| Previous changeset 2:c46a5807f2b6 (2014-06-03) Next changeset 4:015dc921d814 (2018-05-08) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter commit a1517c9d22029095120643bbe2c8fa53754dd2b7 |
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modified:
fastx_barcode_splitter.xml fastx_barcode_splitter_galaxy_wrapper.sh tool_dependencies.xml |
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| diff -r c46a5807f2b6 -r 8abdedf55101 fastx_barcode_splitter.xml --- a/fastx_barcode_splitter.xml Tue Jun 03 14:50:45 2014 -0400 +++ b/fastx_barcode_splitter.xml Wed Nov 11 12:38:37 2015 -0500 |
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| @@ -1,42 +1,38 @@ <tool id="cshl_fastx_barcode_splitter" version="1.0.0" name="Barcode Splitter"> - <description></description> + <description></description> <requirements> <requirement type="package" version="0.0.13">fastx_toolkit</requirement> </requirements> - <command interpreter="bash">fastx_barcode_splitter_galaxy_wrapper.sh $BARCODE $input "$input.name" "$output.files_path" --mismatches $mismatches --partial $partial $EOL > $output </command> + <command interpreter="bash">fastx_barcode_splitter_galaxy_wrapper.sh '$BARCODE' '$input' "$input.name" "$output.files_path" --mismatches $mismatches --partial $partial $EOL > '$output' </command> + + <inputs> + <param format="txt" name="BARCODE" type="data" label="Barcodes to use" /> + <param format="fasta,fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="Library to split" /> - <inputs> - <param format="txt" name="BARCODE" type="data" label="Barcodes to use" /> - <param format="fasta,fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="Library to split" /> + <param name="EOL" type="select" label="Barcodes found at"> + <option value="--bol">Start of sequence (5' end)</option> + <option value="--eol">End of sequence (3' end)</option> + </param> - <param name="EOL" type="select" label="Barcodes found at"> - <option value="--bol">Start of sequence (5' end)</option> - <option value="--eol">End of sequence (3' end)</option> - </param> + <param name="mismatches" type="integer" value="2" label="Number of allowed mismatches" /> - <param name="mismatches" type="integer" size="3" value="2" label="Number of allowed mismatches" /> - - <param name="partial" type="integer" size="3" value="0" label="Number of allowed barcodes nucleotide deletions" /> - - </inputs> - - <tests> - <test> - <!-- Split a FASTQ file --> - <param name="BARCODE" value="fastx_barcode_splitter1.txt" /> - <param name="input" value="fastx_barcode_splitter1.fastq" ftype="fastqsolexa" /> - <param name="EOL" value="Start of sequence (5' end)" /> - <param name="mismatches" value="2" /> - <param name="partial" value="0" /> - <param name="output" file="fastx_barcode_splitter1.out" /> - </test> - </tests> - - <outputs> - <data format="html" name="output" /> - </outputs> -<help> - + <param name="partial" type="integer" value="0" label="Number of allowed barcodes nucleotide deletions" /> + </inputs> + <outputs> + <data format="html" name="output" /> + </outputs> + <tests> + <test> + <!-- Split a FASTQ file --> + <param name="BARCODE" value="fastx_barcode_splitter1.txt" /> + <param name="input" value="fastx_barcode_splitter1.fastq" ftype="fastqsolexa" /> + <param name="EOL" value="Start of sequence (5' end)" /> + <param name="mismatches" value="2" /> + <param name="partial" value="0" /> + <output name="output" file="fastx_barcode_splitter1.out" /> + </test> + </tests> + <help> **What it does** This tool splits a Solexa library (FASTQ file) or a regular FASTA file into several files, using barcodes as the split criteria. @@ -50,11 +46,11 @@ Example:: #This line is a comment (starts with a 'number' sign) - BC1 GATCT - BC2 ATCGT - BC3 GTGAT + BC1 GATCT + BC2 ATCGT + BC3 GTGAT BC4 TGTCT - + For each barcode, a new FASTQ file will be created (with the barcode's identifier as part of the file name). Sequences matching the barcode will be stored in the appropriate file. @@ -72,7 +68,6 @@ This tool is based on `FASTX-toolkit`__ by Assaf Gordon. .. __: http://hannonlab.cshl.edu/fastx_toolkit/ - -</help> + </help> <!-- FASTX-barcode-splitter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) --> </tool> |
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| diff -r c46a5807f2b6 -r 8abdedf55101 fastx_barcode_splitter_galaxy_wrapper.sh --- a/fastx_barcode_splitter_galaxy_wrapper.sh Tue Jun 03 14:50:45 2014 -0400 +++ b/fastx_barcode_splitter_galaxy_wrapper.sh Wed Nov 11 12:38:37 2015 -0500 |
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| @@ -62,7 +62,7 @@ PREFIX="$BASEPATH""${LIBNAME}__" SUFFIX=".txt" -RESULTS=`zcat -f "$FASTQ_FILE" | fastx_barcode_splitter.pl --bcfile "$BARCODE_FILE" --prefix "$PREFIX" --suffix "$SUFFIX" "$@"` +RESULTS=`zcat -f < "$FASTQ_FILE" | fastx_barcode_splitter.pl --bcfile "$BARCODE_FILE" --prefix "$PREFIX" --suffix "$SUFFIX" "$@"` if [ $? != 0 ]; then echo "error" fi |
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| diff -r c46a5807f2b6 -r 8abdedf55101 tool_dependencies.xml --- a/tool_dependencies.xml Tue Jun 03 14:50:45 2014 -0400 +++ b/tool_dependencies.xml Wed Nov 11 12:38:37 2015 -0500 |
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| @@ -1,6 +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" /> + <repository changeset_revision="ec66ae4c269b" name="package_fastx_toolkit_0_0_13" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency> |