| Previous changeset 12:bd3a1e0de84c (2016-12-30) Next changeset 14:051eba708f43 (2017-06-01) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 3442b18860bc4398d917e3a35943351a9cf031ea |
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modified:
bwa-mem.xml bwa.xml |
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added:
test-data/bwa-mem-fastq1.fq.gz |
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| diff -r bd3a1e0de84c -r 53646aaaafef bwa-mem.xml --- a/bwa-mem.xml Fri Dec 30 08:11:12 2016 -0500 +++ b/bwa-mem.xml Mon Jan 30 08:49:26 2017 -0500 |
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| @@ -114,8 +114,8 @@ <option value="paired_iv">Paired Interleaved</option> </param> <when value="paired"> - <param name="fastq_input1" type="data" format="fastqsanger" label="Select first set of reads" help="Specify dataset with forward reads"/> - <param name="fastq_input2" type="data" format="fastqsanger" label="Select second set of reads" help="Specify dataset with reverse reads"/> + <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz" label="Select first set of reads" help="Specify dataset with forward reads"/> + <param name="fastq_input2" type="data" format="fastqsanger,fastqsanger.gz" label="Select second set of reads" help="Specify dataset with reverse reads"/> <param name="iset_stats" type="text" optional="True" label="Enter mean, standard deviation, max, and min for insert lengths." help="-I; This parameter is only used for paired reads. Only mean is required while sd, max, and min will be inferred. Examples: both "250" and "250,25" will work while "250,,10" will not. See below for details."> <sanitizer invalid_char=""> <valid initial="string.digits"><add value=","/> </valid> @@ -123,10 +123,10 @@ </param> </when> <when value="single"> - <param name="fastq_input1" type="data" format="fastqsanger" label="Select fastq dataset" help="Specify dataset with single reads"/> + <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz" label="Select fastq dataset" help="Specify dataset with single reads"/> </when> <when value="paired_collection"> - <param name="fastq_input1" format="fastqsanger" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/> + <param name="fastq_input1" format="fastqsanger,fastqsanger.gz" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/> <param name="iset_stats" type="text" optional="True" label="Enter mean, standard deviation, max, and min for insert lengths." help="-I; This parameter is only used for paired reads. Only mean is required while sd, max, and min will be inferred. Examples: both "250" and "250,25" will work while "250,,10" will not. See below for details."> <sanitizer invalid_char=""> <valid initial="string.digits"><add value=","/> </valid> @@ -134,7 +134,7 @@ </param> </when> <when value="paired_iv"> - <param name="fastq_input1" type="data" format="fastqsanger" label="Select fastq dataset" help="Specify dataset with interleaved reads"/> + <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz" label="Select fastq dataset" help="Specify dataset with interleaved reads"/> <param name="iset_stats" type="text" optional="True" label="Enter mean, standard deviation, max, and min for insert lengths." help="-I; This parameter is only used for paired reads. Only mean is required while sd, max, and min will be inferred. Examples: both "250" and "250,25" will work while "250,,10" will not. See below for details."> <sanitizer invalid_char=""> <valid initial="string.digits"><add value=","/> </valid> @@ -261,6 +261,15 @@ <test> <param name="reference_source_selector" value="history" /> <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> + <param name="fastq_input_selector" value="paired"/> + <param name="fastq_input1" ftype="fastqsanger.gz" value="bwa-mem-fastq1.fq.gz"/> + <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/> + <param name="analysis_type_selector" value="illumina"/> + <output name="bam_output" ftype="bam" file="bwa-mem-test1.bam" lines_diff="2" /> + </test> + <test> + <param name="reference_source_selector" value="history" /> + <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> <param name="index_a" value="is"/> <param name="fastq_input_selector" value="paired"/> <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/> |
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| diff -r bd3a1e0de84c -r 53646aaaafef bwa.xml --- a/bwa.xml Fri Dec 30 08:11:12 2016 -0500 +++ b/bwa.xml Mon Jan 30 08:49:26 2017 -0500 |
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| @@ -233,8 +233,8 @@ <option value="single_bam">Single BAM</option> </param> <when value="paired"> - <param name="fastq_input1" type="data" format="fastqsanger" label="Select first set of reads" help="Specify dataset with forward reads"/> - <param name="fastq_input2" type="data" format="fastqsanger" label="Select second set of reads" help="Specify dataset with reverse reads"/> + <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz" label="Select first set of reads" help="Specify dataset with forward reads"/> + <param name="fastq_input2" type="data" format="fastqsanger,fastqsanger.gz" label="Select second set of reads" help="Specify dataset with reverse reads"/> <conditional name="adv_pe_options"> <expand macro="advanced_pe_options" /> @@ -243,7 +243,7 @@ </when> <when value="paired_collection"> - <param name="fastq_input1" format="fastqsanger" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/> + <param name="fastq_input1" format="fastqsanger,fastqsanger.gz" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/> <conditional name="adv_pe_options"> <expand macro="advanced_pe_options" /> @@ -252,7 +252,7 @@ </when> <when value="single"> - <param name="fastq_input1" type="data" format="fastqsanger" label="Select fastq dataset" help="Specify dataset with single reads"/> + <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz" label="Select fastq dataset" help="Specify dataset with single reads"/> <conditional name="adv_se_options"> <expand macro="advanced_se_options" /> @@ -331,6 +331,15 @@ <test> <param name="reference_source_selector" value="history" /> <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> + <param name="input_type_selector" value="paired"/> + <param name="fastq_input1" ftype="fastqsanger.gz" value="bwa-mem-fastq1.fq.gz"/> + <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/> + <param name="analysis_type_selector" value="illumina"/> + <output name="bam_output" ftype="bam" file="bwa-aln-test1.bam" lines_diff="2" /> + </test> + <test> + <param name="reference_source_selector" value="history" /> + <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> <param name="input_type_selector" value="paired_bam"/> <param name="bam_input" ftype="bam" value="bwa-aln-bam-input.bam"/> <param name="analysis_type_selector" value="illumina"/> |
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| diff -r bd3a1e0de84c -r 53646aaaafef test-data/bwa-mem-fastq1.fq.gz |
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| Binary file test-data/bwa-mem-fastq1.fq.gz has changed |