc27be9a draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit 4c002e52261da2e7609735883d91fa1610ce6ce7"
author | iuc |
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date | Thu, 30 Jan 2020 13:29:38 -0500 |
parents | 02a5f43cd5d1 |
children | 8979c288aefb |
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02a5f43cd5d1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit 3953b65f6b1c0336e9cadbe0792a5d3b14b5643a
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1 <tool id="cshl_fastq_to_fasta" name="FASTQ to FASTA" version="1.0.2"> |
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ce309f4ff17f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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2 <description>converter from FASTX-toolkit</description> |
ce309f4ff17f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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3 <macros> |
ce309f4ff17f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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4 <import>macros.xml</import> |
ce309f4ff17f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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5 </macros> |
ce309f4ff17f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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6 <expand macro="requirements" /> |
ce309f4ff17f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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7 <command detect_errors="exit_code"><![CDATA[ |
ce309f4ff17f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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8 @CATS@ fastq_to_fasta |
ce309f4ff17f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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9 $SKIPN |
ce309f4ff17f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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10 $RENAMESEQ |
ce309f4ff17f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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11 -v @FQQUAL@ |
4
e282bc27be9a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit 4c002e52261da2e7609735883d91fa1610ce6ce7"
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12 @GZIP@ > '$output' |
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ce309f4ff17f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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13 ]]></command> |
ce309f4ff17f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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14 <inputs> |
ce309f4ff17f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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15 <expand macro="fastq_input" /> |
ce309f4ff17f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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16 <param name="SKIPN" type="select" label="Discard sequences with unknown (N) bases "> |
ce309f4ff17f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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17 <option value="">yes</option> |
ce309f4ff17f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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18 <option value="-n">no</option> |
ce309f4ff17f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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19 </param> |
ce309f4ff17f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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20 <param name="RENAMESEQ" type="select" label="Rename sequence names in output file (reduces file size)"> |
ce309f4ff17f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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21 <option value="-r">yes</option> |
ce309f4ff17f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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22 <option value="">no</option> |
ce309f4ff17f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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23 </param> |
ce309f4ff17f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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24 </inputs> |
ce309f4ff17f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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25 <outputs> |
ce309f4ff17f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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26 <data name="output" format="fasta" metadata_source="input" /> |
ce309f4ff17f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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27 </outputs> |
ce309f4ff17f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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28 <tests> |
ce309f4ff17f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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29 <test> |
ce309f4ff17f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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30 <!-- FASTQ-To-FASTA, keep N, don't rename --> |
ce309f4ff17f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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31 <param name="input" value="fastq_to_fasta1.fastq" ftype="fastqsolexa" /> |
ce309f4ff17f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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32 <param name="SKIPN" value=""/> |
ce309f4ff17f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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33 <param name="RENAMESEQ" value=""/> |
ce309f4ff17f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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34 <output name="output" file="fastq_to_fasta1a.out" /> |
ce309f4ff17f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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35 </test> |
ce309f4ff17f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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36 <test> |
ce309f4ff17f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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37 <!-- FASTQ-To-FASTA, discard N, rename --> |
ce309f4ff17f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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38 <param name="input" value="fastq_to_fasta1.fastq" ftype="fastqsolexa" /> |
ce309f4ff17f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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39 <param name="SKIPN" value="no"/> |
ce309f4ff17f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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40 <param name="RENAMESEQ" value="yes"/> |
ce309f4ff17f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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41 <output name="output" file="fastq_to_fasta1b.out" /> |
ce309f4ff17f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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42 </test> |
ce309f4ff17f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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43 <test> |
ce309f4ff17f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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44 <!-- FASTQ-To-FASTA, discard N, rename --> |
ce309f4ff17f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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45 <param name="input" value="fastq_to_fasta-in2.fastq" ftype="fastqsanger" /> |
ce309f4ff17f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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46 <param name="SKIPN" value="no"/> |
ce309f4ff17f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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47 <param name="RENAMESEQ" value="yes"/> |
ce309f4ff17f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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48 <output name="output" file="fastq_to_fasta-out2.out" /> |
ce309f4ff17f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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49 </test> |
ce309f4ff17f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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50 </tests> |
ce309f4ff17f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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51 <help><![CDATA[ |
0 | 52 **What it does** |
53 | |
54 This tool converts data from Solexa format to FASTA format (scroll down for format description). | |
55 | |
56 -------- | |
57 | |
58 **Example** | |
59 | |
60 The following data in Solexa-FASTQ format:: | |
61 | |
62 @CSHL_4_FC042GAMMII_2_1_517_596 | |
63 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT | |
64 +CSHL_4_FC042GAMMII_2_1_517_596 | |
65 40 40 40 40 40 40 40 40 40 40 38 40 40 40 40 40 14 40 40 40 40 40 36 40 13 14 24 24 9 24 9 40 10 10 15 40 | |
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186b8d913e6c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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66 |
0 | 67 Will be converted to FASTA (with 'rename sequence names' = NO):: |
68 | |
69 >CSHL_4_FC042GAMMII_2_1_517_596 | |
70 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT | |
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186b8d913e6c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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71 |
0 | 72 Will be converted to FASTA (with 'rename sequence names' = YES):: |
73 | |
74 >1 | |
75 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT | |
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186b8d913e6c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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76 |
0 | 77 ------ |
78 | |
79 This tool is based on `FASTX-toolkit`__ by Assaf Gordon. | |
80 | |
1
186b8d913e6c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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81 .. __: http://hannonlab.cshl.edu/fastx_toolkit/ |
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ce309f4ff17f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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82 ]]></help> |
ce309f4ff17f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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83 <expand macro="citations" /> |
0 | 84 <!-- FASTQ-to-FASTA is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) --> |
85 </tool> |