| Next changeset 1:d77c9c6ecf68 (2013-12-03) |
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Commit message:
Uploaded tool tarball. |
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added:
fastx_trimmer.xml test-data/fastx_trimmer1.fasta test-data/fastx_trimmer1.out test-data/fastx_trimmer2.fastq test-data/fastx_trimmer2.out tool_dependencies.xml |
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| diff -r 000000000000 -r 9cb372481a71 fastx_trimmer.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fastx_trimmer.xml Wed Sep 25 11:21:27 2013 -0400 |
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| @@ -0,0 +1,83 @@ +<tool id="cshl_fastx_trimmer" version="1.0.0" name="Trim sequences"> + <description></description> + <requirements> + <requirement type="package" version="0.0.13">fastx_toolkit</requirement> + </requirements> + <command>zcat -f '$input' | fastx_trimmer -v -f $first -l $last -o $output +#if $input.ext == "fastqsanger": +-Q 33 +#end if + </command> + + <inputs> + <param format="fasta,fastqsolexa,fastqsanger" version="1.0.0" name="input" type="data" label="Library to clip" /> + + <param version="1.0.0" name="first" size="4" type="integer" value="1"> + <label>First base to keep</label> + </param> + + <param version="1.0.0" name="last" size="4" type="integer" value="21"> + <label>Last base to keep</label> + </param> + </inputs> + + <tests> + <test> + <!-- Trim a FASTA file - remove first four bases (e.g. a barcode) --> + <param version="1.0.0" name="input" value="fastx_trimmer1.fasta" /> + <param version="1.0.0" name="first" value="5"/> + <param version="1.0.0" name="last" value="36"/> + <output version="1.0.0" name="output" file="fastx_trimmer1.out" /> + </test> + <test> + <!-- Trim a FASTQ file - remove last 9 bases (e.g. keep only miRNA length sequences) --> + <param version="1.0.0" name="input" value="fastx_trimmer2.fastq" ftype="fastqsolexa"/> + <param version="1.0.0" name="first" value="1"/> + <param version="1.0.0" name="last" value="27"/> + <output version="1.0.0" name="output" file="fastx_trimmer2.out" /> + </test> + </tests> + + <outputs> + <data format="input" version="1.0.0" name="output" metadata_source="input" /> + </outputs> + <help> +**What it does** + +This tool trims (cut bases from) sequences in a FASTA/Q file. + +-------- + +**Example** + +Input Fasta file (with 36 bases in each sequences):: + + >1-1 + TATGGTCAGAAACCATATGCAGAGCCTGTAGGCACC + >2-1 + CAGCGAGGCTTTAATGCCATTTGGCTGTAGGCACCA + + +Trimming with First=1 and Last=21, we get a FASTA file with 21 bases in each sequences (starting from the first base):: + + >1-1 + TATGGTCAGAAACCATATGCA + >2-1 + CAGCGAGGCTTTAATGCCATT + +Trimming with First=6 and Last=10, will generate a FASTA file with 5 bases (bases 6,7,8,9,10) in each sequences:: + + >1-1 + TCAGA + >2-1 + AGGCT + + ------ + +This tool is based on `FASTX-toolkit`__ by Assaf Gordon. + + .. __: http://hannonlab.cshl.edu/fastx_toolkit/ + +</help> +<!-- FASTX-Trimmer is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) --> +</tool> |
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| diff -r 000000000000 -r 9cb372481a71 test-data/fastx_trimmer1.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastx_trimmer1.fasta Wed Sep 25 11:21:27 2013 -0400 |
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| @@ -0,0 +1,4 @@ +>CSHL__2_FC042NGABCD:8:1:120:202 +ACGATAGATCGGAAGAGCTAGTATGCCGTTTTCTGC +>CSHL__2_FC042NGABCD:8:1:103:1185 +ATCACGATAGATCGGCAGAGCTCGTTTACCGTCTTC |
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| diff -r 000000000000 -r 9cb372481a71 test-data/fastx_trimmer1.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastx_trimmer1.out Wed Sep 25 11:21:27 2013 -0400 |
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| @@ -0,0 +1,4 @@ +>CSHL__2_FC042NGABCD:8:1:120:202 +TAGATCGGAAGAGCTAGTATGCCGTTTTCTGC +>CSHL__2_FC042NGABCD:8:1:103:1185 +CGATAGATCGGCAGAGCTCGTTTACCGTCTTC |
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| diff -r 000000000000 -r 9cb372481a71 test-data/fastx_trimmer2.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastx_trimmer2.fastq Wed Sep 25 11:21:27 2013 -0400 |
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| @@ -0,0 +1,8 @@ +@CSHL__2_FC042NGABCD:8:1:120:202 +ACGATAGATCGGAAGAGCTAGTATGCCGTTTTCTGC ++CSHL__2_FC042NGABCD:8:1:120:202 +40 40 40 40 20 40 40 40 40 6 40 40 28 40 40 25 40 20 40 -1 30 40 14 27 40 8 1 3 7 -1 11 10 -1 21 10 8 +@CSHL__2_FC042NGABCD:8:1:103:1185 +ATCACGATAGATCGGCAGAGCTCGTTTACCGTCTTC ++CSHL__2_FC042NGABCD:8:1:103:1185 +40 40 40 40 40 35 33 31 40 40 40 32 30 22 40 -0 9 22 17 14 8 36 15 34 22 12 23 3 10 -0 8 2 4 25 30 2 |
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| diff -r 000000000000 -r 9cb372481a71 test-data/fastx_trimmer2.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastx_trimmer2.out Wed Sep 25 11:21:27 2013 -0400 |
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| @@ -0,0 +1,8 @@ +@CSHL__2_FC042NGABCD:8:1:120:202 +ACGATAGATCGGAAGAGCTAGTATGCC ++CSHL__2_FC042NGABCD:8:1:120:202 +40 40 40 40 20 40 40 40 40 6 40 40 28 40 40 25 40 20 40 -1 30 40 14 27 40 8 1 +@CSHL__2_FC042NGABCD:8:1:103:1185 +ATCACGATAGATCGGCAGAGCTCGTTT ++CSHL__2_FC042NGABCD:8:1:103:1185 +40 40 40 40 40 35 33 31 40 40 40 32 30 22 40 0 9 22 17 14 8 36 15 34 22 12 23 |
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| diff -r 000000000000 -r 9cb372481a71 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Wed Sep 25 11:21:27 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> |