| Previous changeset 2:b007d9642911 (2015-07-16) |
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Commit message:
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastq_join commit a7f8461032de196092033c9ceae9f4407a469c44 |
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modified:
fastq-join.xml |
| b |
| diff -r b007d9642911 -r 8ec3dfde378b fastq-join.xml --- a/fastq-join.xml Thu Jul 16 17:36:11 2015 -0400 +++ b/fastq-join.xml Wed Dec 16 16:01:08 2015 -0500 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="fastq_join" name="fastq-join" version="1.1.2-806"> +<tool id="fastq_join" name="fastq-join" version="1.1.2-806.1"> <description> - Joins two paired-end reads on the overlapping ends</description> <requirements> @@ -11,21 +11,39 @@ <command><![CDATA[ fastq-join - -v '$splitChar' - -p $pctMaxDiff - -m $minOverlap + -v "${splitChar}" + -p "${pctMaxDiff}" + -m "${minOverlap}" #if $stitchLengthReport: - -r $outputStitchLengthReport + -r "${outputStitchLengthReport}" #end if - $read1 - $read2 - -o $outputUnmatched1 -o $outputUnmatched2 -o $outputJoined + #if str( $input_type.input_type_selector ) == 'paired': + "${input_type.read1}" + "${input_type.read2}" + #else: + "${input_type.input_collection.forward}" + "${input_type.input_collection.reverse}" + #end if + -o "${outputUnmatched1}" -o "${outputUnmatched2}" -o "${outputJoined}" ]]> </command> <inputs> - <param format="fastq, fastqillumina, fastqsanger, fastqsolexa" name="read1" type="data" label="Read 1 Fastq" /> - <param format="fastq, fastqillumina, fastqsanger, fastqsolexa" name="read2" type="data" label="Read 2 Fastq" /> + <conditional name="input_type"> + <param name="input_type_selector" type="select" label="Dataset type"> + <option value="paired">Paired-end</option> + <option value="paired_collection">Paired-end Dataset Collection</option> + </param> + <when value="paired"> + <param format="fastqsanger" name="read1" type="data" label="Read 1 Fastq" help="Nucleotide-space: Must have PHRED-scaled quality values with offset 33 (fastqsanger)." /> + <param format="fastqsanger" name="read2" type="data" label="Read 2 Fastq" help="Nucleotide-space: Must have PHRED-scaled quality values with offset 33 (fastqsanger)." /> + </when> + <when value="paired_collection"> + <param name="input_collection" format="fastqsanger" + type="data_collection" collection_type="paired" + label="FASTQ Paired Dataset" help="Nucleotide-space: Must have PHRED-scaled quality values with offset 33 (fastqsanger)." /> + </when> + </conditional> <param name="splitChar" type="text" value=" " label="Split read ids on this character" help="Default is space ' ' for Illumina reads" /> <param name="pctMaxDiff" type="float" value="8" min="0" max="100" label="Maximum percentage difference between matching segments" /> <param name="minOverlap" type="integer" value="6" min="1" label="Minimum length of matching segements" /> @@ -33,9 +51,9 @@ </inputs> <outputs> - <data format_source="read1" name="outputJoined" label="${tool.name} on ${on_string} (joined)"/> - <data format_source="read1" name="outputUnmatched1" label="${tool.name} on ${on_string} (unmatched1)"/> - <data format_source="read2" name="outputUnmatched2" label="${tool.name} on ${on_string} (unmatched2)"/> + <data format="fastqsanger" name="outputJoined" label="${tool.name} on ${on_string} (joined)"/> + <data format="fastqsanger" name="outputUnmatched1" label="${tool.name} on ${on_string} (unmatched1)"/> + <data format="fastqsanger" name="outputUnmatched2" label="${tool.name} on ${on_string} (unmatched2)"/> <data format="tabular" name="outputStitchLengthReport" label="${tool.name} on ${on_string} (stitch length report)"> <filter>stitchLengthReport</filter> </data> @@ -43,8 +61,8 @@ <tests> <test> - <param name="read1" value="test_read1.fastq" /> - <param name="read2" value="test_read3.fastq" /> + <param name="read1" value="test_read1.fastq" ftype="fastqsanger" /> + <param name="read2" value="test_read3.fastq" ftype="fastqsanger" /> <output name="outputJoined" file="testout.join.fastq" /> <output name="outputUnmatched1" file="testout.un1.fastq" /> <output name="outputUnmatched2" file="testout.un2.fastq" /> |