Mercurial > repos > devteam > fasta_compute_length
annotate fasta_compute_length.xml @ 1:2811169ce62b draft
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
| author | devteam |
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| date | Tue, 13 Oct 2015 12:19:36 -0400 |
| parents | 86f00ebe7be7 |
| children | d75972d4bd2a |
| rev | line source |
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2811169ce62b
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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1 <tool id="fasta_compute_length" name="Compute sequence length" version="1.0.0"> |
| 0 | 2 <description></description> |
| 3 <command interpreter="python">fasta_compute_length.py $input $output $keep_first</command> | |
| 4 <inputs> | |
| 5 <param name="input" type="data" format="fasta" label="Compute length for these sequences"/> | |
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2811169ce62b
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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6 <param name="keep_first" type="integer" value="0" label="How many title characters to keep?" help="'0' = keep the whole thing"/> |
| 0 | 7 </inputs> |
| 8 <outputs> | |
| 9 <data name="output" format="tabular"/> | |
| 10 </outputs> | |
| 11 <tests> | |
| 12 <test> | |
| 13 <param name="input" value="454.fasta" /> | |
| 14 <param name="keep_first" value="0"/> | |
| 15 <output name="output" file="fasta_tool_compute_length_1.out" /> | |
| 16 </test> | |
| 17 | |
| 18 <test> | |
| 19 <param name="input" value="extract_genomic_dna_out1.fasta" /> | |
| 20 <param name="keep_first" value="0"/> | |
| 21 <output name="output" file="fasta_tool_compute_length_2.out" /> | |
| 22 </test> | |
| 23 | |
| 24 <test> | |
| 25 <param name="input" value="454.fasta" /> | |
| 26 <param name="keep_first" value="14"/> | |
| 27 <output name="output" file="fasta_tool_compute_length_3.out" /> | |
| 28 </test> | |
| 29 </tests> | |
| 30 <help> | |
| 31 | |
| 32 **What it does** | |
| 33 | |
| 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. | |
| 35 | |
| 36 ----- | |
| 37 | |
| 38 **Example** | |
| 39 | |
| 40 Suppose you have the following FASTA formatted sequences from a Roche (454) FLX sequencing run:: | |
| 41 | |
| 42 >EYKX4VC02EQLO5 length=108 xy=1826_0455 region=2 run=R_2007_11_07_16_15_57_ TCCGCGCCGAGCATGCCCATCTTGGATTCCGGCGCGATGACCATCGCCCGCTCCACCACG TTCGGCCGGCCCTTCTCGTCGAGGAATGACACCAGCGCTTCGCCCACG >EYKX4VC02D4GS2 length=60 xy=1573_3972 region=2 run=R_2007_11_07_16_15_57_ AATAAAACTAAATCAGCAAAGACTGGCAAATACTCACAGGCTTATACAATACAAATGTAAfa | |
| 43 | |
| 44 Running this tool while setting **How many characters to keep?** to **14** will produce this:: | |
| 45 | |
| 46 EYKX4VC02EQLO5 108 | |
| 47 EYKX4VC02D4GS2 60 | |
| 48 | |
| 49 | |
| 50 </help> | |
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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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51 </tool> |