# HG changeset patch # User devteam # Date 1444754452 14400 # Node ID 4286abbc87a2f0bfa7b3e89abdec7f35b370195e # Parent 08495cd1d93e638a4418d4cf93aaf700ab2f1827 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 diff -r 08495cd1d93e -r 4286abbc87a2 fastx_clipper.xml --- a/fastx_clipper.xml Tue Jun 03 14:53:42 2014 -0400 +++ b/fastx_clipper.xml Tue Oct 13 12:40:52 2015 -0400 @@ -1,80 +1,77 @@ - - adapter sequences - - fastx_toolkit - - - zcat -f $input | fastx_clipper -l $minlength -a $clip_source.clip_sequence -d $keepdelta -o $output -v $KEEP_N $DISCARD_OPTIONS + + adapter sequences + + fastx_toolkit + + + - - - - - - Minimum sequence length (after clipping, sequences shorter than this length will be discarded) - +]]> + - - - - - + + - - - + + Minimum sequence length (after clipping, sequences shorter than this length will be discarded) + - - - - - - - - - + + + + + + + + + - - enter non-zero value to keep the adapter sequence and x bases that follow it - use this for hairpin barcoding. keep at 0 unless you know what you're doing. - + + + + + + + + + - - - - + + enter non-zero value to keep the adapter sequence and x bases that follow it + use this for hairpin barcoding. keep at 0 unless you know what you're doing. + - - - - - + + + + - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + **What it does** This tool clips adapters from the 3'-end of the sequences in a FASTA/FASTQ file. @@ -84,34 +81,21 @@ **Clipping Illustration:** -.. image:: fastx_clipper_illustration.png - - - - - - - +.. image:: fastx_clipper_illustration.png **Clipping Example:** -.. image:: fastx_clipper_example.png +.. image:: 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/ - - + diff -r 08495cd1d93e -r 4286abbc87a2 test-data/fastx_clipper1a.out --- a/test-data/fastx_clipper1a.out Tue Jun 03 14:53:42 2014 -0400 +++ b/test-data/fastx_clipper1a.out Tue Oct 13 12:40:52 2015 -0400 @@ -2,18 +2,6 @@ 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 diff -r 08495cd1d93e -r 4286abbc87a2 tool_dependencies.xml --- a/tool_dependencies.xml Tue Jun 03 14:53:42 2014 -0400 +++ b/tool_dependencies.xml Tue Oct 13 12:40:52 2015 -0400 @@ -1,6 +1,6 @@ - +