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comparison bwa-mem.xml @ 12:bd3a1e0de84c draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 13b3ab10ff1a2e4be39b44f885df6bbe7c23099a
author devteam
date Fri, 30 Dec 2016 08:11:12 -0500
parents 546ada4a9f43
children 53646aaaafef
comparison
equal deleted inserted replaced
11:546ada4a9f43 12:bd3a1e0de84c
24 #end if 24 #end if
25 #end if 25 #end if
26 26
27 #if str( $analysis_type.analysis_type_selector ) == "pacbio": 27 #if str( $analysis_type.analysis_type_selector ) == "pacbio":
28 -x pacbio 28 -x pacbio
29 #elif str( $analysis_type.analysis_type_selector ) == "ont2d":
30 -x ont2d
31 #elif str( $analysis_type.analysis_type_selector ) == "intractg":
32 -x intractg
29 #elif str( $analysis_type.analysis_type_selector ) == "full": 33 #elif str( $analysis_type.analysis_type_selector ) == "full":
30 #if str( $analysis_type.algorithmic_options.algorithmic_options_selector ) == "set": ## Algorithmic options 34 #if str( $analysis_type.algorithmic_options.algorithmic_options_selector ) == "set": ## Algorithmic options
31 -k "${analysis_type.algorithmic_options.k}" 35 -k "${analysis_type.algorithmic_options.k}"
32 -w "${analysis_type.algorithmic_options.w}" 36 -w "${analysis_type.algorithmic_options.w}"
33 -d "${analysis_type.algorithmic_options.d}" 37 -d "${analysis_type.algorithmic_options.d}"
94 #else: 98 #else:
95 "${reference_fasta_filename}" 99 "${reference_fasta_filename}"
96 "${fastq_input.fastq_input1}" 100 "${fastq_input.fastq_input1}"
97 #end if 101 #end if
98 102
99 | samtools view -Sb - > temporary_bam_file.bam && 103 | samtools sort -O bam -o '$bam_output'
100
101 samtools sort -f temporary_bam_file.bam ${bam_output}
102 ]]> 104 ]]>
103 </command> 105 </command>
104 106
105 <inputs> 107 <inputs>
106 <expand macro="reference_source_conditional" /> 108 <expand macro="reference_source_conditional" />
145 147
146 <conditional name="analysis_type"> 148 <conditional name="analysis_type">
147 <param name="analysis_type_selector" type="select" label="Select analysis mode"> 149 <param name="analysis_type_selector" type="select" label="Select analysis mode">
148 <option value="illumina">1.Simple Illumina mode</option> 150 <option value="illumina">1.Simple Illumina mode</option>
149 <option value="pacbio">2.PacBio mode (-x pacbio)</option> 151 <option value="pacbio">2.PacBio mode (-x pacbio)</option>
150 <option value="full">3.Full list of options</option> 152 <option value="ont2d">3.Nanopore 2D-reads mode (-x ont2d)</option>
153 <option value="intractg">4.Intra-species contigs mode (-x intractg)</option>
154 <option value="full">5.Full list of options</option>
151 </param> 155 </param>
152 <when value="illumina"> 156 <when value="illumina">
153 <!-- do nothing --> 157 <!-- do nothing -->
154 </when> 158 </when>
155 <when value="pacbio"> 159 <when value="pacbio">
160 <!-- do nothing. all magic happens within <command> tag -->
161 </when>
162 <when value="ont2d">
163 <!-- do nothing. all magic happens within <command> tag -->
164 </when>
165 <when value="intractg">
156 <!-- do nothing. all magic happens within <command> tag --> 166 <!-- do nothing. all magic happens within <command> tag -->
157 </when> 167 </when>
158 <when value="full"> 168 <when value="full">
159 <conditional name="algorithmic_options"> 169 <conditional name="algorithmic_options">
160 <param name="algorithmic_options_selector" type="select" label="Set algorithmic options?" help="Sets -k, -w, -d, -r, -y, -c, -D, -W, -m, -S, -P, and -e options."> 170 <param name="algorithmic_options_selector" type="select" label="Set algorithmic options?" help="Sets -k, -w, -d, -r, -y, -c, -D, -W, -m, -S, -P, and -e options.">