Mercurial > repos > devteam > fastx_clipper
changeset 0:2fe2d2b9e8e4 draft
Uploaded tool tarball.
| author | devteam |
|---|---|
| date | Wed, 25 Sep 2013 11:07:38 -0400 |
| parents | |
| children | 8192b4014977 |
| files | fastx_clipper.xml test-data/fastx_clipper1.fastq test-data/fastx_clipper1a.out tool-data/fastx_clipper_sequences.txt.sample tool_dependencies.xml |
| diffstat | 5 files changed, 192 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fastx_clipper.xml Wed Sep 25 11:07:38 2013 -0400 @@ -0,0 +1,117 @@ +<tool id="cshl_fastx_clipper" name="Clip" version="1.0.1" > + <description>adapter sequences</description> + <requirements> + <requirement type="package" version="0.0.13">fastx_toolkit</requirement> + </requirements> + <command> + zcat -f $input | fastx_clipper -l $minlength -a $clip_source.clip_sequence -d $keepdelta -o $output -v $KEEP_N $DISCARD_OPTIONS +#if $input.ext == "fastqsanger": + -Q 33 +#end if + </command> + + <inputs> + <param format="fasta,fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="Library to clip" /> + + <param name="minlength" size="4" type="integer" value="15"> + <label>Minimum sequence length (after clipping, sequences shorter than this length will be discarded)</label> + </param> + + <conditional name="clip_source"> + <param name="clip_source_list" type="select" label="Source"> + <option value="prebuilt" selected="true">Standard (select from the list below)</option> + <option value="user">Enter custom sequence</option> + </param> + + <when value="user"> + <param name="clip_sequence" size="30" label="Enter custom clipping sequence" type="text" value="AATTGGCC" /> + </when> + + <when value="prebuilt"> + <param name="clip_sequence" type="select" label="Choose Adapter"> + <options from_file="fastx_clipper_sequences.txt"> + <column name="name" index="1"/> + <column name="value" index="0"/> + </options> + </param> + </when> + </conditional> + + <param name="keepdelta" size="2" type="integer" value="0"> + <label>enter non-zero value to keep the adapter sequence and x bases that follow it</label> + <help>use this for hairpin barcoding. keep at 0 unless you know what you're doing.</help> + </param> + + <param name="KEEP_N" type="select" label="Discard sequences with unknown (N) bases"> + <option value="">Yes</option> + <option value="-n">No</option> + </param> + + <param name="DISCARD_OPTIONS" type="select" label="Output options"> + <option value="-c">Output only clipped sequences (i.e. sequences which contained the adapter)</option> + <option value="-C">Output only non-clipped sequences (i.e. sequences which did not contained the adapter)</option> + <option value="">Output both clipped and non-clipped sequences</option> + </param> + + </inputs> + <!-- + #functional test with param value starting with - fails. + --> + <tests> + <test> + <param name="input" value="fastx_clipper1.fastq" ftype="fastqsolexa"/> + <param name="maxmismatches" value="2" /> + <param name="minlength" value="15" /> + <param name="clip_source_list" value="user" /> + <param name="clip_sequence" value="CAATTGGTTAATCCCCCTATATA" /> + <param name="keepdelta" value="0" /> + <param name="KEEP_N" value="+-n" /> + <param name="DISCARD_OPTIONS" value="+-c" /> + <output name="output" file="fastx_clipper1a.out" /> + </test> + </tests> + <outputs> + <data format="input" name="output" metadata_source="input" /> + </outputs> + +<help> +**What it does** + +This tool clips adapters from the 3'-end of the sequences in a FASTA/FASTQ file. + +-------- + + +**Clipping Illustration:** + +.. image:: ${static_path}/fastx_icons/fastx_clipper_illustration.png + + + + + + + + +**Clipping Example:** + +.. image:: ${static_path}/fastx_icons/fastx_clipper_example.png + + + +**In the above example:** + +* Sequence no. 1 was discarded since it wasn't clipped (i.e. didn't contain the adapter sequence). (**Output** parameter). +* Sequence no. 5 was discarded --- it's length (after clipping) was shorter than 15 nt (**Minimum Sequence Length** parameter). + + + + +------ + +This tool is based on `FASTX-toolkit`__ by Assaf Gordon. + + .. __: http://hannonlab.cshl.edu/fastx_toolkit/ + +</help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastx_clipper1.fastq Wed Sep 25 11:07:38 2013 -0400 @@ -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastx_clipper1a.out Wed Sep 25 11:07:38 2013 -0400 @@ -0,0 +1,20 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GTACGCATGACCGAACCCCCCNCCCCC ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaaabbXEZabaa +@CSHL_3_FC042AGLLWW:1:2:7:169 +GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCC ++CSHL_3_FC042AGLLWW:1:2:7:169 +a_M^a\Uaaa_M_aaaaaaaaaaaaaaaV\ZUGUU +@CSHL_3_FC042AGLLWW:1:2:7:1819 +AATTCAAACCACCCCAACCCACACACAGAGATA ++CSHL_3_FC042AGLLWW:1:2:7:1819 +a\\QVVVLaaLOEXUWUUEKUULEMUEUUKULI +@CSHL_3_FC042AGLLWW:1:2:7:1875 +GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCC ++CSHL_3_FC042AGLLWW:1:2:7:1875 +aaaaaaaaaXUXXEXaaaaa`_ZaaaaaaaaaXEX +@CSHL_3_FC042AGLLWW:1:2:8:250 +TGCCGCGCACACTGATG ++CSHL_3_FC042AGLLWW:1:2:8:250 +aaaaaaaa^aaaaaabb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/fastx_clipper_sequences.txt.sample Wed Sep 25 11:07:38 2013 -0400 @@ -0,0 +1,13 @@ +# +# Adapter/Linker sequences for FASTX-Clipper tool. +# +# Format: +# Adapter Sequence <TAB> Descriptive name +# +# Example: +# AAATTTGATAAGATA Our-Adapter +# +# Some adapters can be found here: +# http://seqanswers.com/forums/showthread.php?t=198 +# +#TGTAGGCC Dummy-Adapter (don't use me)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Wed Sep 25 11:07:38 2013 -0400 @@ -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>