| Next changeset 1:186b8d913e6c (2015-11-11) |
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Commit message:
Uploaded tool tarball. |
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added:
fastq_to_fasta.xml test-data/fastq_to_fasta1.fastq test-data/fastq_to_fasta1a.out test-data/fastq_to_fasta1b.out tool_dependencies.xml |
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| diff -r 000000000000 -r 04614cf6ed39 fastq_to_fasta.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fastq_to_fasta.xml Wed Sep 25 11:04:26 2013 -0400 |
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| @@ -0,0 +1,82 @@ +<tool id="cshl_fastq_to_fasta" name="FASTQ to FASTA"> + <description>converter</description> + <requirements> + <requirement type="package" version="0.0.13">fastx_toolkit</requirement> + </requirements> + <command>gunzip -cf $input | fastq_to_fasta $SKIPN $RENAMESEQ -o $output -v +#if $input.ext == "fastqsanger": +-Q 33 +#end if + </command> + + <inputs> + <param format="fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="FASTQ Library to convert" /> + + <param name="SKIPN" type="select" label="Discard sequences with unknown (N) bases "> + <option value="">yes</option> + <option value="-n">no</option> + </param> + + <param name="RENAMESEQ" type="select" label="Rename sequence names in output file (reduces file size)"> + <option value="-r">yes</option> + <option value="">no</option> + </param> + + </inputs> + + <tests> + <test> + <!-- FASTQ-To-FASTA, keep N, don't rename --> + <param name="input" value="fastq_to_fasta1.fastq" ftype="fastqsolexa" /> + <param name="SKIPN" value=""/> + <param name="RENAMESEQ" value=""/> + <output name="output" file="fastq_to_fasta1a.out" /> + </test> + <test> + <!-- FASTQ-To-FASTA, discard N, rename --> + <param name="input" value="fastq_to_fasta1.fastq" ftype="fastqsolexa" /> + <param name="SKIPN" value="no"/> + <param name="RENAMESEQ" value="yes"/> + <output name="output" file="fastq_to_fasta1b.out" /> + </test> + </tests> + + <outputs> + <data format="fasta" name="output" metadata_source="input" /> + </outputs> + +<help> + +**What it does** + +This tool converts data from Solexa format to FASTA format (scroll down for format description). + +-------- + +**Example** + +The following data in Solexa-FASTQ format:: + + @CSHL_4_FC042GAMMII_2_1_517_596 + GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT + +CSHL_4_FC042GAMMII_2_1_517_596 + 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 + +Will be converted to FASTA (with 'rename sequence names' = NO):: + + >CSHL_4_FC042GAMMII_2_1_517_596 + GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT + +Will be converted to FASTA (with 'rename sequence names' = YES):: + + >1 + GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT + +------ + +This tool is based on `FASTX-toolkit`__ by Assaf Gordon. + + .. __: http://hannonlab.cshl.edu/fastx_toolkit/ +</help> +<!-- FASTQ-to-FASTA is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) --> +</tool> |
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| diff -r 000000000000 -r 04614cf6ed39 test-data/fastq_to_fasta1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastq_to_fasta1.fastq Wed Sep 25 11:04:26 2013 -0400 |
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| @@ -0,0 +1,36 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GTACGCATGACCGAACCCCCCNCCCCCCAATTGGTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaaabbXEZabaaaaaaaa]]` +@CSHL_3_FC042AGLLWW:1:2:7:33 +CAATGCCTCCAATTGGTTAATCCCCCTATATATACT ++CSHL_3_FC042AGLLWW:1:2:7:33 +Waaa^aZaaW^U_XaWaa\WMEP^KEZXRPEEEGaa +@CSHL_3_FC042AGLLWW:1:2:7:169 +GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC ++CSHL_3_FC042AGLLWW:1:2:7:169 +a_M^a\Uaaa_M_aaaaaaaaaaaaaaaV\ZUGUUR +@CSHL_3_FC042AGLLWW:1:2:7:1436 +AATTATTTATTAAATTTTAATAATATGGGAGACACT ++CSHL_3_FC042AGLLWW:1:2:7:1436 +a^aaaaaaaaaaaaaaa_U`aaaaa_S_aaaaaVV[ +@CSHL_3_FC042AGLLWW:1:2:7:292 +GGAGAAATACACACAATTGGTTAATCCCCCTATATA ++CSHL_3_FC042AGLLWW:1:2:7:292 +babaaaaaaaUMaaaaaaaaaaa\XEUUEP_]UERE +@CSHL_3_FC042AGLLWW:1:2:7:1819 +AATTCAAACCACCCCAACCCACACACAGAGATACAA ++CSHL_3_FC042AGLLWW:1:2:7:1819 +a\\QVVVLaaLOEXUWUUEKUULEMUEUUKULIQMU +@CSHL_3_FC042AGLLWW:1:2:7:1875 +GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC ++CSHL_3_FC042AGLLWW:1:2:7:1875 +aaaaaaaaaXUXXEXaaaaa`_ZaaaaaaaaaXEXU +@CSHL_3_FC042AGLLWW:1:2:8:624 +ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG ++CSHL_3_FC042AGLLWW:1:2:8:624 +aa[S^`X`aa_]]OOXMU^_[MU_aaaaaaaaaaaa +@CSHL_3_FC042AGLLWW:1:2:8:250 +TGCCGCGCACACTGATGCAATTGGTTAATCCCCCTA ++CSHL_3_FC042AGLLWW:1:2:8:250 +aaaaaaaa^aaaaaabbb[KXPEU[RXZ^JUKRKXE |
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| diff -r 000000000000 -r 04614cf6ed39 test-data/fastq_to_fasta1a.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastq_to_fasta1a.out Wed Sep 25 11:04:26 2013 -0400 |
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| @@ -0,0 +1,16 @@ +>CSHL_3_FC042AGLLWW:1:2:7:33 +CAATGCCTCCAATTGGTTAATCCCCCTATATATACT +>CSHL_3_FC042AGLLWW:1:2:7:169 +GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC +>CSHL_3_FC042AGLLWW:1:2:7:1436 +AATTATTTATTAAATTTTAATAATATGGGAGACACT +>CSHL_3_FC042AGLLWW:1:2:7:292 +GGAGAAATACACACAATTGGTTAATCCCCCTATATA +>CSHL_3_FC042AGLLWW:1:2:7:1819 +AATTCAAACCACCCCAACCCACACACAGAGATACAA +>CSHL_3_FC042AGLLWW:1:2:7:1875 +GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC +>CSHL_3_FC042AGLLWW:1:2:8:624 +ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG +>CSHL_3_FC042AGLLWW:1:2:8:250 +TGCCGCGCACACTGATGCAATTGGTTAATCCCCCTA |
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| diff -r 000000000000 -r 04614cf6ed39 test-data/fastq_to_fasta1b.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastq_to_fasta1b.out Wed Sep 25 11:04:26 2013 -0400 |
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| @@ -0,0 +1,18 @@ +>1 +GTACGCATGACCGAACCCCCCNCCCCCCAATTGGTT +>2 +CAATGCCTCCAATTGGTTAATCCCCCTATATATACT +>3 +GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC +>4 +AATTATTTATTAAATTTTAATAATATGGGAGACACT +>5 +GGAGAAATACACACAATTGGTTAATCCCCCTATATA +>6 +AATTCAAACCACCCCAACCCACACACAGAGATACAA +>7 +GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC +>8 +ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG +>9 +TGCCGCGCACACTGATGCAATTGGTTAATCCCCCTA |
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| diff -r 000000000000 -r 04614cf6ed39 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Wed Sep 25 11:04:26 2013 -0400 |
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| @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="fastx_toolkit" version="0.0.13"> + <repository changeset_revision="ec66ae4c269b" name="package_fastx_toolkit_0_0_13" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |