Mercurial > repos > devteam > fastq_to_fasta
annotate fastq_to_fasta.xml @ 3:4498e994e31b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit 3953b65f6b1c0336e9cadbe0792a5d3b14b5643a
author | iuc |
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date | Wed, 22 Aug 2018 11:02:27 -0400 |
parents | 44ed3f74ea7a |
children | 5dbca5fbdc45 |
rev | line source |
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3
4498e994e31b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit 3953b65f6b1c0336e9cadbe0792a5d3b14b5643a
iuc
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1 <tool id="cshl_fastq_to_fasta" name="FASTQ to FASTA" version="1.0.2"> |
2
44ed3f74ea7a
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> |
44ed3f74ea7a
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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3 <macros> |
44ed3f74ea7a
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> |
44ed3f74ea7a
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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5 </macros> |
44ed3f74ea7a
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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6 <expand macro="requirements" /> |
44ed3f74ea7a
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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7 <command detect_errors="exit_code"><![CDATA[ |
44ed3f74ea7a
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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8 @CATS@ fastq_to_fasta |
44ed3f74ea7a
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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9 $SKIPN |
44ed3f74ea7a
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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10 $RENAMESEQ |
44ed3f74ea7a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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11 -o '$output' |
44ed3f74ea7a
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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12 -v @FQQUAL@ |
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4498e994e31b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit 3953b65f6b1c0336e9cadbe0792a5d3b14b5643a
iuc
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13 @GZIP@ |
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44ed3f74ea7a
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 ]]></command> |
44ed3f74ea7a
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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15 <inputs> |
44ed3f74ea7a
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 <expand macro="fastq_input" /> |
44ed3f74ea7a
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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17 <param name="SKIPN" type="select" label="Discard sequences with unknown (N) bases "> |
44ed3f74ea7a
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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18 <option value="">yes</option> |
44ed3f74ea7a
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 <option value="-n">no</option> |
44ed3f74ea7a
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> |
44ed3f74ea7a
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 <param name="RENAMESEQ" type="select" label="Rename sequence names in output file (reduces file size)"> |
44ed3f74ea7a
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="-r">yes</option> |
44ed3f74ea7a
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 <option value="">no</option> |
44ed3f74ea7a
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 </param> |
44ed3f74ea7a
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 </inputs> |
44ed3f74ea7a
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 <outputs> |
44ed3f74ea7a
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 <data name="output" format="fasta" metadata_source="input" /> |
44ed3f74ea7a
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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28 </outputs> |
44ed3f74ea7a
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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29 <tests> |
44ed3f74ea7a
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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30 <test> |
44ed3f74ea7a
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 <!-- FASTQ-To-FASTA, keep N, don't rename --> |
44ed3f74ea7a
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="input" value="fastq_to_fasta1.fastq" ftype="fastqsolexa" /> |
44ed3f74ea7a
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="SKIPN" value=""/> |
44ed3f74ea7a
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 <param name="RENAMESEQ" value=""/> |
44ed3f74ea7a
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 <output name="output" file="fastq_to_fasta1a.out" /> |
44ed3f74ea7a
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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36 </test> |
44ed3f74ea7a
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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37 <test> |
44ed3f74ea7a
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 <!-- FASTQ-To-FASTA, discard N, rename --> |
44ed3f74ea7a
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="input" value="fastq_to_fasta1.fastq" ftype="fastqsolexa" /> |
44ed3f74ea7a
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="SKIPN" value="no"/> |
44ed3f74ea7a
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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41 <param name="RENAMESEQ" value="yes"/> |
44ed3f74ea7a
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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42 <output name="output" file="fastq_to_fasta1b.out" /> |
44ed3f74ea7a
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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43 </test> |
44ed3f74ea7a
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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44 <test> |
44ed3f74ea7a
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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45 <!-- FASTQ-To-FASTA, discard N, rename --> |
44ed3f74ea7a
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="input" value="fastq_to_fasta-in2.fastq" ftype="fastqsanger" /> |
44ed3f74ea7a
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="SKIPN" value="no"/> |
44ed3f74ea7a
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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48 <param name="RENAMESEQ" value="yes"/> |
44ed3f74ea7a
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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49 <output name="output" file="fastq_to_fasta-out2.out" /> |
44ed3f74ea7a
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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50 </test> |
44ed3f74ea7a
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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51 </tests> |
44ed3f74ea7a
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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52 <help><![CDATA[ |
0 | 53 **What it does** |
54 | |
55 This tool converts data from Solexa format to FASTA format (scroll down for format description). | |
56 | |
57 -------- | |
58 | |
59 **Example** | |
60 | |
61 The following data in Solexa-FASTQ format:: | |
62 | |
63 @CSHL_4_FC042GAMMII_2_1_517_596 | |
64 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT | |
65 +CSHL_4_FC042GAMMII_2_1_517_596 | |
66 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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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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67 |
0 | 68 Will be converted to FASTA (with 'rename sequence names' = NO):: |
69 | |
70 >CSHL_4_FC042GAMMII_2_1_517_596 | |
71 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT | |
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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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72 |
0 | 73 Will be converted to FASTA (with 'rename sequence names' = YES):: |
74 | |
75 >1 | |
76 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT | |
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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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77 |
0 | 78 ------ |
79 | |
80 This tool is based on `FASTX-toolkit`__ by Assaf Gordon. | |
81 | |
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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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82 .. __: http://hannonlab.cshl.edu/fastx_toolkit/ |
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44ed3f74ea7a
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 ]]></help> |
44ed3f74ea7a
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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84 <expand macro="citations" /> |
0 | 85 <!-- FASTQ-to-FASTA is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) --> |
86 </tool> |