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annotate fasta_compute_length.xml @ 1:d8cc2c8eef14 draft

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planemo upload commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
author devteam
date Tue, 21 Jul 2015 14:18:55 -0400
parents ece409f6573c
children de2db1bdfbf8
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d8cc2c8eef14 planemo upload commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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1 <tool id="fasta_compute_length" name="Compute sequence length" version="1.0.0">
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2 <description></description>
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3 <command interpreter="python">fasta_compute_length.py $input $output $keep_first</command>
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4 <inputs>
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5 <param name="input" type="data" format="fasta" label="Compute length for these sequences"/>
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6 <param name="keep_first" type="integer" size="5" value="0" label="How many title characters to keep?" help="'0' = keep the whole thing"/>
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7 </inputs>
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8 <outputs>
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9 <data name="output" format="tabular"/>
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10 </outputs>
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11 <tests>
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12 <test>
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13 <param name="input" value="454.fasta" />
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14 <param name="keep_first" value="0"/>
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15 <output name="output" file="fasta_tool_compute_length_1.out" />
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16 </test>
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18 <test>
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19 <param name="input" value="extract_genomic_dna_out1.fasta" />
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20 <param name="keep_first" value="0"/>
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21 <output name="output" file="fasta_tool_compute_length_2.out" />
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22 </test>
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23
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24 <test>
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25 <param name="input" value="454.fasta" />
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26 <param name="keep_first" value="14"/>
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27 <output name="output" file="fasta_tool_compute_length_3.out" />
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28 </test>
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29 </tests>
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30 <help>
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31
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32 **What it does**
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34 This tool counts the length of each fasta sequence in the file. The output file has two columns per line (separated by tab): fasta titles and lengths of the sequences. The option *How many characters to keep?* allows to select a specified number of letters from the beginning of each FASTA entry.
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35
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36 -----
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37
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38 **Example**
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39
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40 Suppose you have the following FASTA formatted sequences from a Roche (454) FLX sequencing run::
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42 &gt;EYKX4VC02EQLO5 length=108 xy=1826_0455 region=2 run=R_2007_11_07_16_15_57_ TCCGCGCCGAGCATGCCCATCTTGGATTCCGGCGCGATGACCATCGCCCGCTCCACCACG TTCGGCCGGCCCTTCTCGTCGAGGAATGACACCAGCGCTTCGCCCACG &gt;EYKX4VC02D4GS2 length=60 xy=1573_3972 region=2 run=R_2007_11_07_16_15_57_ AATAAAACTAAATCAGCAAAGACTGGCAAATACTCACAGGCTTATACAATACAAATGTAAfa
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43
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44 Running this tool while setting **How many characters to keep?** to **14** will produce this::
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46 EYKX4VC02EQLO5 108
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47 EYKX4VC02D4GS2 60
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49
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50 </help>
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51 </tool>