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comparison fastq_combiner.xml @ 2:56389130cb63 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_combiner commit f2582539542b33240234e8ea6093e25d0aee9b6a
author devteam
date Sat, 30 Sep 2017 14:57:41 -0400
parents e711d52c7509
children b05e39b9c170
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1:e711d52c7509 2:56389130cb63
1 <tool id="fastq_combiner" name="Combine FASTA and QUAL" version="1.0.1"> 1 <tool id="fastq_combiner" name="Combine FASTA and QUAL" version="1.1.1">
2 <description>into FASTQ</description> 2 <description>into FASTQ</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.0.0">galaxy_sequence_utils</requirement> 4 <requirement type="package" version="1.1.1">galaxy_sequence_utils</requirement>
5 </requirements> 5 </requirements>
6 <command interpreter="python">fastq_combiner.py '$fasta_file' '${fasta_file.extension}' '$qual_file' '${qual_file.extension}' '$output_file' '$force_quality_encoding'</command> 6 <command><![CDATA[
7 <inputs> 7 gx-fastq-combiner '$fasta_file' '${fasta_file.extension}' '$qual_file' '${qual_file.extension}' '$output_file' $force_quality_encoding
8 <param name="fasta_file" type="data" format="fasta,csfasta" label="FASTA File" /> 8 ]]></command>
9 <param name="qual_file" type="data" format="qual" label="Quality Score File" optional="True" /> 9 <inputs>
10 <param name="force_quality_encoding" type="select" label="Force Quality Score encoding"> 10 <param name="fasta_file" type="data" format="fasta,csfasta" label="FASTA File" />
11 <option value="None">Use Source Encoding</option> 11 <param name="qual_file" type="data" format="qual" optional="true" label="Quality Score File" />
12 <option value="ascii" selected="True">ASCII</option> 12 <param name="force_quality_encoding" type="select" label="Force Quality Score encoding">
13 <option value="decimal">Decimal</option> 13 <option value="None">Use Source Encoding</option>
14 </param> 14 <option value="ascii" selected="true">ASCII</option>
15 </inputs> 15 <option value="decimal">Decimal</option>
16 <outputs> 16 </param>
17 <data name="output_file" format="fastqsanger"> 17 </inputs>
18 <change_format> 18 <outputs>
19 <when input_dataset="fasta_file" attribute="extension" value="csfasta" format="fastqcssanger" /> 19 <data name="output_file" format="fastqsanger">
20 <when input_dataset="qual_file" attribute="extension" value="qualsolid" format="fastqcssanger" /> 20 <change_format>
21 <when input_dataset="qual_file" attribute="extension" value="qualsolexa" format="fastqsolexa" /> 21 <when input="fasta_file" value="csfasta" format="fastqcssanger" />
22 <when input_dataset="qual_file" attribute="extension" value="qualillumina" format="fastqillumina" /> 22 <when input="qual_file" value="qualsolid" format="fastqcssanger" />
23 </change_format> 23 <when input="qual_file" value="qualsolexa" format="fastqsolexa" />
24 </data> 24 <when input="qual_file" value="qualillumina" format="fastqillumina" />
25 </outputs> 25 </change_format>
26 <tests> 26 </data>
27 <test> 27 </outputs>
28 <param name="fasta_file" value="s2fq_phiX.csfasta" ftype="csfasta" /> 28 <tests>
29 <param name="qual_file" value="s2fq_phiX.qualsolid" ftype="qualsolid" /> 29 <test>
30 <param name="force_quality_encoding" value="None" /> 30 <param name="fasta_file" value="s2fq_phiX.csfasta" ftype="csfasta" />
31 <output name="output_file" file="combine_phiX_out_1.fastqcssanger" /> 31 <param name="qual_file" value="s2fq_phiX.qualsolid" ftype="qualsolid" />
32 </test> 32 <param name="force_quality_encoding" value="None" />
33 <test> 33 <output name="output_file" file="combine_phiX_out_1.fastqcssanger" />
34 <param name="fasta_file" value="s2fq_phiX.csfasta" ftype="csfasta" /> 34 </test>
35 <param name="qual_file" value="s2fq_phiX.qualsolid" ftype="qualsolid" /> 35 <test>
36 <param name="force_quality_encoding" value="ascii" /> 36 <param name="fasta_file" value="s2fq_phiX.csfasta" ftype="csfasta" />
37 <output name="output_file" file="combine_phiX_out_2.fastqcssanger" /> 37 <param name="qual_file" value="s2fq_phiX.qualsolid" ftype="qualsolid" />
38 </test> 38 <param name="force_quality_encoding" value="ascii" />
39 <test> 39 <output name="output_file" file="combine_phiX_out_2.fastqcssanger" />
40 <param name="fasta_file" value="fastq_combiner_in_1.fasta" ftype="fasta" /> 40 </test>
41 <param name="qual_file" value="fastq_combiner_in_1.qual454" ftype="qual454" /> 41 <test>
42 <param name="force_quality_encoding" value="None" /> 42 <param name="fasta_file" value="fastq_combiner_in_1.fasta" ftype="fasta" />
43 <output name="output_file" file="wrapping_as_sanger.fastqsanger" /> 43 <param name="qual_file" value="fastq_combiner_in_1.qual454" ftype="qual454" />
44 </test> 44 <param name="force_quality_encoding" value="None" />
45 <test> 45 <output name="output_file" file="wrapping_as_sanger.fastqsanger" />
46 <param name="fasta_file" value="fastq_combiner_in_1.fasta" ftype="fasta" /> 46 </test>
47 <param name="qual_file" value="fastq_combiner_in_1.qual454" ftype="qual454" /> 47 <test>
48 <param name="force_quality_encoding" value="decimal" /> 48 <param name="fasta_file" value="fastq_combiner_in_1.fasta" ftype="fasta" />
49 <output name="output_file" file="wrapping_as_sanger_decimal.fastqsanger" /> 49 <param name="qual_file" value="fastq_combiner_in_1.qual454" ftype="qual454" />
50 </test> 50 <param name="force_quality_encoding" value="decimal" />
51 <test> 51 <output name="output_file" file="wrapping_as_sanger_decimal.fastqsanger" />
52 <param name="fasta_file" value="fastq_combiner_in_1.fasta" ftype="fasta" /> 52 </test>
53 <param name="qual_file" /> 53 <test>
54 <param name="force_quality_encoding" value="decimal" /> 54 <param name="fasta_file" value="fastq_combiner_in_1.fasta" ftype="fasta" />
55 <output name="output_file" file="fastq_combiner_no_qual_decimal_out_1.fastqsanger" /> 55 <param name="qual_file" />
56 </test> 56 <param name="force_quality_encoding" value="decimal" />
57 <test> 57 <output name="output_file" file="fastq_combiner_no_qual_decimal_out_1.fastqsanger" />
58 <param name="fasta_file" value="s2fq_phiX.csfasta" ftype="csfasta" /> 58 </test>
59 <param name="qual_file" /> 59 <test>
60 <param name="force_quality_encoding" value="ascii" /> 60 <param name="fasta_file" value="s2fq_phiX.csfasta" ftype="csfasta" />
61 <output name="output_file" file="fastq_combiner_no_qual_ascii_out_1.fastqcssanger" /> 61 <param name="qual_file" />
62 </test> 62 <param name="force_quality_encoding" value="ascii" />
63 </tests> 63 <output name="output_file" file="fastq_combiner_no_qual_ascii_out_1.fastqcssanger" />
64 <help> 64 </test>
65 </tests>
66 <help><![CDATA[
65 **What it does** 67 **What it does**
66 68
67 This tool joins a FASTA file to a Quality Score file, creating a single FASTQ block for each read. 69 This tool joins a FASTA file to a Quality Score file, creating a single FASTQ block for each read.
68 70
69 Specifying a set of quality scores is optional; when not provided, the output will be fastqsanger or fastqcssanger (when a csfasta is provided) with each quality score being the maximal allowed value (93). 71 Specifying a set of quality scores is optional; when not provided, the output will be fastqsanger or fastqcssanger (when a csfasta is provided) with each quality score being the maximal allowed value (93).
70 72
71 Use this tool, for example, to convert 454-type output to FASTQ. 73 Use this tool, for example, to convert 454-type output to FASTQ.
72 74 ]]></help>
73 </help> 75 <citations>
74 76 <citation type="doi">10.1093/bioinformatics/btq281</citation>
75 <citations> 77 </citations>
76 <citation type="doi">10.1093/bioinformatics/btq281</citation>
77 </citations>
78
79 </tool> 78 </tool>