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comparison fastq-join.xml @ 3:8ec3dfde378b draft default tip

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planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastq_join commit a7f8461032de196092033c9ceae9f4407a469c44
author lparsons
date Wed, 16 Dec 2015 16:01:08 -0500
parents b007d9642911
children
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2:b007d9642911 3:8ec3dfde378b
1 <tool id="fastq_join" name="fastq-join" version="1.1.2-806"> 1 <tool id="fastq_join" name="fastq-join" version="1.1.2-806.1">
2 <description> - Joins two paired-end reads on the overlapping ends</description> 2 <description> - Joins two paired-end reads on the overlapping ends</description>
3 3
4 <requirements> 4 <requirements>
5 <requirement type="package" version="1.1.2-806">ea-utils</requirement> 5 <requirement type="package" version="1.1.2-806">ea-utils</requirement>
6 </requirements> 6 </requirements>
9 <exit_code range="1:" level="fatal" description="Unknown error occurred" /> 9 <exit_code range="1:" level="fatal" description="Unknown error occurred" />
10 </stdio> 10 </stdio>
11 11
12 <command><![CDATA[ 12 <command><![CDATA[
13 fastq-join 13 fastq-join
14 -v '$splitChar' 14 -v "${splitChar}"
15 -p $pctMaxDiff 15 -p "${pctMaxDiff}"
16 -m $minOverlap 16 -m "${minOverlap}"
17 #if $stitchLengthReport: 17 #if $stitchLengthReport:
18 -r $outputStitchLengthReport 18 -r "${outputStitchLengthReport}"
19 #end if 19 #end if
20 $read1 20 #if str( $input_type.input_type_selector ) == 'paired':
21 $read2 21 "${input_type.read1}"
22 -o $outputUnmatched1 -o $outputUnmatched2 -o $outputJoined 22 "${input_type.read2}"
23 #else:
24 "${input_type.input_collection.forward}"
25 "${input_type.input_collection.reverse}"
26 #end if
27 -o "${outputUnmatched1}" -o "${outputUnmatched2}" -o "${outputJoined}"
23 ]]> 28 ]]>
24 </command> 29 </command>
25 30
26 <inputs> 31 <inputs>
27 <param format="fastq, fastqillumina, fastqsanger, fastqsolexa" name="read1" type="data" label="Read 1 Fastq" /> 32 <conditional name="input_type">
28 <param format="fastq, fastqillumina, fastqsanger, fastqsolexa" name="read2" type="data" label="Read 2 Fastq" /> 33 <param name="input_type_selector" type="select" label="Dataset type">
34 <option value="paired">Paired-end</option>
35 <option value="paired_collection">Paired-end Dataset Collection</option>
36 </param>
37 <when value="paired">
38 <param format="fastqsanger" name="read1" type="data" label="Read 1 Fastq" help="Nucleotide-space: Must have PHRED-scaled quality values with offset 33 (fastqsanger)." />
39 <param format="fastqsanger" name="read2" type="data" label="Read 2 Fastq" help="Nucleotide-space: Must have PHRED-scaled quality values with offset 33 (fastqsanger)." />
40 </when>
41 <when value="paired_collection">
42 <param name="input_collection" format="fastqsanger"
43 type="data_collection" collection_type="paired"
44 label="FASTQ Paired Dataset" help="Nucleotide-space: Must have PHRED-scaled quality values with offset 33 (fastqsanger)." />
45 </when>
46 </conditional>
29 <param name="splitChar" type="text" value=" " label="Split read ids on this character" help="Default is space ' ' for Illumina reads" /> 47 <param name="splitChar" type="text" value=" " label="Split read ids on this character" help="Default is space ' ' for Illumina reads" />
30 <param name="pctMaxDiff" type="float" value="8" min="0" max="100" label="Maximum percentage difference between matching segments" /> 48 <param name="pctMaxDiff" type="float" value="8" min="0" max="100" label="Maximum percentage difference between matching segments" />
31 <param name="minOverlap" type="integer" value="6" min="1" label="Minimum length of matching segements" /> 49 <param name="minOverlap" type="integer" value="6" min="1" label="Minimum length of matching segements" />
32 <param name="stitchLengthReport" type="boolean" value="False" label="Output verbose stitch length report" /> 50 <param name="stitchLengthReport" type="boolean" value="False" label="Output verbose stitch length report" />
33 </inputs> 51 </inputs>
34 52
35 <outputs> 53 <outputs>
36 <data format_source="read1" name="outputJoined" label="${tool.name} on ${on_string} (joined)"/> 54 <data format="fastqsanger" name="outputJoined" label="${tool.name} on ${on_string} (joined)"/>
37 <data format_source="read1" name="outputUnmatched1" label="${tool.name} on ${on_string} (unmatched1)"/> 55 <data format="fastqsanger" name="outputUnmatched1" label="${tool.name} on ${on_string} (unmatched1)"/>
38 <data format_source="read2" name="outputUnmatched2" label="${tool.name} on ${on_string} (unmatched2)"/> 56 <data format="fastqsanger" name="outputUnmatched2" label="${tool.name} on ${on_string} (unmatched2)"/>
39 <data format="tabular" name="outputStitchLengthReport" label="${tool.name} on ${on_string} (stitch length report)"> 57 <data format="tabular" name="outputStitchLengthReport" label="${tool.name} on ${on_string} (stitch length report)">
40 <filter>stitchLengthReport</filter> 58 <filter>stitchLengthReport</filter>
41 </data> 59 </data>
42 </outputs> 60 </outputs>
43 61
44 <tests> 62 <tests>
45 <test> 63 <test>
46 <param name="read1" value="test_read1.fastq" /> 64 <param name="read1" value="test_read1.fastq" ftype="fastqsanger" />
47 <param name="read2" value="test_read3.fastq" /> 65 <param name="read2" value="test_read3.fastq" ftype="fastqsanger" />
48 <output name="outputJoined" file="testout.join.fastq" /> 66 <output name="outputJoined" file="testout.join.fastq" />
49 <output name="outputUnmatched1" file="testout.un1.fastq" /> 67 <output name="outputUnmatched1" file="testout.un1.fastq" />
50 <output name="outputUnmatched2" file="testout.un2.fastq" /> 68 <output name="outputUnmatched2" file="testout.un2.fastq" />
51 </test> 69 </test>
52 </tests> 70 </tests>