Mercurial > repos > devteam > bwa
diff bwa-mem.xml @ 7:d8c9597bfb09 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit ddb8bdb9d62399f086b06b3469450d0aad2113bd
| author | devteam |
|---|---|
| date | Tue, 03 Nov 2015 09:36:45 -0500 |
| parents | 09a7281d24c5 |
| children | 7bee165c3a44 |
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--- a/bwa-mem.xml Tue Jul 21 14:12:49 2015 -0400 +++ b/bwa-mem.xml Tue Nov 03 09:36:45 2015 -0500 @@ -1,14 +1,11 @@ <?xml version="1.0"?> -<tool id="bwa_mem" name="Map with BWA-MEM" version="0.3.1"> +<tool id="bwa_mem" name="Map with BWA-MEM" version="0.4.1"> <description>- map medium and long reads (> 100 bp) against reference genome</description> <macros> <import>read_group_macros.xml</import> <import>bwa_macros.xml</import> </macros> - <requirements> - <requirement type="package" version="0.7.10.039ea20639">bwa</requirement> - <requirement type="package" version="1.1">samtools</requirement> - </requirements> + <expand macro="requirements" /> <expand macro="stdio" /> <command> #set $reference_fasta_filename = "localref.fa" @@ -170,7 +167,7 @@ <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="iset_stats" type="text" optional="True" size="10" 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."> + <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> </sanitizer> @@ -181,7 +178,7 @@ </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="iset_stats" type="text" optional="True" size="10" 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."> + <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> </sanitizer> @@ -189,7 +186,7 @@ </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="iset_stats" type="text" optional="True" size="10" 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."> + <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> </sanitizer>